Effect of hay nets on horse bodyweight, body condition score, hay usage, and dental health in mature adult horses.

Hay nets are a commonly used management practice to increase intake time and reduce hay waste but may impact horse health. The objectives were to compare hay usage, dental wear, and dental conditions between horses fed with (NET) or without (CON) hay nets during a 2-year cross-over study. In September 2021, 13 mature adult horses were blocked by bodyweight (BW) and randomly assigned to the NET or CON treatments for one year. After one year (September 2022), horses switched treatments and the trial concluded in September 2023. Horses were housed in adjacent dry lots with shelter, ad libitum water, and free choice access to round bales with or without hay nets (4.45 cm openings). Blinded dental work, including incisor length measurements and recording of dental abnormalities and conditions, and recording of horse BW and body condition score (BCS) were completed in September 2021, 2022, and 2023. Digital images were taken monthly to determine rostral oral cavity scores (ROCS). Round bales were weighed prior to being placed in the dry lot and the date fed was recorded to calculate hay usage. Significance was set at P≤0.05. Horse BW, BCS, and hay usage were greater in horses consuming hay without hay nets (P<0.05). No differences were observed in incisor length, presence of incisor bevels, ROCS, or dental abnormalities and conditions (P>0.05). These data suggest that hay nets do not result in negative impacts on dental health but can reduce hay usage and help to control horse BW and BCS.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.

Obesity significantly alters the human sperm proteome, with potential implications for fertility.

PURPOSE: In men, obesity may lead to poor semen parameters and reduced fertility. However, the causative links between obesity and male infertility are not totally clear, particularly on a molecular level. As such, we investigated how obesity modifies the human sperm proteome, to elucidate any important implications for fertility. METHODS: Sperm protein lysates from 5 men per treatment, classified as a healthy weight (body mass index (BMI) ≤ 25 kg/m2) or obese (BMI ≥ 30 kg/m2), were FASP digested, submitted to liquid chromatography tandem mass spectrometry, and compared by label-free quantification. Findings were confirmed for several proteins by qualitative immunofluorescence and a quantitative protein immunoassay. RESULTS: A total of 2034 proteins were confidently identified, with 24 proteins being significantly (p < 0.05) less abundant (fold change < 0.05) in the spermatozoa of obese men and 3 being more abundant (fold change > 1.5) compared with healthy weight controls. Proteins with altered abundance were involved in a variety of biological processes, including oxidative stress (GSS, NDUFS2, JAGN1, USP14, ADH5), inflammation (SUGT1, LTA4H), translation (EIF3F, EIF4A2, CSNK1G1), DNA damage repair (UBEA4), and sperm function (NAPA, RNPEP, BANF2). CONCLUSION: These results suggest that oxidative stress and inflammation are closely tied to reproductive dysfunction in obese men. These processes likely impact protein translation and folding during spermatogenesis, leading to poor sperm function and subfertility. The observation of these changes in obese men with no overt andrological diagnosis further suggests that traditional clinical semen assessments fail to detect important biochemical changes in spermatozoa which may compromise fertility.

Cryopreservation of bull semen: Evolution from egg yolk based to soybean based extenders.

Since the inception of bovine semen cryopreservation, egg yolk and milk based extenders have been used to protect sperm from the detrimental effects of cooling and freezing. In recent years, demand for alternatives to conventional commercial extenders has arisen as the risk of introducing exotic diseases through transporting egg yolk based products has been recognized. Egg yolk can also interfere with sperm evaluation and the presence of particulate material in the extender may reduce fertility. Soybeans contain lecithin, a phospholipid fraction that can substitute for high molecular weight lipoprotein and phospholipids from egg yolk and prevent or ameliorate damage to the sperm plasma membrane that occurs during extension, cooling, and cryopreservation. Soy lecithin based extenders have been evaluated for processing and freezing bovine semen, although extender from soybean milk has not been studied as extensively. Commercially available soy lecithin based extenders are used increasingly but remain under scrutiny and are not universally accepted. With these observations in mind, this review is intended to examine effects of conventional cryopreservation procedures, methods of assessment, and potential for developing soybean extract as an acceptable alternative to traditional egg yolk and milk based extenders for bull sperm cryopreservation.

Modeling Mercury in Proteins.

Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively nontoxic, other forms such as Hg(2+) and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg(2+) can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg(2+) to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed molecular picture and circumvent issues associated with toxicity. Here, we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intraprotein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand-binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confer mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multiscale model of environmental mercury cycling.

Enhancement of ARROW Photonic Device Performance via Thermal Annealing of PECVD-based SiO2 Waveguides.

Silicon-based optofluidic devices are very attractive for applications in biophotonics and chemical sensing. Understanding and controlling the properties of their dielectric waveguides is critical for the performance of these chips. We report that thermal annealing of PECVD-grown silicon dioxide (SiO2) ridge waveguides results in considerable improvements to optical transmission and particle detection. There are two fundamental changes that yield higher optical transmission: (1) propagation loss in solid-core waveguides is reduced by over 70%, and (2) coupling efficiencies between solid- and liquid-core waveguides are optimized. The combined effects result in improved optical chip transmission by a factor of 100-1000 times. These improvements are shown to arise from the elimination of a high-index layer at the surface of the SiO2 caused by water absorption into the porous oxide. The effects of this layer on optical transmission and mode confinement are shown to be reversible by alternating subjection of waveguides to water and subsequent low temperature annealing. Finally, we show that annealing improves detection of fluorescent analytes in optofluidic chips with a signal-to-noise ratio improvement of 166x and a particle detection efficiency improvement of 94%.

On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood.

We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids -BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples.

Optofluidic analysis system for amplification-free, direct detection of Ebola infection.

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

Integration of programmable microfluidics and on-chip fluorescence detection for biosensing applications.

We describe the integration of an actively controlled programmable microfluidic sample processor with on-chip optical fluorescence detection to create a single, hybrid sensor system. An array of lifting gate microvalves (automaton) is fabricated with soft lithography, which is reconfigurably joined to a liquid-core, anti-resonant reflecting optical waveguide (ARROW) silicon chip fabricated with conventional microfabrication. In the automaton, various sample handling steps such as mixing, transporting, splitting, isolating, and storing are achieved rapidly and precisely to detect viral nucleic acid targets, while the optofluidic chip provides single particle detection sensitivity using integrated optics. Specifically, an assay for detection of viral nucleic acid targets is implemented. Labeled target nucleic acids are first captured and isolated on magnetic microbeads in the automaton, followed by optical detection of single beads on the ARROW chip. The combination of automated microfluidic sample preparation and highly sensitive optical detection opens possibilities for portable instruments for point-of-use analysis of minute, low concentration biological samples.

Public engagement with information on renewable energy developments: The case of single, semi-urban wind turbines.

This paper explores perceptions of public engagement with information on renewable energy developments. It draws on a case study of proposals by a major supermarket chain to construct single wind turbines in two semi-urban locations in the UK, analysing data from interviews with key actors in the planning process and focus groups with local residents. The paper concludes that key actors often had high expectations of how local people should engage with information, and sometimes implied that members of the public who were incapable of filtering or processing information in an organised or targeted fashion had no productive role to play in the planning process. It shows how the specific nature of the proposals (single wind turbines in semi-urban locations proposed by a commercial private sector developer) shaped local residents' information needs and concerns in a way that challenged key actors' expectations of how the public should engage with information.

Effect of n-3 fatty acids and α-tocopherol on post-thaw parameters and fatty acid composition of bovine sperm.

PURPOSE: This study was designed to determine the combined effects of adding source of n-3 fatty acids (FA) and α-tocopherol (vitamin E, VE) to semen extender on freezability and FA composition of Brown Swiss bull sperm. METHODS: Semen samples were collected from 6 Brown Swiss bulls and pooled. In the first trial, semen was divided into 12 groups including 4 levels of n-3 FA (0, 1, 10, 100 ng ml(-1)) and 3 levels of VE (0. 0.2, 0.4 mM). Motility, viability and fatty acid composition of sperm were measured. RESULTS: The treatment of 10 ng ml(-1) n-3 FA and 0.4 mM VE had the best post-thaw sperm characteristics (P < 0.01). In the second trial, sperm lipid composition of this treatment and control (without FA and VE) was determined. Supplementing n-3 fatty acids during cryopreservation increased docosahexaenoic acid (DHA) and the ratio of n-3 to n-6 FA in sperm before freezing and after thawing. CONCLUSIONS: The results suggest that combining the optimal level of n-3 FA (10 ng ml(-1)) with the highest level of VE tested (0.4 mM) in a semen extender changed the membrane lipid composition and improved freezablity of Brown Swiss bull sperm.

Common polymorphisms in the GH/IGF-1 axis contribute to growth in extremely tall subjects.

CONTEXT/OBJECTIVE: The growth hormone (GH)/insulin-like growth factor-1(IGF-1) axis is the key regulator of somatic growth in humans and its genes are plausible candidates to study the genetics of height variation. Here, we studied polymorphic variation in the GH/IGF-1 axis in the extremely tall Dutch. METHODS: Case-control study of 166 tall cases with height >2 SDS and 206 controls with normally distributed height <2 SDS. Excluded were subjects with endocrine disorders or growth syndromes. We analyzed genomic DNA at 7 common polymorphisms in the GH-1, GH receptor (GHR), IGF-1 and IGFBP-3 genes. RESULTS: The association of the GH-1 1663 SNP with tall stature approached statistical significance, with the T-allele more present in the tall (allele frequency (AF): 0.44 vs. 0.36; p=0.084). Moreover, haplotype frequencies at this locus were significantly different between cases and controls, with the GGT haplotype most commonly seen in cases (p=0.01). Allele frequencies of GHR polymorphisms were not different. For the IGF-1 CA-repeat we observed a higher frequency of homozygous 192-bp carriers among tall males compared to control males (AF: 0.62 vs. 0.55; p=0.02). The IGFBP-3 -202 C-allele occurred more frequently in cases than in controls (AF: 0.58 vs. 0.50; p=0.002). Within cases, those carrying one or two copies of the -202 C-allele were significantly taller than AA genotype carriers (AC, p=0.028 and CC, p=0.009). Serum IGFBP-3 levels were highest in AA genotype carriers, the -202 SNP explained 5.8% of the variation. CONCLUSION: Polymorphic variation in the GH-1, IGF-1 and IGFBP-3 genes is associated with extremely tall stature. In particular, the IGFBP-3 -202 SNP is associated not only with being very tall but also with height variation within the tall.

Genetic variation in candidate genes like the HMGA2 gene in the extremely tall.

BACKGROUND/AIMS: Genetic variation in several candidate genes has been associated with short stature. Recently, a high-mobility group A2 (HMGA2) gene SNP has been robustly associated with height in the general population. Only few have attempted to study these genes in extremely tall stature. We therefore studied common genetic variation in candidate genes for height in extremely tall Dutch. METHODS: We included 116 constitutionally tall cases with height >2 SD and 103 controls with normally distributed height <2 SD. We genotyped 10 common polymorphisms previously associated with height variation. RESULTS: The HMGA2 gene SNP was significantly associated with tall stature. Using a logistic regression model, we calculated that carrying the HMGA2 (rs1042725) C allele significantly increased the odds of being tall (OR = 1.53, 95% CI 1.02-2.28; p = 0.03). In addition, controls with one or two copies of the C allele were significantly taller than controls carrying the TT genotype [TC: mean (SD) +0.61 (0.21) SDS; p = 0.004, and CC: +0.77 (0.25) SDS; p = 0.003]. CONCLUSION: Our study shows that a common polymorphism in the HMGA2 gene is not only associated with height variation in the general population but also plays an important role in one of the extremes of the height distribution.

Mechanical control of spin states in spin-1 molecules and the underscreened Kondo effect.

The ability to make electrical contact to single molecules creates opportunities to examine fundamental processes governing electron flow on the smallest possible length scales. We report experiments in which we controllably stretched individual cobalt complexes having spin S = 1, while simultaneously measuring current flow through the molecule. The molecule's spin states and magnetic anisotropy were manipulated in the absence of a magnetic field by modification of the molecular symmetry. This control enabled quantitative studies of the underscreened Kondo effect, in which conduction electrons only partially compensate the molecular spin. Our findings demonstrate a mechanism of spin control in single-molecule devices and establish that they can serve as model systems for making precision tests of correlated-electron theories.

Right pulmonary agenesis converts an incomplete vascular ring into a near-complete vascular ring.

A unique combination of pulmonary agenesis and anatomic left aortic arch with aberrant right subclavian artery was identified in two patients. Because of the right pulmonary agenesis, there is rotation of mediastinal contents, especially the aortic arch, into the right chest, converting an incomplete vascular ring to a near-complete vascular ring. The anterior portion of the ring is formed by the ascending aorta and aortic arch, whereas the posterior portion is formed by the aberrant right subclavian artery. Subclavian artery reimplantation and aortopexy effectively relieve the anterior and posterior tracheoesophageal compressive forces.

Tuning the Kondo effect with a mechanically controllable break junction.

We study electron transport through C(60) molecules in the Kondo regime using a mechanically controllable break junction. By varying the electrode spacing, we are able to change both the width and the height of the Kondo resonance, indicating modification of the Kondo temperature and the relative strength of coupling to the two electrodes. The linear conductance as a function of T/T(K) agrees with the scaling function expected for the spin-1/2 Kondo problem. We are also able to tune finite-bias Kondo features which appear at the energy of the first C(60) intracage vibrational mode.

Effect of semen thaw method on conception rate in four large commercial dairy heifer herds.

Semen processed with procedures intended to permit a flexible thaw method is used to breed millions of cows yearly. One method of thawing straws, the "pocket thaw" is used extensively with semen prepared with these procedures. Published field data is lacking for thaw method comparisons with semen processed to permit flexible-thawing. The objective of the present study was to measure the effect of semen thaw method (warm-water or pocket thaw) over all seasons and its interaction with herds, inseminators, straw package size, and sperm number on conception rate in commercial dairy heifer herds using semen processed with procedures historically optimized for success with flexible-thawing. Professional inseminators performed 11,215 services over a 16-month period in four large herds, achieving a 67.6% conception rate. Thaw method was alternated weekly. Thaw effect on conception status, determined by 70 days non-return rate, was estimated by a generalized linear mixed model. Neither thaw method nor number of sperm per straw significantly affected probability of conception (P=0.658 and 0.769, respectively). No interactions of thaw method with herd, sperm number, season, straw size, and straw size by season were detected (P=0.297, 0.526, 0.365, 0.723, and 0.824, respectively). Bull, herd, inseminator within herd, year, season, and straw size affected conception rate (P=0.002, 0.000, 0.000, 0.000, 0.000, and 0.014, respectively). In conclusion, for semen processed with procedures that permit flexible-thawing, thaw method (pocket thaw versus warm-water thaw) did not affect conception rate under commercial conditions and with routine semen handling methods.