Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of colostral volume, interval between calving and first milking, and photoperiod on colostral IgG concentrations in dairy cows.

OBJECTIVE To identify cow and management factors associated with colostral IgG concentration in dairy cows. DESIGN Prospective observational study. ANIMALS 81 multiparous Holstein-Friesian cows from a single herd. PROCEDURES Serum was obtained at the start of the nonlactating period, and cows were assigned to 1 of 4 photoperiod groups: natural day length (n = 22 cows), long days (16 h of light/d [21]) or short days (8 h of light/d [20]) for the entire nonlactating period, or natural day length followed by short days for the last 21 days of the nonlactating period (18). Serum and colostrum were collected at the first milking after calving. Regression analysis was used to investigate associations between colostral IgG concentration and the interval between calving and first milking, colostral volume, photoperiod, length of the nonlactating period, and season of calving. RESULTS Colostral IgG concentration decreased by 3.7% during each subsequent hour after calving because of postparturient secretion by the mammary glands. The interval between calving and first milking and the colostral volume were significantly and negatively associated with colostral IgG concentration, with the former effect predominating. Photoperiod had no effect on colostral IgG concentration or volume. Serum protein concentration at calving correlated poorly with colostral IgG concentration. CONCLUSIONS AND CLINICAL RELEVANCE Dairy producers should harvest colostrum as soon as possible after calving to optimize transfer of passive immunity in neonatal calves. Photoperiod can be manipulated without adversely affecting colostral IgG concentration.
Approximately-Optimal Queries for Planning in Reward-Uncertain Markov Decision Processes

When planning actions to take on behalf of its human operator, a robot might be uncertain about its operator's reward function. We address the problem of how the robot should formulate an (approximately) optimal query to pose to the operator, given how its uncertainty affects which policies it should plan to pursue. We explain how a robot whose queries ask the operator to choose the best from among k choices can, without loss of optimality, restrict consideration to choices only over alternative policies. Further, we present a method for constructing an approximately-optimal policy query that enjoys a performance bound, where the method need not enumerate all policies. Finally, because queries posed to the operator of a robotic system are often expressed in terms of preferences over trajectories rather than policies, we show how our constructed policy query can be projected into the space of trajectory queries. Our empirical results demonstrate that our projection technique can outperform prior techniques for choosing trajectory queries, particularly when the number of trajectories the operator is asked to compare is small.
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.

The complexity of biological systems provides for a great diversity of relationships between genes. The current analysis of whole-genome expression data focuses on relationships based on global correlation over a whole time-course, identifying clusters of genes whose expression levels simultaneously rise and fall. There are, of course, other potential relationships between genes, which are missed by such global clustering. These include activation, where one expects a time-delay between related expression profiles, and inhibition, where one expects an inverted relationship. Here, we propose a new method, which we call local clustering, for identifying these time-delayed and inverted relationships. It is related to conventional gene-expression clustering in a fashion analogous to the way local sequence alignment (the Smith-Waterman algorithm) is derived from global alignment (Needleman-Wunsch). An integral part of our method is the use of random score distributions to assess the statistical significance of each cluster. We applied our method to the yeast cell-cycle expression dataset and were able to detect a considerable number of additional biological relationships between genes, beyond those resulting from conventional correlation. We related these new relationships between genes to their similarity in function (as determined from the MIPS scheme) or their having known protein-protein interactions (as determined from the large-scale two-hybrid experiment); we found that genes strongly related by local clustering were considerably more likely than random to have a known interaction or a similar cellular role. This suggests that local clustering may be useful in functional annotation of uncharacterized genes. We examined many of the new relationships in detail. Some of them were already well-documented examples of inhibition or activation, which provide corroboration for our results. For instance, we found an inverted expression profile relationship between genes YME1 and YNT20, where the latter has been experimentally documented as a bypass suppressor of the former. We also found new relationships involving uncharacterized yeast genes and were able to suggest functions for many of them. In particular, we found a time-delayed expression relationship between J0544 (which has not yet been functionally characterized) and four genes associated with the mitochondria. This suggests that J0544 may be involved in the control or activation of mitochondrial genes. We have also looked at other, less extensive datasets than the yeast cell-cycle and found further interesting relationships. Our clustering program and a detailed website of clustering results is available at http://www.bioinfo. mbb.yale. edu/expression/cluster (or http://www.genecensus.org/expression/cluster).
More severe white matter changes in the elderly with jugular venous reflux

The etiology of age‐related white matter changes is unclear. Cerebral white matter changes on magnetic resonance imaging (MRI) and progressive dementia have been reported in patients with dural arteriovenous fistulas of the sigmoid sinus. The frequency of jugular venous reflux, which mimics a dural arteriovenous fistula, significantly increases with age. We investigated whether jugular venous reflux was associated with the severity of age‐related white matter changes in 97 persons (aged 55–90 years, mean [standard deviation]: 75.77 [8.19] years; 55 men) from a medical center memory clinic.
Surveillance of Viral Gastroenteritis in Japan: Pediatric Cases and Outbreak Incidents

Abstract Surveillance results from pediatric cases and outbreaks of viral gastroenteritis in Japan are presented. In winter, both small round structured virus (SRSV, or Norwalk-like viruses) and rotavirus were detected from infants with gastroenteritis; however, in recent years, the prevailing time of SRSV infection has preceded that of rotavirus infection. Most nonbacterial gastroenteritis outbreaks were related to SRSV infection, and >60% of the outbreaks were caused by contaminated food. In small-sized outbreaks, raw oysters were the primary source of transmission. In large-sized outbreaks, school lunches and catered meals that were served at schools, banquet halls, and hospitals were most often implicated in the transmission of foodborne gastroenteritis.
Trade Intensity and Output Synchronisation: On the Endogeneity Properties of EMU

Using annual bilateral data over the period 1988-2011 for a panel of 24 industrialised and emerging economies, we analyse in a time-varying framework the determinants of output synchronisation in EMU (European Monetary Union) distinguishing between core and peripheral member states. The results support the specialisation paradigm rather than the endogeneity hypothesis. Evidence is found in the euro period of diverging patterns between the core and the peripheral EMU countries raising questions about the future stability of EMU.
Properties of delay-period neuronal activity in the monkey dorsolateral prefrontal cortex during a spatial delayed matching-to-sample task.

The dorsolateral prefrontal cortex (PFC) has been implicated in visuospatial memory, and its cellular basis has been extensively studied with the delayed-response paradigm in monkeys. However, using this paradigm, it is difficult to dissociate neuronal activities related to visuospatial memory from those related to motor preparation, and few studies have provided evidence for the involvement of PFC neurons in visuospatial memory of a sensory cue, rather than in motor preparation. To extend this finding, we examined neuronal activities in the dorsolateral PFC while a rhesus monkey performed a spatial delayed matching-to-sample (SDMTS) task, which allows us to adequately access visuospatial memory independent of any sensorimotor components. The SDMTS task required the subject to make a lever-holding NOGO response or a lever-releasing GO response when a visuospatial matching cue (white spot, one of four peripheral locations, 15 degrees in eccentricity) matched or did not match a sample cue (physically the same as the matching cue) that had been presented prior to a delay period (3 s). Thus, the SDMTS task requires the subject to remember visuospatial information regarding the sample cue location during the delay period and is suitable for accessing visuospatial memory independent of any sensorimotor components, such as motor preparation, for directed movements. Of a total of 385 task-related neurons, 184 showed a sustained increase in activity during the delay period ("delay-period activity"). Most of these neurons (n = 165/184, 90%) showed positional delay-period activity, i.e., delay-period activity where the magnitude differed significantly with the position of the sample cue. This activity appears to be involved in visuospatial memory and to form a "memory field. " To quantitatively examine the properties of positional delay-period activity, we introduced a tuning index (TI) and a discriminative index (DI), which represent the sharpness of tuning and the discriminative ability, respectively, of positional delay-period activity. Both TI and DI varied among neurons with positional delay-period activity and were closely related to the time from the onset of the sample cue to the onset of positional delay-period activity; positional delay-period activity with sharper tuning and a greater discriminative ability had a slower onset. Furthermore, at the population level, both TI and DI were increased during the delay period in the neuronal population with a high DI value. These results extend previous findings to suggest that integrative, convergent processes of neuronal activities for increasing the accuracy of visuospatial memory may occur in the dorsolateral PFC. Thus, a critical role of the dorsolateral PFC in visuospatial memory may be to sharpen it to guide behaviors/decisions requiring accurate visuospatial memory.
Polarization splitter with hybrid plasmonic waveguide

We propose a design for a CMOS compatible three-core directional-coupler-based polarization splitter that incorporates a hybrid plasmonic waveguide. The large polarization selectivity of the hybrid plasmonic waveguide allows only the TM mode to evanescently couple to the cross port of the directional coupler, while the TE mode is confined to the through port. FDTD simulations show that the proposed polarization splitter can achieve peak extinction ratios of 23 dB over a 15 dB bandwidth of 82 nm, while having low insertion losses of <;1 dB.
Serum Prostate-Specific Antigen Hemodilution Among Obese Men Undergoing Screening in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial

Background: Previous studies have shown an inverse relationship between prostate-specific antigen (PSA) concentration and body mass index (BMI). It has been recently proposed that this relationship may be explained by the larger plasma volume of obese men diluting a fixed amount of PSA (hemodilution effect). We examined this hypothesis in a cohort of men enrolled in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Methods: Of 38,349 men ages 55 to 74 years randomized in PLCO to receive annual PSA and digital rectal examination screening, 28,380 had a baseline PSA, complete demographic information, and no prostate cancer diagnosis within 6 years from baseline. Self-reported height and weight were used to calculate BMI and to estimate plasma volume. PSA mass was estimated as PSA concentration times plasma volume. Multivariable linear regression models were used to investigate the relationship between PSA concentration, plasma volume, PSA mass, and BMI. Results: PSA concentration significantly decreased with increasing BMI (P < 0.001); mean PSA values were 1.27, 1.25, 1.18, and 1.07 ng/mL among normal (BMI, 18.5-25), overweight (BMI, 25-30), obese (BMI, 30-35), and morbidly obese (BMI, >35) men, respectively. However, plasma volume also increased with increasing BMI and PSA mass showed no association with BMI, with mean values of 3.78, 3.95, 3.97, and 3.82 μg across the four BMI categories (P = 0.10). Conclusions: This study confirms earlier findings that the inverse relationship between PSA concentration and BMI may be explained by a hemodilution effect. These findings could have implications for prostate cancer screening in large men. (Cancer Epidemiol Biomarkers Prev 2009;18(3):748–51)
A REVIEW OF THE RHEOLOGY OF FILLED VISCOELASTIC SYSTEMS

We are concerned here with the effect of added filler particles on the linear and non-linear rheological properties of viscoelastic systems. Whilst the addition of spherical or near-spherical filler particles will almost always increase the level of both the linear and the non-linear viscometric properties (so leading to increases in pressure drops, etc.), we usually find a decrease in the level of the elasticity (in its various measures combining the first normal stress difference and the shear stress), as manifested in such important practical features such as extrudate swell, melt fracture, size of entry vortices, stress relaxation, Weissenberg effect, etc. However, the addition of high-aspect-ratio, fibre-like fillers can increase the elasticity as well as the viscosity. Occasionally, the absorption of chemical species from the continuous phase onto the surface of the disperse phase particles can complicate matters due to depletion of the continuous phase.
The Heterotrimeric Laminin Coiled-Coil Domain Exerts Anti-Adhesive Effects and Induces a Pro-Invasive Phenotype

Laminins are large heterotrimeric cross-shaped extracellular matrix glycoproteins with terminal globular domains and a coiled-coil region through which the three chains are assembled and covalently linked. Laminins are key components of basement membranes, and they serve as attachment sites for cell adhesion, migration and proliferation. In this work, we produced a recombinant fragment comprising the entire laminin coiled-coil of the α1-, β1-, and γ1-chains that assemble into a stable heterotrimeric coiled-coil structure independently of the rest of the molecule. This domain was biologically active and not only failed to serve as a substrate for cell attachment, spreading and focal adhesion formation but also inhibited cell adhesion to laminin when added to cells in a soluble form at the time of seeding. Furthermore, gene array expression profiling in cells cultured in the presence of the laminin coiled-coil domain revealed up-regulation of genes involved in cell motility and invasion. These findings were confirmed by real-time quantitative PCR and zymography assays. In conclusion, this study shows for the first time that the laminin coiled-coil domain displays anti-adhesive functions and has potential implications for cell migration during matrix remodeling.
Benign plexiform (multinodular) schwannoma: a rare tumour unassociated with neurofibromatosis

In reviewing a large series of soft tissue tumours, seven cases of benign plexiform schwannoma have been retrieved. These were solitary lesions, not associated with von Recklinghausen's neurofibromatosis, which arose in the dermis or subcutaneous tissue, predominantly in young adults. None has recurred. While the schwannomatous nature of these rare lesions is readily appreciated, the frequent presence of nuclear pleomorphism and the plexiform growth pattern should not be regarded as having sinister prognostic significance.
The Effectiveness of FES-Evoked EMG Potentials to Assess Muscle Force and Fatigue in Individuals with Spinal Cord Injury

The evoked electromyographic signal (eEMG) potential is the standard index used to monitor both electrical changes within the motor unit during muscular activity and the electrical patterns during evoked contraction. However, technical and physiological limitations often preclude the acquisition and analysis of the signal especially during functional electrical stimulation (FES)-evoked contractions. Hence, an accurate quantification of the relationship between the eEMG potential and FES-evoked muscle response remains elusive and continues to attract the attention of researchers due to its potential application in the fields of biomechanics, muscle physiology, and rehabilitation science. We conducted a systematic review to examine the effectiveness of eEMG potentials to assess muscle force and fatigue, particularly as a biofeedback descriptor of FES-evoked contractions in individuals with spinal cord injury. At the outset, 2867 citations were identified and, finally, fifty-nine trials met the inclusion criteria. Four hypotheses were proposed and evaluated to inform this review. The results showed that eEMG is effective at quantifying muscle force and fatigue during isometric contraction, but may not be effective during dynamic contractions including cycling and stepping. Positive correlation of up to r = 0.90 (p < 0.05) between the decline in the peak-to-peak amplitude of the eEMG and the decline in the force output during fatiguing isometric contractions has been reported. In the available prediction models, the performance index of the eEMG signal to estimate the generated muscle force ranged from 3.8% to 34% for 18 s to 70 s ahead of the actual muscle force generation. The strength and inherent limitations of the eEMG signal to assess muscle force and fatigue were evident from our findings with implications in clinical management of spinal cord injury (SCI) population.
Chemical Similarities Between Galactic Bulge And Local Thick Disk Red Giant Stars

Context. The evolution of the Milky Way bulge and its relationship with the other Galactic populations is still poorly understood. The bulge has been suggested to be either a merger-driven classical bulge or the product of a dynamical instability of the inner disk. Aims. To probe the star formation history, the initial mass function and stellar nucleosynthesis of the bulge, we performed an elemental abundance analysis of bulge red giant stars. We also completed an identical study of local thin disk, thick disk and halo giants to establish the chemical differences and similarities between the various populations. Methods. High-resolution infrared spectra of 19 bulge giants and 49 comparison giants in the solar neighborhood were acquired with Gemini/Phoenix. All stars have similar stellar parameters but cover a broad range in metallicity. A standard 1D local thermodynamic equilibrium analysis yielded the abundances of C, N, O and Fe. A homogeneous and differential analysis of the bulge, halo, thin disk and thick disk stars ensured that systematic errors were minimized. Results. We confirm the well-established differences for [O/Fe] (at a given metallicity) between the local thin and thick disks. For the elements investigated, we find no chemical distinction between the bulge and the local thick disk, which is in contrast to previous studies relying on literature values for disk dwarf stars in the solar neighborhood. Conclusions. Our findings suggest that the bulge and local thick disk experienced similar, but not necessarily shared, chemical evolution histories. We argue that their formation timescales, star formation rates and initial mass functions were similar.
Neoadjuvant and adjuvant therapy in relation to surgery for colorectal liver metastases

Abstract Liver resection is associated with prolonged survival in patients with colorectal liver metastases. At diagnosis, 15–20% of patients have resectable colorectal liver metastases whereas other patients have too advanced disease to enable surgical treatment and receive chemotherapy. In patients undergoing resection of colorectal liver metastases, disease relapse occurs in up to 70%. Therefore, a combined approach including preoperative or postoperative chemotherapy or both has been tested to improve outcome after surgery. In patients with unresectable colorectal liver metastases, chemotherapy is initially the sole treatment option. The considerable improvement of the efficacy of anticancer agents has contributed to increase the response rate in patients with advanced colorectal cancer. In case of major response to chemotherapy, surgery with curative intent can be offered to patients with initially unresectable liver metastases.
A tale of two metrics: simultaneous bounds on competitiveness and regret

We consider algorithms for “smoothed online convex optimization” (SOCO) problems, which are a hybrid between online convex optimization (OCO) and metrical task system (MTS) problems. Historically, the performance metric for OCO was regret and that for MTS was competitive ratio (CR). There are algorithms with either sublinear regret or constant CR, but no known algorithm achieves both simultaneously. We show that this is a fundamental limitation – no algorithm (deterministic or randomized) can achieve sublinear regret and a constant CR, even when the objective functions are linear and the decision space is one dimensional. However, we present an algorithm that, for the important one dimensional case, provides sublinear regret and a CR that grows arbitrarily slowly.