Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic parameters of postnatal mortality and birth weight in Japanese Black calves.

Postnatal mortality (PM) of calves is an economically important trait, because a high mortality rate of calves decreases farm income and significantly increases production costs. In spite of the economic importance of PM, genetic studies on PM have been scarce for Japanese Black cattle. The objectives of this study were to estimate the direct and maternal heritability for PM using a Bayesian threshold model with Gibbs sampling in Japanese Black cattle. The original data consisted of 43 723 records of animals born from January 2005 to June 2006. Four binary traits of mortality were considered: D1-14, D15-60, D61-180 and D1-180 with numbers indicating the period of risk in days after birth. Direct heritabilities for PM ranged from 0.12 to 0.31 and maternal heritabilities for PM were lower than the direct heritabilities and ranged from 0.02 to 0.16. Direct genetic correlations between D1-14 and D15-60, between D15-60 and D61-180, and between D1-14 and D61-180 were 0.501, 0.689 and 0.062, respectively. Direct genetic correlations of birth weight with D1-14, D15-60, D61-180 and D1-180 were 0.089, 0.482, 0.434 and 0.394, respectively. These results indicated that different genes were responsible for early and late PM and early PM (D1-14) can be genetically reduced without influencing birth weight.
Regulation of plant immune receptors by ubiquitination

From pathogen perception and the activation of signal transduction cascades to the deployment of defense responses, protein ubiquitination plays a key role in the modulation of plant immunity. Ubiquitination is mediated by three enzymes, of which the E3 ubiquitin ligases, the substrate determinants, have been the major focus of attention. Accumulating evidence suggests that ubiquitination modulates signaling mediated by pattern recognition receptors and is important for the accumulation of nucleotide-binding leucine-rich repeat type intracellular immune sensors. Recent studies also indicate that ubiquitination directs vesicle trafficking, a function that has been clearly established for immune signaling in animals. In this mini review, we discuss these and other recent advances and highlight important open questions.
Clinical conundrums and challenges during geriatric orthopedic emergency surgeries

Despite so many advancements and innovations in anesthetic techniques, expectations and challenges have also grown in plenty. Cardiac, pediatric, obstetric and neuro-anesthesia have perfectly developed to fulfill the desired needs of respective patient population. However, geriatric anesthesia has been shown a lesser interest in teaching and clinical practices over the years as compared with other anesthetic sub-specialties. The large growing geriatric population globally is also associated with an increase number of elderly patients presenting for orthopedic emergency surgeries. Orthopedic emergency surgery in geriatric population is not only a daunting clinical challenge but also has numerous socio-behavioral and economic ramifications. Decision making in anesthesia is largely influenced by the presence of co-morbidities, neuro-cognitive functions and the current socio-behavioral status. Pre-anesthetic evaluation and optimization are extremely important for a better surgical outcome but is limited by time constraints during emergency surgery. The current review aims to highlight comprehensively the various clinical, social, behavioral and psychological aspects during pre-anesthetic evaluation associated with emergency orthopedic surgery in geriatric population.
Scalable Internet Routing on Topology-Independent Node Identities

Unmanaged Internet Protocol (UIP) is a fully selforganizing network-layer protocol that implements scalable identity-based routing. In contrast with addressbased routing protocols, which depend for scalability on centralized hierarchical address management, UIP nodes use a flat namespace of cryptographic node identifiers. Node identities can be created locally on demand and remain stable across network changes. Unlike locationindependent name services, the UIP routing protocol can stitch together many conventional address-based networks with disjoint or discontinuous address domains, providing connectivity between any pair of participating nodes even when no underlying network provides direct connectivity. The UIP routing protocol works on networks with arbitrary topologies and global traffic patterns, and requires only O(log N) storage per node for routing state, enabling even small, ubiquitous edge devices to act as ad-hoc selfconfiguring routers. The protocol rapidly recovers from network partitions, bringing every node up-to-date in a multicast-based chain reaction of O(log N) depth. Simulation results indicate that UIP finds routes that are on average within 2× the length of the best possible route. This technical report describes a work in progress and does not contain complete, final, or polished results. This research was conducted as part of the IRIS project (http://project-iris.net/), supported by the National Science Foundation under Cooperative Agreement No. ANI-0225660.
Diagnostic paleoradiology of mummified tissue: interpretation and pitfalls.

D ead human and animal tissue can, because of natural conditions or artificial attempts, escape postmortem decay partially or even completely. This process called " mummification " derives linguistically from the Persian word mum or mom, which means beeswax. 1 In order to conduct an accurate radiologic diagnosis of the anatomical and pathologic changes in mummies, and thereby advance research in this area, a thorough knowledge of the process of mummification itself is required. The purpose of this article is to review the role of diagnostic paleoradiology in mummy studies. Natural mummification may occur under contrasting climatic conditions: the alpine/arctic process of freeze-drying, which requires sufficient air flow to sublimate body water; preservation in northern European peat bogs, in which acids interfere with enzymatic soft-tissue decomposition; or the mummification that can happen in the hot and arid environment of deserts. Artificial mummification can be achieved by embalming a body, as seen in the funerary tradition of Ancient Egypt where a physically well-preserved body was essential to gain immortality. Surprisingly, this method has been described very rarely in historical times and is passed on to us de facto only by Herodotus of Halicarnassus (fifth century BC) and by Diodorus Siculus (first century BC). Essentially, it involved the complete or incomplete removal of the internal organs using diverse tools. 2 Desiccation of the body was obtained by using natron, 3,4 a blend of NaCl, Na 2 CO 3 , NaHCO 3 and NaP 2 SO 4. 5 The term " natron " was coined after the Wadi Natrun region in Egypt. The embalming substance was a still mostly unknown mixture of natron with various preserving and aromatic products. 6–12 Finally, the corpse was wrapped with bandages and kept within a coffin in a well-sealed tomb. Since antiquity, the presence of valuable burial goods, such as jewellery and religious objects, in Egyptian tombs has attracted many thieves. Mummies recovered in modern times usually bear several stigmata of these acts of vandalism caused by tomb looters. Burial artifacts have also been removed during archaeological excavations and the scientific unwrapping of mummies. Mysterious deaths of scientists have been linked with the " curse of the Pharaohs, " a romantic speculation without any strong scientific basis. 13 Postmortem alterations of soft tissues and bone caused by artificial mummification are numerous. Internal organs were either removed completely and kept in jars or were put back in the …
Development of a Risk Reduction Intervention to Reduce Bacterial and Viral Infections for Injection Drug Users

Bacterial infections are widespread problems among drug injectors, requiring novel preventive intervention. As part of a NIDA-funded study, we developed an intervention based on the Information-Motivation-Behavioral Skills model, past research, injection hygiene protocols, and data collected from focus groups with 32 injectors in Denver in 2009. Qualitative responses from focus groups indicated that most participants had experienced skin abscesses and believed that bacterial infections were commonly a result of drug cut, injecting intramuscularly, and reusing needles. Access to injection supplies and experiencing withdrawal were the most frequently reported barriers to utilizing risk reduction. Implications for intervention development are discussed.
EyePrint: Using Passive Eye Trace From Reading to Enhance Document Access and Comprehension

The improvement of digital document technologies is changing our document browsing style. We browse a lot of documents in a short time, jumping from one to another by following the hyperlinks. This makes document management difficult; we sometimes feel it is difficult to keep track of all of the information. To overcome this problem, this article proposes a novel method that uses the user's eye movement to create passive traces of document comprehension for digital documents. The eye gaze traces so generated become metadata of the document; they can be used in the next search, document browsing, and zooming. A prototype system that works with a gaze tracking system is developed. Two experiments are conducted to evaluate the usefulness of eye gaze traces in digital document browsing. The first experiment examines the validity of trace generation, where generated eye gaze traces are compared with the ‘participants’ self-judgment of reading. In the second experiment, participants browse a set of documents to gather information, where the ‘participants’ reading behavior with the eye gaze trace and the efficiency of keyword search is studied. The results confirm that EyePrint is the answer to keeping track of digital documents.
Galena oxidation investigations on oxygen and sulphur isotopes

Batch experiments with the lead sulphide ore mineral galena were carried out in order to get information about the oxidation mechanisms and to contribute to the understanding of field data, especially those obtained from the mining-affected sites. Results indicate that oxygen and sulphur isotopes of dissolved sulphate may be useful tools for the investigation of galena oxidation mechanisms. However, some methodological modifications are necessary to obtain sufficient sulphate yields, which are a prerequisite for the reduction of the analytical uncertainty. Surface and hydrochemical investigations indicated that galena was dissolved non-oxidatively during the experiment at initial pH 2, whereas the oxidative dissolution of galena dominated in experiments at initial pH 6 and 8. No isotope results could be obtained from the experiment at initial pH 2 due to the low sulphate production. The oxidative dissolution of galena resulted in somewhat higher sulphate yields. Thus, the oxygen isotope composition of sulphate produced from galena oxidation could be determined for the first time. Oxygen in sulphate derived largely from water molecules; but minor amounts of molecular oxygen could be also observed. Both molecular oxygen and ferric iron may act as oxidants of galena. A variety of intermediate reactions allow for a variable oxygen isotope composition of sulphate. Sulphur isotopes of sulphate showed an enrichment of 32S in sulphate (relative to galena), which increases with increasing pH. Sulphur isotope enrichment processes may be associated with the formation of anglesite.
Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region

Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.
The Relationship between Pedal Force and Crank Angular Velocity in Sprint Cycling.

PURPOSE Relationships between tangential pedal force and crank angular velocity in sprint cycling tend to be linear. We set out to understand why they are not hyperbolic, like the intrinsic force-velocity relationship of muscles. METHODS We simulated isokinetic sprint cycling at crank angular velocities ranging from 30 to 150 rpm with a forward dynamic model of the human musculoskeletal system actuated by eight lower extremity muscle groups. The input of the model was muscle stimulation over time, which we optimized to maximize average power output over a cycle. RESULTS Peak tangential pedal force was found to drop more with crank angular velocity than expected based on intrinsic muscle properties. This linearizing effect was not due to segmental dynamics but rather due to active state dynamics. Maximizing average power in cycling requires muscles to bring their active state from as high as possible during shortening to as low as possible during lengthening. Reducing the active state is a relatively slow process, and hence must be initiated a certain amount of time before lengthening starts. As crank angular velocity goes up, this amount of time corresponds to a greater angular displacement, so the instant of switching off extensor muscle stimulation must occur earlier relative to the angle at which pedal force was extracted for the force-velocity relationship. CONCLUSION Relationships between pedal force and crank angular velocity in sprint cycling do not reflect solely the intrinsic force-velocity relationship of muscles but also the consequences of activation dynamics.
Medical Management of Crohn's Disease

The clinical course of Crohn's disease (CD) is characterized by unpredictable phases of disease activity and quiescence. The majority of CD patients experience mild to moderate disease or are in clinical remission over significant periods during the course of their disease. These patients can be treated conservatively with 5-aminosalicylates or budesonide depending on the disease location. Those patients with more severe forms of the disease who require corticosteroids should be treated more aggressively with early introduction of immunomodulator and/or biologic therapy, which may help to prevent the complications associated with CD. It has been suggested that therapies directed at mucosal healing may favorably modify the natural history of CD. As newer, more effective medications become available and new therapeutic approaches are introduced (top-down therapy), mucosal healing, and not solely clinical remission, may well become the preferred treatment objective.
Echoes of Persuasion: The Effect of Euphony in Persuasive Communication

While the effect of various lexical, syntactic, semantic and stylistic features have been addressed in persuasive language from a computational point of view, the persuasive effect of phonetics has received little attention. By modeling a notion of euphony and analyzing four datasets comprising persuasive and non-persuasive sentences in different domains (political speeches, movie quotes, slogans and tweets), we explore the impact of sounds on different forms of persuasiveness. We conduct a series of analyses and prediction experiments within and across datasets. Our results highlight the positive role of phonetic devices on persuasion.
Evaluation of D-dimer in the diagnosis of suspected aortic dissection

Abstract Background: The goal of this study was to evaluate plasma D-dimer as a diagnostic marker for exclusion of suspected aortic dissection (AD). Methods: Two-hundred and sixty suspected AD patients were enrolled, including acute AD, n=107; chronic AD, n=17; acute myocardial infarction (AMI), n=70; pulmonary embolism (PE), n=18; non-ST elevation myocardial infarction (NSTEMI), n=28; and unstable angina (UA), n=20. All patients had D-dimer testing performed (Roche Diagnostics GmbH) immediately following admission. Results: The D-dimer concentrations in both the acute AD group [median: 3.47; 95% confidence interval (CI): 2.43–4.50 μg/mL] and chronic AD group (median: 1.09; 95% CI: 0.36–3.81 μg/mL) were significantly higher than those in patients in the AMI, NSTEMI and UA groups (p=0.000), but not when compared to the PE group. One (0.8%) patient was identified in the acute AD group who presented with a low D-dimer value (0.04 μg/mL), indicating the existence of intramural hematoma as demonstrated by CT. Conclusions: D-dimer may be used as a potential marker for suspected AD, with high sensitivity of up to 99.2% (1/124). Regardless of the cut-off threshold selected, the sensitivity of D-dimer was unable to reach 100%. Further examinations, including imaging technology, were necessary to diagnose the suspected AD patients who had negative D-dimer result. Clin Chem Lab Med 2010;48:1733–7.
Improved Forest Biomass and Carbon Estimations Using Texture Measures from WorldView-2 Satellite Data

Accurate estimation of aboveground biomass and carbon stock has gained importance in the context of the United Nations Framework Convention on Climate Change (UNFCCC) and the Kyoto Protocol. In order to develop improved forest stratum–specific aboveground biomass and carbon estimation models for humid rainforest in northeast Madagascar, this study analyzed texture measures derived from WorldView-2 satellite data. A forest inventory was conducted to develop stratum-specific allometric equations for dry biomass. On this basis, carbon was calculated by applying a conversion factor. After satellite data preprocessing, vegetation indices, principal components, and texture measures were calculated. The strength of their relationships with the stratum-specific plot data was analyzed using Pearson’s correlation. Biomass and carbon estimation models were developed by performing stepwise multiple linear regression. Pearson’s correlation coefficients revealed that (a) texture measures correlated more with biomass and carbon than spectral parameters, and (b) correlations were stronger for degraded forest than for non-degraded forest. For degraded forest, the texture measures of Correlation, Angular Second Moment, and Contrast, derived from the red band, contributed to the best estimation model, which explained 84% of the variability in the field data (relative RMSE = 6.8%). For non-degraded forest, the vegetation index EVI and the texture measures of Variance, Mean, and Correlation, derived from the newly introduced coastal blue band, both NIR bands, and the red band, contributed to the best model, which explained 81% of the variability in the field data (relative RMSE = 11.8%). These results indicate that estimation of tropical rainforest biomass/carbon, based on very high resolution satellite data, can be improved by (a) developing and applying forest stratum–specific models, and (b) including textural information in addition to spectral information.
The Role of Adaptation in Bacterial Speed Races

Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli. A paradigm among prokaryotes is the chemotaxis system, which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion. A notable feature of chemotaxis is adaptation: after the application of a step stimulus, the bacterial running time relaxes to its pre-stimulus level. The response to the amino acid aspartate is precisely adapted whilst the response to serine is not, in spite of the same pathway processing the signals preferentially sensed by the two receptors Tar and Tsr, respectively. While the chemotaxis pathway in E. coli is well characterized, the role of adaptation, its functional significance and the ecological conditions where chemotaxis is selected, are largely unknown. Here, we investigate the role of adaptation in the climbing of gradients by E. coli. We first present theoretical arguments that highlight the mechanisms that control the efficiency of the chemotactic up-gradient motion. We discuss then the limitations of linear response theory, which motivate our subsequent experimental investigation of E. coli speed races in gradients of aspartate, serine and combinations thereof. By using microfluidic techniques, we engineer controlled gradients and demonstrate that bacterial fronts progress faster in equal-magnitude gradients of serine than aspartate. The effect is observed over an extended range of concentrations and is not due to differences in swimming velocities. We then show that adding a constant background of serine to gradients of aspartate breaks the adaptation to aspartate, which results in a sped-up progression of the fronts and directly illustrate the role of adaptation in chemotactic gradient-climbing.
Ciliary biology: Understanding the cellular and genetic basis of human ciliopathies

Motile cilia have long been known to play a role in processes such as cell locomotion and fluid movement whereas the functions of primary cilia have remained obscure until recent years. To date, ciliary dysfunction has been shown to be causally linked to a number of clinical manifestations that characterize the group of human disorders known as ciliopathies. This classification reflects a common or shared cellular basis and implies that it is possible to associate a series of different human conditions with ciliary dysfunction, which allows gaining insight into the cellular defect in disorders of unknown etiology solely based on phenotypic observations. Furthermore, to date we know that the cilium participates in a number of biological processes ranging from chemo‐ and mechanosensation to the transduction of a growing list of paracrine signaling cascades that are critical for the development and maintenance of different tissues and organs. Consequently, the primary cilium has been identified as a key structure necessary to regulate and maintain cellular and tissue homeostasis and thus its study is providing significant information to understand the pathogenesis of the different phenotypes that characterize these human conditions. Finally, the similarities between different ciliopathies at the phenotypic level are proving to be due to their shared cellular defect and also their common genetic basis. To this end, recent studies are showing that mutations in a given ciliary gene often appear involved in the pathogenesis of more than one clinical entity, complicating their genetic dissection, and hindering our ability to generate accurate genotype–phenotype correlations. © 2009 Wiley‐Liss, Inc.