Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of internal markers for predicting digestibility and fecal output by cattle fed bermudagrass hays of varying quality

The potential of in situ rumen undegradable dry matter (RUDM), indigestible neutr aldetergent fiber (INDF), indigestible acid-detergent fiber (IADF), a cid-detergent insoluble ash (ADIA), alkaline-peroxide lignin (APL), and acid-detergent lignin (ADL) to predict digestibility (DMD) and fecal output (FO) by cattle fed bermudagrass [ Cynodon dactylon (L.) Pers. ] haydiets categorized by their low (L), medium low (ML), medium high (MH), or high (H) C P concentrations (79, 111, 131, and 164 g/kg DM, respectively) was evaluated. The second objective was to evaluate the effects of time (0600, 1200, 1800, and 2400 h) of fecal sampling on the prediction of FO and DMD. A replicated 4 × 4 Latin-Square with one period miss ing was employed where diets were offered in three 15-d periods to provide 2 replicates per di et r period (n = 24). Actual DMI, FO, and DMD were determined based on hay offered, orts, and feces excreted. Hay, orts, and feces were analyzed for RUDM, INDF, I A , ADL, APL, and ADIA concentrations. Fecal recoveries of internal markers were expres sed as the ratio of the quantity of marker excreted per unit of marker consumed. Estimate of FO and DM D were calculated by the marker ratio technique. All in situ markers and ADL recoveries differed from 1. Estimates of DMD w ere underestimated while FO estimates were overestimated for all in situ m arkers. Recovery of APL tended to differ from 1, but ADIA recovery was not different from 1. Estimates of F O and DMD derived using APL and ADIA were not different from TC. Time of sampling affecte d th concentration of IADFa while ADIA and APL concentrations in fecal samples were not different. Estimates of FO and DMD by all fecal sampling times and their differe nt combinations were not different from actual FO and DMD. Therefore APL and ADIA have the pote ntial to predict FO and DMD of bermudagrass of various qualities fed to cattle and fecal sampling tim e may not be an issue when using internal markers. This dissertation is approved for recommendation to the Graduate Council. Dissertation Director: _______________________________________ Dr. Kenneth P. Coffey Dissertation Committee: _______________________________________
What determines family structure?

We estimate the effects of policy and labor market variables on the fertility, union formation and dissolution, type of union (cohabiting versus married), and partner choices of the NLSY79 cohort of women. These demographic behaviors interact to determine the family structure experienced by the children of these women: living with the biological mother and the married or cohabiting biological father, a married or cohabiting step father, or no man. We find that the average wage rates available to men and women have substantial effects on family structure for children of black and Hispanic mothers, but not for whites. The tax treatment of children also affects family structure. Implementation of welfare reform and passage of unilateral divorce laws had much smaller effects on family structure for the children of this cohort of women, as did changes in welfare benefits. The estimates imply that observed changes from the 1970s to the 2000s in the policy and labor market variables considered here contributed to a reduction in the proportion of time spent living without a father by children of the NLSY79 cohort of women. This suggests that the observed increase in this non-traditional family structure in the U.S. in the last three decades was caused by other factors.
Emotional Intelligence and Perceived Stress among Young Adults during COVID-19

The study intends to explore the relationship of emotional intelligence and perceived stress among young adults during covid-19. Through online survey two questionnaires were distributed to group of young adults aged between 18 and 25 years (N=65 females and N=60 males). A total of 125 samples were selected from various colleges and working sectors of Kerala for the study. Quantitative approach was used along with Cross-sectional descriptive research design was adopted and the sampling technique was purposive. Emotional Intelligence Self-Administered Tool (Sterrett, 2000) was used to assess the emotional intelligence among young adults and Perceived Stress Scale (Cohen et al., 1994) was used to determine the perceived stress levels among young adults. Pearson Correlation and Independent sample t-test was incorporated to reach the findings. According to Pearson Correlation the results indicated a significant negative low correlation between emotional intelligence and perceived stress levels. Independent sample t-test was computed on gender and results were found to be rejecting the null hypothesis, females were found to be higher in perceived stress than males and it was found that emotional intelligence has no significant difference based on gender, therefore the hypothesis was accepted. Hence there is a need to take measures by the authorities to reduce the stress among female adult population.
Abnormal Traffic Detection Circuit with Real-time Cardinality Counter

: To identify abnormal tra ﬃ c such as P2P ﬂows, DDoS attacks, and Internet worms, this paper discusses a circuit design to realize real-time abnormal tra ﬃ c detection in broadband networks. Real-time counting of cardinality is the key feature of the circuit. Although our previous study showed that cardinality counting is e ﬀ ective for detecting various types of abnormal tra ﬃ c, the slowness of DRAM access prevented us from deploying cardinality counting in backbone networks. To address the problem of DRAM access time, this paper proposes a new algorithm for cardinality counting. By changing the order of the cardinality counting process, the proposed algorithm enables parallel accesses of DRAM circuits, which hides the slow DRAM access time through a pipeline circuit. In addition, we propose a new hashing function that also hides the DRAM access problem. It partially replaces scattered addresses with successive addresses, in order to use a faster DRAM burst access. We also report the accuracy of the cardinality counting of the new algorithm, and describe the estimated processing performance based on a pipeline tact level circuit simulation. Our experimental results show that the use of the self-timed pipeline circuit can help realize cardinality counting at rates up to 100Gbps.
b -Adrenergic Blocking Agents in Heart Failure Benefits of Vasodilating and Nonvasodilating Agents According to Patients’ Characteristics: A Meta-analysis of Clinical Trials

Background: In patients with heart failure, b -adrener-gic blocking agents reduce overall and cardiovascular mortality. This meta-analysis aimed at clarifying their effect on sudden death, the magnitude of their benefit according to the cause of heart failure, and whether there is any difference between vasodilating and nonvasodilating agents. Methods: Randomized,clinicaltrialswereincludedifthey evaluated a b -adrenergic blocking agent without intrinsic sympathomimetic activity, included a control group receiving placebo or standard treatment, evaluated mortal-ityonanintention-to-treatbasis,andlastedatleast8weeks. Results: Twenty-one trials with 5849 patients (3130 receiving b -blockers) were included. Median length of treatment was 6 months. Most patients had mild or mod-erate heart failure and were treated with angiotensin-converting enzyme inhibitors, diuretics, and digitalis. The b -blockers significantly reduced overall mortality, cardiovascular mortality, and mortality due to pump failure and sudden death by 34% to 39%. The decrease in overall mortality in patients with ischemic heart disease (IHD) (30%) was no different from that among patients with non-IHD (26%) ( P = .08). The reduction in overall mortality was greater with vasodilating than with nonvasodilating agents (45% vs 27%; P = .007), particularly in patients without IHD (62%), compared with those with IHD (22%; P = .03). Conclusions: In patients with heart failure, b -blockers and cardiovascular mortality the expense
Sickle red blood cell derived extracellular vesicles activate endothelial cells and enhance sickle red cell adhesion mediated by von Willebrand factor

Endothelial activation and sickle red blood cell (RBC) adhesion are central to the pathogenesis of sickle cell disease (SCD). Quantitatively, RBC-derived extracellular vesicles, REVs, are more abundant from SS RBCs compared with healthy RBCs (AA RBCs). Sickle RBC-derived REVs (SS REVs) are known to promote endothelial cell (EC) activation through cell signaling and transcriptional regulation at longer terms. However, the SS REV-mediated short term non transcriptional response of EC is unclear. Here, we examined the impact of SS REVs on acute microvascular EC activation and RBC adhesion at 2 hours. Compared with AA REVs, SS REVs promoted human pulmonary microvascular endothelial cells (HPMEC) activation indicated by increased von Willebrand Factor (vWF) expression. Under microfluidic conditions, we found abnormal SS RBC adhesion to HPMECs exposed to SS REVs. This enhanced SS RBC adhesion was reduced by vWF cleaving protease ADAMTS13 to a level similar to HPMECs treated with AA REVs. Consistent with these observations, studies in SS mice with implanted dorsal skin-fold chambers found hemin-induced stasis was inhibited by ADAMTS13. The adhesion induced by SS REVs was variable, and was higher with SS RBCs from patients with increased markers of hemolysis (LDH and reticulocyte count) or a concomitant clinical diagnosis of deep vein thrombosis. Our results emphasize the critical contribution made by REVs to the pathophysiology of SCD by triggering acute microvascular EC activation and abnormal RBC adhesion. These findings may help to better understand acute pathophysiological mechanism of SCD and thereby the development of new treatment strategies using vWF as a potential target.
Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5

After the global spread of SARS-CoV-2 Omicron BA.2 lineage, some BA.2-related variants that acquire mutations in the L452 residue of spike protein, such as BA.2. 9.1 and BA.2. 13 (L452M), BA.2. 12.1 (L452Q), and BA.2. 11, BA.4 and BA.5 (L452R), emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these L452R/M/Q-bearing BA.2-related Omicron variants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1 and BA.2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2. 12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. Furthermore, infection experiments using hamsters indicated that BA.4/5 is more pathogenic than BA.2. Altogether, our multiscale investigations suggest that the risk of L452R/M/Q-bearing BA.2-related Omicron variants, particularly BA.4 and BA.5, to global health is potentially greater than that of original BA.2. Highlights Spike L452R/Q/M mutations increase the effective reproduction number of BA.2 BA.4/5 is resistant to the immunity induced by BA.1 and BA.2 infections BA.2. 12.1 and BA.4/5 more efficiently spread in human lung cells than BA.2 BA.4/5 is more pathogenic than BA.2 in hamsters
TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies

Aggregation of the RNA-binding protein TDP-43 is the main common neuropathological feature of TDP-43 proteinopathies. In physiological conditions, TDP-43 is predominantly nuclear and contained in biomolecular condensates formed via liquid-liquid phase separation (LLPS). However, in disease, TDP-43 is depleted from these compartments and forms cytoplasmic or, sometimes, intranuclear inclusions. How TDP-43 transitions from physiological to pathological states remains poorly understood. Here, we show that self-oligomerization and RNA binding cooperatively govern TDP-43 stability, functionality, LLPS and cellular localization. Importantly, our data reveal that TDP-43 oligomerization is connected to, and conformationally modulated by, RNA binding. Mimicking the impaired proteasomal activity observed in patients, we found that TDP-43 forms nuclear aggregates via LLPS and cytoplasmic aggregates via aggresome formation. The favored aggregation pathway depended on the TDP-43 state –monomeric/oligomeric, RNA-bound/-unbound– and the subcellular environment –nucleus/cytoplasm. Our work unravels the origins of heterogeneous pathological species occurring in TDP-43 proteinopathies.
Physical resilience in the brain: The effect of white matter disease on brain networks in cognitively normal older adults

BACKGROUND Physical resilience with age is considered a key feature of healthy aging, but current understanding of the neural contributions to resilience is limited. Additionally, few methods exist to identify physical resilience and observe the mechanisms through which resilience manifests. METHODS To address these gaps, we used data from 189 participants from the Brain Networks and Mobility (B-NET) study who completed the short physical performance battery (SPPB) as well as its expanded version (eSPPB), magnetic resonance imaging (MRI), and functional MRI (fMRI). Functional brain networks were generated using graph theory methods. We grouped participants based on SPPB scores (<10=unhealthy & 10-12=healthy) and median splits of white matter hyperintensity volumes: Expected Healthy (EH: low WMH, healthy SPPB, n=81), Expected Impaired (EI: high WMH, unhealthy SPPB, n=42), Unexpected Healthy (UH: high WMH, healthy SPPB, n=53), and Unexpected Impaired (UI: low WMH, unhealthy SPPB, n=13). UH is considered the “resilient” group due to their maintained function despite elevated WMH burden. Continuous analyses assessed the relationships between network properties, mobility, and cognition. RESULTS Higher SPPB scores were associated (p<0.01) with greater sensorimotor cortex community structure (SMN-CS) consistency. While no main effect of the resilience interaction term (SPPB*WMH) was found on SMN-CS, UH showed higher numbers of second-order connections between the SMN and anterior cingulate cortex (ACC) than EI (p<0.01). CONCLUSIONS Increased connectivity between SMN and ACC may be a marker of physical resilience within the brain.
The Budding Yeast Heterochromatic Protein Sir3 is a Global Modulator of Gene Expression

The SIR complex (Silent Information Regulator) is the building block of heterochromatic structures that silence underlying genes. It is well established that the silenced state is epigenetically inherited but it is not known how the SIR complex survives perturbations caused by DNA replication nor how it is maintained when cells are exposed to environmental challenges such as nutrient deprivation. The biological function of heterochromatin located in subtelomeric regions is also unclear since heterochromatin coverage appears to be limited to a few kbps near chromosome ends and the expression of subtelomeric genes is only marginally affected in the absence of the SIR complex. We use a three pronged approach to address these questions. First, nanopore-MetID, an in vivo foot printing technique similar to DamID that uses nanopore sequencing technology, identified hundreds of new transient contacts between Sir3 and euchromatic genes that are not detectable by ChIP-seq and revealed a high and a previously undocumented low-density mode of Sir3 binding to subtelomeric regions. Second, our measurements of genome-wide Sir3 exchange rates after exit from starvation show that heterochromatin is a highly dynamic structure in optimal growth conditions. Third, “spike-in” RNA-seq time course experiments in the same conditions reveal that Sir3 modulates global mRNA levels in correlation with fluctuations in nutrient availability. We now propose that subtelomeric regions serve as Sir3 hubs from which Sir3 diffuses down the chromosome arm and transiently contacts euchromatic genes in its path. We hypothesize
Inference of Electrical Stimulation Sensitivity from Recorded Activity of Primate Retinal Ganglion Cells

High-fidelity electronic implants can in principle restore the function of neural circuits by precisely activating neurons via extracellular stimulation. However, direct characterization of the individual electrical sensitivity of a large population of target neurons, to precisely control their activity, can be difficult or impossible. A potential solution is to leverage biophysical principles to infer sensitivity to electrical stimulation from features of spontaneous electrical activity, which can be recorded relatively easily. Here, this approach is developed and its potential value for vision restoration is tested quantitatively using large-scale multielectrode stimulation and recording from retinal ganglion cells (RGCs) of male and female macaque monkeys ex vivo. Electrodes recording larger spikes from a given cell exhibited lower stimulation thresholds across cell types, retinas, and eccentricities, with systematic and distinct trends for somas and axons. Thresholds for somatic stimulation increased with distance from the axon initial segment. The dependence of spike probability on injected current was inversely related to threshold, and was substantially steeper for axonal than somatic compartments, which could be identified by their recorded electrical signatures. Dendritic stimulation was largely ineffective for eliciting spikes. These trends were quantitatively reproduced with biophysical simulations. Results from human RGCs were broadly similar. The inference of stimulation sensitivity from recorded electrical features was tested in a data-driven simulation of visual reconstruction, revealing that the approach could significantly improve the function of future high-fidelity retinal implants. SIGNIFICANCE STATEMENT This study demonstrates that individual in situ primate retinal ganglion cells of different types respond to artificially generated, external electrical fields in a systematic manner, in accordance with theoretical predictions, that allows for prediction of electrical stimulus sensitivity from recorded spontaneous activity. It also provides evidence that such an approach could be immensely helpful in the calibration of clinical retinal implants.
Estimating chromosome sizes from karyotype images enables validation of de novo assemblies

Highly contiguous genome assemblies are essential for genomic research. Chromosome-scale assembly is feasible with the modern sequencing techniques in principle, but in practice, scaffolding errors frequently occur, leading to incorrect number and sizes of chromosomes. Relating the observed chromosome sizes from karyotype images to the generated assembly scaffolds offers a method for detecting these errors. Here, we present KICS, a semi-automated approach for estimating relative chromosome sizes from karyotype images and their subsequent comparison to the corresponding assembly scaffolds. The method relies on threshold-based image segmentation and uses the computed areas of the chromosome-related connected components as a proxy for the actual chromosome size. We demonstrate the validity and practicality of our approach by applying it to karyotype images of humans and various amphibians, birds, fish, insects, mammals, and plants. We found a strong linear relationship between pixel counts and the DNA content of chromosomes. Averaging estimates from eight human karyotype images, KICS predicts most of the chromosome sizes within an error margin of just 6 Mb. Our method provides additional means of validating genome assemblies at low costs. An interactive implementation of KICS is available at https://github.com/mpicbg-csbd/napari-kics.
Common facultative endosymbionts do not influence sensitivity of cereal aphids to pyrethroids

Cereal aphids, including the bird cherry-oat aphid, Rhopalosiphum padi, and the grain aphid, Sitobion avenae, can transmit viruses that significantly reduce crop yields. To mitigate against yield losses, insecticides are routinely used to manage aphid populations. Aphids can form relationships with endosymbionts that confer fitness benefits or consequences to the aphid. Recent artificial inoculation experiments indicate that endosymbionts could increase aphid susceptibility to insecticides, but this has not been explored using aphid populations naturally infected with endosymbionts. Here, we sampled aphids from an important cereal production region in Lower Saxony, Germany. We characterised the endosymbiont profile of these aphid populations and conducted pyrethroid dose-response assays to test the hypothesis that facultative endosymbionts increase aphid susceptibility to insecticides. We find that the level of insecticide susceptibility is highly variable in S. avenae and we identify populations that are sensitive and tolerant to pyrethroids, including populations collected from the same field. For R. padi, we find evidence for decreased sensitivity to pyrethroids, representing the first report of reduced sensitivity to pyrethroids in R. padi sampled from Central Europe. We detected high endosymbiont infection frequencies in the aphid populations. 84% of aphids carry one facultative endosymbiont and 9% of aphids carry two facultative endosymbionts. We detected associations with Regiella insecticola, Fukatsia symbiotica, and Hamiltonella defensa. However, we do not identify a link between endosymbiont infection and insecticide susceptibility, indicating that other factors may govern the development of insecticide resistance and the need for alternative management strategies.
Input-Specific Inhibitory Plasticity Improves Decision Accuracy Under Noise

Inhibitory interneurons regulate excitability, information flow, and plasticity in neural circuits. Inhibitory synapses are also plastic and can be modified by changes in experience or activity, often together with changes to excitatory synapses. However, given the diversity of inhibitory cell types within the cerebral cortex, it is unclear if plasticity is similar for various inhibitory inputs or what the functional significance of inhibitory plasticity might be. Here we examined spike-timing-dependent plasticity of inhibitory synapses from four major subtypes of GABAergic cells onto layer 2/3 pyramidal cells in mouse auditory cortex. The likelihood of inhibitory potentiation varied across cell types, with somatostatin-positive (SST+) interneuron inputs exhibiting the most potentiation on average. A network simulation of perceptual decision-making revealed that plasticity of SST+-like inputs provided robustness from higher input noise levels to maintain decision accuracy. Differential plasticity at specific inhibitory inputs therefore may be important for network function and sensory perception.