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At least 37 records · Page 2

Identification of key bacterial populations affecting early embryonic development in cattle uterus

Abstract Superovulation is an important animal breeding biotechnology, while the quality of embryos obtained from superovulation is unstable in cattle. The relationship between the microorganisms in the cattle uterus and embryo qualities was determined to identify the key bacterial populations affecting early embryonic development. A total of 10 Xia Nan cows underwent superovulation, we collected cervical mucus and flush samples to investigated by 16S rDNA sequencing. Results showed that there were abundant microorganisms in cervical mucus, but no obvious relationship with the quality of embryos. The clustering results of flush samples were consistent with the grouping of embryo quality. Proteobacteria accounted for more than 95% of the total bacterial community in group A with the best embryo quality (qualified embryo ratio above 0.8), and as embryo quality decreased, the Proteobacteria proportion also decreased. In contrast to the proportion of Proteobacteria, the proportions of Firmicutes and Bacteroidetes significantly increased as embryo quality decreased. For group C with the worst embryo quality, the proportions of Firmicutes and Bacteroidetes increased to 4.7 times and 12.3 times of group A, respectively. These results showed that the quantities and proportions of Firmicutes and Bacteroidetes may be related to early embryonic development in cattle.

Lyu, Chenchen↗

ATTNChecker: Highly-Optimized Fault Tolerant Attention for Large Language Model Training

Large Language Models (LLMs) have demonstrated remarkable performance in various natural language processing tasks. However, the training of these models is computationally intensive and susceptible to faults, particularly in the attention mechanism, which is a critical component of transformer-based LLMs. In this paper, we investigate the impact of faults on LLM training, focusing on INF, NaN, and near-INF values in the computation results with systematic fault injection experiments. We observe the propagation patterns of these errors, which can trigger non-trainable states in the model and disrupt training, forcing the procedure to load from checkpoints. To mitigate the impact of these faults, we propose ATTNChecker, the first Algorithm-Based Fault Tolerance (ABFT) technique tailored for the attention mechanism in LLMs. ATTNChecker is designed based on fault propagation patterns of LLM and incorporates performance optimization to adapt to both system reliability and model vulnerability while providing lightweight protection for fast LLM training. Evaluations on four LLMs show that ATTNChecker on average incurs on average 7% overhead on training while detecting and correcting all extreme errors. Compared with the state-of-the-art checkpoint/restore approach, ATTNChecker reduces recovery overhead by up to 49×.

Liang, Yuhang [University of Alabama - Birmingham]↗

BinFPE

BinFPE is a tool that detects floating-point exceptions (NaN, infinity, and subnormal quantities) in NVIDIA GPU applications using binary instrumentation. It requires no re-compilation of the application and can analyze libraries. The tool extends NVBit (https://github.com/NVlabs/NVBit), which is provided by NVIDIA Labs to analyze binaries. When the tool detects a floating-point exception it reports to the user the location of the exception (file and line number).

Laguna Peralta, Ignacio↗

XScope

XScope finds inputs that trigger floating-point exceptions, such as NaN (not a number) and infinity, in CUDA functions using Bayesian optimization (BO). XScope assumes that the CUDA functions are a black box, i.e., the source code is not available. It searches the input space using several methods to guide BO into extreme cases. When an input is found to trigger an exception in the target CUDA function, the input is shown to the user.

Laguna Peralta, Ignacio↗

Soil Temperature and Moisture within the Kougarok Fire Complex, Kougarok Road Mile Marker 86, Seward Peninsula, Alaska, 2019-2023

Daily averages of soil temperature and moisture measured once every hour at different heights located at Intensive Monitoring Stations within the Kougarok Fire Complex, Kougarok Road Mile Marker 86 site. Data were retrieved annually from 2019-2023. Package contains 21 *.CSV data files plus a file level metadata *.CSV, data dictionary *.CSV, data file inventory *.CSV, and sensor location site map *.JPG. Data files have header rows, NaN fields indicate invalid or missing data, and negative vertical offsets are above ground.The Kougarok tundra fire complex (KFC) is located north of Nome and the Kigluaik Mountains, near Quartz Creek and the Kougarok River. The site is accessed by foot from the end of the Nome-Taylor Highway (mile marker 86; also called the Kougarok or Beam Road). The KFC burned in six major fires in the decades since 1950 (Alaska Interagency Coordination Center, unpublished data). Lightning ignited five of these fires (1971, 1997, 2015, and 2019) and one was human caused (2002). The mosaic of overlapping fire scars allows for the study of repeat fires in the tundra which, until recently, was not a common phenomenon outside the boreal forest in Alaska. Our reference unburned tundra fire site is south of the KFC located at mile marker 80 of the Nome-Taylor Highway.The two most recent fires are the Mingvk Lake (2015; 21,698 acres burned from 7/27/2015 to 9/28/2015) and Garfield Creek (2019; 422 acres burned from 7/31/2019 to 8/20/19). The Mingvk Lake fire scar includes areas that burned 1-4x (1971, 1997, 2002), while the entirety of the Garfield Creek fire scar has burned 2x previously (1971, 2002).Previous research at the KFC focused on permafrost (Liljedahl et al. 2007; Narita et al. 2015; Iwahana et al. 2016; Tsuyuzaki, Iwahana, and Saito 2017) and vegetation (Narita et al. 2015; Hollingsworth et al. 2021) response to fire. The central Seward Peninsula is characterized by continuous permafrost with a thickness of 15 to 30 m and a mean active layer thickness of 56 cm (Hinzman et al. 2003). Sloping hills with mixed shrub–tussock tundra and tussock tundra vegetation in the uplands are characteristic of the region. Three micrometeorological towers near the Kougarok field site recorded a mean annual temperature of −2.4°C, mean January temperature of −23.1°C, mean July temperature of +11°C, and mean summer rainfall (June–August) of 94 mm from 2000 to 2006 (Liljedahl et al. 2007).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Materials Data on NaC2N3 by Materials Project

NaN(CN)2 crystallizes in the monoclinic P2_1/c space group. The structure is three-dimensional. there are three inequivalent Na1+ sites. In the first Na1+ site, Na1+ is bonded in a 6-coordinate geometry to six N3- atoms. There are a spread of Na–N bond distances ranging from 2.40–2.90 Å. In the second Na1+ site, Na1+ is bonded in a 7-coordinate geometry to seven N3- atoms. There are a spread of Na–N bond distances ranging from 2.57–2.90 Å. In the third Na1+ site, Na1+ is bonded to six N3- atoms to form distorted edge-sharing NaN6 octahedra. There are a spread of Na–N bond distances ranging from 2.42–3.02 Å. There are six inequivalent C4+ sites. In the first C4+ site, C4+ is bonded in a linear geometry to two N3- atoms. There is one shorter (1.18 Å) and one longer (1.30 Å) C–N bond length. In the second C4+ site, C4+ is bonded in a trigonal planar geometry to three N3- atoms. There are a spread of C–N bond distances ranging from 1.35–1.37 Å. In the third C4+ site, C4+ is bonded in a trigonal planar geometry to three N3- atoms. All C–N bond lengths are 1.36 Å. In the fourth C4+ site, C4+ is bonded in a trigonal planar geometry to three N3- atoms. All C–N bond lengths are 1.36 Å. In the fifth C4+ site, C4+ is bonded in a linear geometry to two N3- atoms. There is one shorter (1.19 Å) and one longer (1.29 Å) C–N bond length. In the sixth C4+ site, C4+ is bonded in a linear geometry to two N3- atoms. There is one shorter (1.19 Å) and one longer (1.30 Å) C–N bond length. There are nine inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted bent 120 degrees geometry to two Na1+ and two C4+ atoms. In the second N3- site, N3- is bonded in a distorted bent 120 degrees geometry to two equivalent Na1+ and two C4+ atoms. In the third N3- site, N3- is bonded in a 4-coordinate geometry to three Na1+ and one C4+ atom. In the fourth N3- site, N3- is bonded in a 4-coordinate geometry to three equivalent Na1+ and one C4+ atom. In the fifth N3- site, N3- is bonded in a 2-coordinate geometry to one Na1+ and two C4+ atoms. In the sixth N3- site, N3- is bonded in a 2-coordinate geometry to two equivalent Na1+ and two C4+ atoms. In the seventh N3- site, N3- is bonded in a 2-coordinate geometry to two equivalent Na1+ and two C4+ atoms. In the eighth N3- site, N3- is bonded in a 2-coordinate geometry to two equivalent Na1+ and two C4+ atoms. In the ninth N3- site, N3- is bonded in a 3-coordinate geometry to two Na1+ and one C4+ atom.

36 MATERIALS SCIENCE↗

Materials Data on NaC2N3 by Materials Project

NaN(CN)2 crystallizes in the monoclinic P2_1/c space group. The structure is three-dimensional. Na1+ is bonded to six N3- atoms to form edge-sharing NaN6 octahedra. There are a spread of Na–N bond distances ranging from 2.49–2.57 Å. There are two inequivalent C4+ sites. In the first C4+ site, C4+ is bonded in a linear geometry to two N3- atoms. There is one shorter (1.19 Å) and one longer (1.30 Å) C–N bond length. In the second C4+ site, C4+ is bonded in a linear geometry to two N3- atoms. There is one shorter (1.18 Å) and one longer (1.30 Å) C–N bond length. There are three inequivalent N3- sites. In the first N3- site, N3- is bonded in a rectangular see-saw-like geometry to three equivalent Na1+ and one C4+ atom. In the second N3- site, N3- is bonded in a 3-coordinate geometry to two equivalent Na1+ and one C4+ atom. In the third N3- site, N3- is bonded in a trigonal planar geometry to one Na1+ and two C4+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on NaS2N(O2F)2 by Materials Project

NaN(SO2F)2 crystallizes in the monoclinic P2_1/c space group. The structure is three-dimensional and consists of four ammonia molecules and one NaS2(O2F)2 framework. In the NaS2(O2F)2 framework, Na1+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Na–O bond distances ranging from 2.33–2.91 Å. There are two inequivalent S2+ sites. In the first S2+ site, S2+ is bonded in a trigonal non-coplanar geometry to two O2- and one F1- atom. There is one shorter (1.43 Å) and one longer (1.44 Å) S–O bond length. The S–F bond length is 1.60 Å. In the second S2+ site, S2+ is bonded in a trigonal non-coplanar geometry to two O2- and one F1- atom. There is one shorter (1.43 Å) and one longer (1.45 Å) S–O bond length. The S–F bond length is 1.60 Å. There are four inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Na1+ and one S2+ atom. In the second O2- site, O2- is bonded in a 1-coordinate geometry to two equivalent Na1+ and one S2+ atom. In the third O2- site, O2- is bonded in a 2-coordinate geometry to two equivalent Na1+ and one S2+ atom. In the fourth O2- site, O2- is bonded in a 2-coordinate geometry to one Na1+ and one S2+ atom. There are two inequivalent F1- sites. In the first F1- site, F1- is bonded in a single-bond geometry to one S2+ atom. In the second F1- site, F1- is bonded in a single-bond geometry to one S2+ atom.

36 MATERIALS SCIENCE↗

Materials Data on NaC2S2N(O2F3)2 by Materials Project

NaN(CF3SO2)2 crystallizes in the monoclinic P2_1/c space group. The structure is two-dimensional and consists of eight ammonia molecules; sixteen fluoroform molecules; and two NaS2O4 sheets oriented in the (0, 0, 1) direction. In each NaS2O4 sheet, there are two inequivalent Na1+ sites. In the first Na1+ site, Na1+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Na–O bond distances ranging from 2.43–2.95 Å. In the second Na1+ site, Na1+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Na–O bond distances ranging from 2.42–2.92 Å. There are four inequivalent S2+ sites. In the first S2+ site, S2+ is bonded in a bent 120 degrees geometry to two O2- atoms. There is one shorter (1.45 Å) and one longer (1.46 Å) S–O bond length. In the second S2+ site, S2+ is bonded in a bent 120 degrees geometry to two O2- atoms. There is one shorter (1.45 Å) and one longer (1.46 Å) S–O bond length. In the third S2+ site, S2+ is bonded in a bent 120 degrees geometry to two O2- atoms. There is one shorter (1.44 Å) and one longer (1.46 Å) S–O bond length. In the fourth S2+ site, S2+ is bonded in a bent 120 degrees geometry to two O2- atoms. There is one shorter (1.44 Å) and one longer (1.46 Å) S–O bond length. There are eight inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted bent 120 degrees geometry to one Na1+ and one S2+ atom. In the second O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Na1+ and one S2+ atom. In the third O2- site, O2- is bonded in a 1-coordinate geometry to two Na1+ and one S2+ atom. In the fourth O2- site, O2- is bonded in a 1-coordinate geometry to two Na1+ and one S2+ atom. In the fifth O2- site, O2- is bonded in a 1-coordinate geometry to two Na1+ and one S2+ atom. In the sixth O2- site, O2- is bonded in a distorted bent 120 degrees geometry to one Na1+ and one S2+ atom. In the seventh O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Na1+ and one S2+ atom. In the eighth O2- site, O2- is bonded in a 1-coordinate geometry to two Na1+ and one S2+ atom.

36 MATERIALS SCIENCE↗

Materials Data on NaC2N3 by Materials Project

NaN(CN)2 crystallizes in the monoclinic P2_1/c space group. The structure is two-dimensional and consists of two CN2 ribbons oriented in the (2, 0, 1) direction and two NaCN sheets oriented in the (0, 1, 0) direction. In each CN2 ribbon, C4+ is bonded in a water-like geometry to two N3- atoms. There is one shorter (1.35 Å) and one longer (1.42 Å) C–N bond length. There are two inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted bent 120 degrees geometry to one C4+ and one N3- atom. The N–N bond length is 1.25 Å. In the second N3- site, N3- is bonded in a distorted bent 120 degrees geometry to one C4+ and one N3- atom. The N–N bond length is 1.29 Å. In each NaCN sheet, Na1+ is bonded in a 3-coordinate geometry to three equivalent N3- atoms. There are a spread of Na–N bond distances ranging from 2.39–2.78 Å. C4+ is bonded in a single-bond geometry to one N3- atom. The C–N bond length is 1.18 Å. N3- is bonded in a 4-coordinate geometry to three equivalent Na1+ and one C4+ atom.

36 MATERIALS SCIENCE↗

Supporting Special Values in ZFP

This white paper outlines potential approaches to supporting special values in the ZFP numerical compressor without breaking backwards compatibility. Other than infinities and NaNs, special values are often used to indicate the absence of data, where no value is defined, for example by designating finite but extreme “fill values” as special. Such fill values are commonly used in earth system science, among other applications, but if left as is during compression lead to artifacts and loss of precision in nearby true values. Multiple candidate solutions that would allow ZFP to recognize special values are here proposed. Until such support is available, we also sketch available workarounds.

97 MATHEMATICS AND COMPUTING↗

Soil Temperature and Moisture, Council Road Mile Marker 71, Seward Peninsula, Alaska, beginning 2016

Daily averages of soil temperature and moisture measured once every hour at different heights, as well as daily averages of hourly measured snow depths located at Intensive Monitoring Stations at Council Road Mile Marker 71 site. Deployed at each site is an Onset HOBO U30 data logger with five smart temperature sensors and three smart soil moisture sensors (10HS). Three sites (CN_IS_4, CN_IS_6A, CN_IS_7) are equipped with a snow depth sensor. Data are retrieved annually since 2016. Contains 53 *.CSV files including a file inventory list by year. Data files have header rows, NaN fields indicate invalid or missing data, and negative vertical offsets are above ground. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Soil Temperature and Moisture, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2016-2023

Daily averages of soil temperature and moisture measured once every hour at different heights located at Intensive Monitoring Stations at Teller Road Mile Marker 27 site. Data are retrieved annually from 2016-2023. This is the final update to this dataset: no changes to previous data files with the addition of 2022-2023 data files. Data files have header rows, NaN fields indicate invalid or missing data, and negative vertical offsets are above ground. UPDATED 2025-07: Seven new data files collected in 2022-2023 were added and no previously archived data were changed. This represents the final collection of data and text in the title was changed to reflect the defined timespan. Other files that were added: file-level metadata, a data dictionary, a site location map, and a data file inventory by year. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Soil Temperature and Moisture, Kougarok Road Mile Marker 64, Seward Peninsula, Alaska, beginning 2016

Daily averages of soil temperature and moisture measured once every hour at different heights located at Intensive Monitoring Stations at Kougarok Road Mile Marker 64 site. Data are retrieved annually since 2016. Package contains 46 *.CSV files including a file inventory list by year. Data files have header rows, NaN fields indicate invalid or missing data, and negative vertical offsets are above ground.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

A Bridge Health Monitoring Method Using the Hilbert-Huang Transform: A Case Study

We have developed a new method for nondestructive instrument method to monitor the health of a bridge. This new method is based on a transient test load and simple data collection. The nuclear of the method is the new invented nonstationary and nonlinear time series analysis method, the Empirical Mode Decomposition and Hilbert Spectral Analysis. The final decision on the health of the bridge structure is based on the nonlinear characteristic of the data, and on the comparison between the free and the forced vibration frequencies. Thus this alternative method enjoys many advantages: (1) no a priori data required, (2) simple data collection, and (3) minimum traffic disruption. Results from a case study of the Shing-Nan Bridge in Hou-Wei will be reported.

Huang, Norden E.↗

Transfer from long to short photoperiods affects production efficiency of day-neutral rice

The day-neutral, semidwarf rice (Oryza sativa L.) cultivar Ai-Nan-Tsao was grown in a greenhouse under summer conditions using high-pressure sodium lamps to extend the natural photoperiod. After allowing 2 weeks for germination, stand establishment, and thinning to a consistent planting density of 212 plants/m2, stands were maintained under continuous lighting for 35 or 49 days before shifting to 8- or 12-h photoperiods until harvest 76 days after planting. Non-shifted control treatments consisting of 8-, 12-, or 24-h photoperiods also were maintained throughout production. Tiller number increased as duration of exposure to continuous light increased before shifting to shorter photoperiods. However, shoot harvest index and yield efficiency rate were lower for all plants receiving continuous light than for those under the 8- or 12-h photoperiods. Stands receiving 12-h photoperiods throughout production had the highest grain yield per plant and equaled the 8-h-photoperiod control plants for the lowest tiller number per plant. As long as stands were exposed to continuous light, tiller formation continued. Shifting to shorter photoperiods late in the cropping cycle resulted in newly formed tillers that were either sterile or unable to mature grain before harvest. Late-forming tillers also suppressed yield of grain in early-forming tillers, presumably by competing for photosynthate or for remobilized assimilate during senescence. Stands receiving 12-h photoperiods throughout production not only produced the highest grain yield at harvest but had the highest shoot harvest index, which is important for resource-recovery strategies in advanced life-support systems proposed for space.

Non-NASA Center↗

A Shape-Memory Alloy Thermal Conduction Switch for Use at Cryogenic Temperatures

The following summarizes the activities performed under NASA grant NAG10-323 from September 1, 2002 through September 30, 2004 at the. Univ ersity of Central Florida. A version of this has already been submitt ed for publication in the international journal Swart Materials and S tructures in December 2004. Additionally, a version of this has alrea dy appeared in print in Advances in Cryogenic Engineering, American Institute of Physics, (2004) 50A 26-3; in an article entitled "A Shape Memory Alloy Based Cryogenic Thermal Conduction Switch" by V.B. Krish nan. J.D. Singh. T.R. Woodruff. W.U. Notardonato and R. Vaidyanathan (article is attached at the end of this report).

Vaidyanathan, Raj↗