Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci

The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.
Benefits from retrieval practice are greater for students with lower working memory capacity

ABSTRACT We examined the effects of retrieval practice for students who varied in working memory capacity as a function of the lag between study of material and its initial test, whether or not feedback was given after the test, and the retention interval of the final test. We sought to determine whether a blend of these conditions exists that maximises benefits from retrieval practice for lower and higher working memory capacity students. College students learned general knowledge facts and then restudied the facts or were tested on them (with or without feedback) at lags of 0–9 intervening items. Final cued recall performance was better for tested items than for restudied items after both 10 minutes and 2 days, particularly for longer study–test lags. Furthermore, on the 2-day delayed test the benefits from retrieval practice with feedback were significantly greater for students with lower working memory capacity than for students with higher working memory capacity (r = −.42). Retrieval practice may be an especially effective learning strategy for lower ability students.
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats

&NA; The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re‐examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
[Pemetrexed + Sorafenib] lethality is increased by inhibition of ERBB1/2/3-PI3K-NFκB compensatory survival signaling

In the completed phase I trial NCT01450384 combining the anti-folate pemetrexed and the multi-kinase inhibitor sorafenib it was observed that 20 of 33 patients had prolonged stable disease or tumor regression, with one complete response and multiple partial responses. The pre-clinical studies in this manuscript were designed to determine whether [pemetrexed + sorafenib] –induced cell killing could be rationally enhanced by additional signaling modulators. Multiplex assays performed on tumor material that survived and re-grew after [pemetrexed + sorafenib] exposure showed increased phosphorylation of ERBB1 and of NFκB and IκB; with reduced IκB and elevated G-CSF and KC protein levels. Inhibition of JAK1/2 downstream of the G-CSF/KC receptors did not enhance [pemetrexed + sorafenib] lethality whereas inhibition of ERBB1/2/4 using kinase inhibitory agents or siRNA knock down of ERBB1/2/3 strongly promoted killing. Inhibition of ERBB1/2/4 blocked [pemetrexed + sorafenib] stimulated NFκB activation and SOD2 expression; and expression of IκB S32A S36A significantly enhanced [pemetrexed + sorafenib] lethality. Sorafenib inhibited HSP90 and HSP70 chaperone ATPase activities and reduced the interactions of chaperones with clients including c-MYC, CDC37 and MCL-1. In vivo, a 5 day transient exposure of established mammary tumors to lapatinib or vandetanib significantly enhanced the anti-tumor effect of [pemetrexed + sorafenib], without any apparent normal tissue toxicities. Identical data to that in breast cancer were obtained in NSCLC tumors using the ERBB1/2/4 inhibitor afatinib. Our data argue that the combination of pemetrexed, sorafenib and an ERBB1/2/4 inhibitor should be explored in a new phase I trial in solid tumor patients.
Medical Exam Question Answering with Large-scale Reading Comprehension

Reading and understanding text is one important component in computer aided diagnosis in clinical medicine, also being a major research problem in the field of NLP. In this work, we introduce a question-answering task called MedQA to study answering questions in clinical medicine using knowledge in a large-scale document collection. The aim of MedQA is to answer real-world questions with large-scale reading comprehension. We propose our solution SeaReader---a modular end-to-end reading comprehension model based on LSTM networks and dual-path attention architecture. The novel dual-path attention models information flow from two perspectives and has the ability to simultaneously read individual documents and integrate information across multiple documents. In experiments our SeaReader achieved a large increase in accuracy on MedQA over competing models. Additionally, we develop a series of novel techniques to demonstrate the interpretation of the question answering process in SeaReader.
Resilience in Elders of the Sardinian Blue Zone: An Explorative Study

Background: older adults from the Sardinian Blue Zone self-report low depressive symptoms and high psychological well-being. However, the role of dispositional resilience as a determinant of these characteristics is unknown. Objectives: the current study had three aims. First, to investigate associations among several putative predictors, including dispositional resilience and three established markers of positive and negative mental health. Second, to determine if gender differences in dispositional resilience, independent of age and cognitive impairment, are present in this population. Third, to examine the relative importance of the predictors of self-reported mental health and well-being. Methods: 160 elders were recruited in the Sardinian Blue Zone. The participants completed self-report measures of dispositional resilience, satisfaction with social ties, physical health, depressive symptoms, and psychological well-being. Results: trait resilience was significantly associated with predictors and markers of mental health. Males had significantly greater trait resilience. In regression analyses, dispositional resilience and satisfaction with social ties were significant predictors of all markers of mental health. Other factors were significantly associated only with certain markers. Conclusions: trait resilience and strong social ties appear to be key determinants of the high mental health of Sardinian Blue Zone older adults.
FieldSAFE: Dataset for Obstacle Detection in Agriculture

In this paper, we present a multi-modal dataset for obstacle detection in agriculture. The dataset comprises approximately 2 h of raw sensor data from a tractor-mounted sensor system in a grass mowing scenario in Denmark, October 2016. Sensing modalities include stereo camera, thermal camera, web camera, 360∘ camera, LiDAR and radar, while precise localization is available from fused IMU and GNSS. Both static and moving obstacles are present, including humans, mannequin dolls, rocks, barrels, buildings, vehicles and vegetation. All obstacles have ground truth object labels and geographic coordinates.
Hand and Wrist Injuries in Elite Boxing

Background: The purpose of this investigation was to explore prospectively the nature and duration of hand and wrist injuries in training and competition in the Great Britain (GB) amateur boxing squad between 2005 and 2012. Methods: Longitudinal prospective injury surveillance of the GB boxing squad was performed from 2005 to 2012. The location, region affected, description, and the duration of each injury were recorded by the team doctor and team physiotherapist. We recorded whether the injury occurred during competition or training and also whether it was a new or a recurrent injury. The injury rate during competition was calculated as the number of injuries per 1000 hours. Results: Finger carpometacarpal instability and finger metacarpophalangeal joint extensor hood and capsule sprain also known as “boxer’s knuckle” injuries were significantly more common than other injury diagnoses. The number of injuries during training or competition was similar, which is remarkable given the far greater number of training hours than competition hours performed. Injury rate for hand and wrist injuries in competition was 347 injuries per 1000 hours, while the estimated injury rate in training was <0.5 injuries per 1000 hours. Conclusion: Carpometacarpal instability and boxer’s knuckle were more common than any other kind of hand and wrist injury in this cohort of elite amateur boxers. The rate of hand and wrist injuries was higher in competition than in training. Our study highlights the importance of hand and wrist injury prevention in the competition environment.
Molecular identification of tick-borne pathogens infecting cattle in Mymensingh district of Bangladesh reveals emerging species of Anaplasma and Babesia.

Tick-borne diseases are considered a major hindrance to the health and productive performance of cattle in Bangladesh. To elucidate the epidemiology of tick-borne pathogens (TBPs) in local cattle, a cross-sectional study was performed in the 12 subdistricts (Upazilas) of Mymensingh district in Bangladesh. Blood samples and ticks were collected from 384 clinically healthy cattle kept by 135 farmers from 96 randomly selected villages. DNA extracted from the blood samples was subsequently screened by polymerase chain reaction (PCR) and a Reverse Line Blot (RLB) hybridization assay using an in-house prepared chemiluminescence solution for the presence of Anaplasma, Ehrlichia, Rickettsia, Babesia and Theileria spp. A total of 2,287 ticks were collected from 232 infested cattle (60.4%, 232/384) and identified morphologically as Rhipicephalus (Boophilus) microplus (n = 1,432, 62.6%) and Haemaphysalis bispinosa (n = 855; 37.4%). The RLB results demonstrated that the majority of the cattle (62.2%) were infected with at least one TBP. Theileria orientalis infections were most common (212/384, 55.2%) followed by infections with Anaplasma bovis (137/384, 35.67%), Anaplasma marginale (16/384, 4.17%), Babesia bigemina (4/384, 1.04%) and Babesia bovis (2/384, 0.52%). A previously uncharacterized Anaplasma sp. (Anaplasma sp. Mymensingh) and Babesia sp. (Babesia sp. Mymensingh), which are genetically closely related to Anaplasma platys and B. bigemina, were detected in 50 of 384 (13.0%) and 1 of 384 (0.3%) of the blood samples, respectively. Key risk factors for the occurrence of T. orientalis, A. marginale and Anaplasma sp. Mymensingh were identified. In conclusion, this study revealed that cattle in Mymensingh district are mainly infested with R. microplus and H. bispinosa ticks and may carry multiple TBPs. In addition, two previously uncharacterized pathogens were detected in the bovine blood samples. The pathogenicity of these species remains to be determined.
The Biomechanics of Bony Facial “Buttresses” in South African Australopiths: An Experimental Study Using Finite Element Analysis

Australopiths exhibit a number of derived facial features that are thought to strengthen the face against high and/or repetitive loads associated with a diet that included mechanically challenging foods. Here, we use finite element analysis (FEA) to test hypotheses related to the purported strengthening role of the zygomatic root and “anterior pillar” in australopiths. We modified our previously constructed models of Sts 5 (Australopithecus africanus) and MH1 (A. sediba) to differ in the morphology of the zygomatic root, including changes to both the shape and positioning of the zygomatic root complex, in addition to creating variants of Sts 5 lacking anterior pillars. We found that both an expanded zygomatic root and the presence of “anterior pillars” reinforce the face against feeding loads. We also found that strain orientations are most compatible with the hypothesis that the pillar evolved to resist loads associated with premolar loading, and that this morphology has an ancillary effect of strengthening the face during all loading regimes. These results provide support for the functional hypotheses. However, we found that an anteriorly positioned zygomatic root increases strain magnitudes even in models with an inflated/reinforced root complex. These results suggest that an anteriorly placed zygomatic root complex evolved to enhance the efficiency of bite force production while facial reinforcement features, such as the anterior pillar and the expanded zygomatic root, may have been selected for in part to compensate for the weakening effect of this facial configuration. Anat Rec, 300:171–195, 2017. © 2016 Wiley Periodicals, Inc.
Timber rattlesnakes and Louisiana pine snakes of the West Gulf Coastal Plain: hypotheses of decline

Timber rattlesnakes (Crotalus horrid=) and Louisiana pine snakes (Pituophis melanoleucus ruthvenq are large-bodied snakes occurring on the West Gulf Coastal Plain. Both species are thought to be declining .due to increasing habitat alteration. Timber rattlesnakes occur in closed canopy hardwood and pine-hardwood forests, and Louisiana pine snakes in pine forests on sandy, well drained soils. While various factors are probably involved in population declines, this study examined one factor for each species that may have widespread consequences for population viability. Results obtained in this study support the premise that timber rattIesnakes are vulnerable to mortality associated with roads and vehicular traffic. Data and discussion are presented suggesting that populations are negatively impacted in areas of eastern Texas having a high road density. Conversely, Louisiana pine snakes appear to be affected by changes in the fire regime which has altered vegetation structure resulting in decreases in pocket gopher (Geomys breviceps) density. Decreases in gopher densities are further hypothesized to result in decrease or extirpation of pine snake populations.
Analysis of Ocular Firework-Related Injuries and Common Eye Traumata: a 5-year Clinical Study

Abstract Background A comparative study of eye injuries related to fireworks or acts of violence around New Yearʼs Eve and the Swiss National Day on August 1st. The two groups were compared with respect to the overall numbers of eye accidents within the period of review. Patients and Methods Retrospective analysis of emergency consultations at the Department of Ophthalmology, University Hospital Zurich with eye accidents around the Swiss National Day on August 1st and New Yearʼs Eve over the last 5 years. Two subgroups were formed: (1) Firework-related eye traumata, (2) Eye injuries due to acts of violence. The groups were analysed by age, gender, active participant or bystander, eye involved, severity of trauma (from clinical findings), surgical interventions, time of follow-up and visits, visual acuity and outcome. Results The study included 97 patients (100 eyes) with 74 male (76 %) and 23 female (24 %) victims. After filtering out 67 common traumata cases (all unilateral), 17 patients (18 eyes) with firework-related injuries and 13 patients (15 eyes) with damage due to an act of violence remained. Firework injuries accounted for 18 % of cases (65 % men); eye injuries caused by an act of violence accounted for 15 % of cases (92 % men). In the fireworks group, women were significantly older than men (mean age men 32 ± 14 years versus women 38 ± 16 years, p = 0.002). 65 % of cases were bystanders. The two subgroups contained 30 patients (33 eyes) with 22 left eyes (67 %, p < 0.001). The anterior segment was most frequently involved (79 %), significantly more often than the posterior part of the eye (p < 0.001). The posterior segment was injured more often in the fireworks group (28 %), than in the violence group (13 %). 87 % of the victims in the group of common traumata were mild trauma, 10 % moderate and 3 % severe. In the fireworks group the distribution was 53 % mild, 12 % moderate and 35 % severe, in the violence group 46 %, 23 % and 31 % respectively. Severe trauma cases occurred significantly more often around the New Year, with 36 % versus August 1st with 18 % (p = 0.0028). They are more often related to firework injuries than caused by violence (40 % versus 33 %). In summary, 7 victims (23 %) needed 8 interventions, with 3 having additional issues with their intraocular pressure. Full final visual acuity was noted in 88 %, which was alike in the two subgroups. On the contrary common traumata happened significantly more often around August 1st (66 %) than New Year (34 %; p < 0.001). Conclusions The number of injured eyes in the two subgroups of fireworks and violence was twice as high around New Yearʼs Eve than around the Swiss National Day. If the two events were combined, eye injuries were caused by an act of violence in 45 % and by fireworks in 55 % of cases. Injuries from fireworks can be decreased by professional fireworks. Both types of accident can be decreased by public awareness.
Serum Sclerostin Levels in Patients with Ankylosing Spondylitis and Rheumatoid Arthritis: A Systematic Review and Meta-Analysis

Objective. Current studies of serum sclerostin levels in AS and RA patients are inconsistent. This meta-analysis was performed to identify the association of serum sclerostin level with AS and RA patients. Methods. Embase, PubMed, MEDLINE, and Cochrane Library databases (up to 25 January 2017) were used to collect all relevant published articles. Studies were pooled and standard mean difference (SMD) with 95% confidence interval (CI) was calculated. All data analyses were performed using RevMan 5.3. Results. Totally eight studies of AS including 420 AS patients and 317 healthy controls (HC) and three studies of RA including 145 RA patients and 127 HC were finally included in this meta-analysis. The results revealed that the serum sclerostin levels in both AS patients (SMD = −0.14; 95% CI = [−0.39,0.11]; P = 0.28) and RA patients (SMD = −0.10; 95% CI = [−0.34,0.15]; P = 0.43) were not significantly different from those in HC. Conclusion. The difference of serum sclerostin levels in AS and RA patients was not significantly different from HC, indicating that the sclerostin may not associate with the development of AS and RA.
Distributionally Robust Submodular Maximization

Submodular functions have applications throughout machine learning, but in many settings, we do not have direct access to the underlying function $f$. We focus on stochastic functions that are given as an expectation of functions over a distribution $P$. In practice, we often have only a limited set of samples $f_i$ from $P$. The standard approach indirectly optimizes $f$ by maximizing the sum of $f_i$. However, this ignores generalization to the true (unknown) distribution. In this paper, we achieve better performance on the actual underlying function $f$ by directly optimizing a combination of bias and variance. Algorithmically, we accomplish this by showing how to carry out distributionally robust optimization (DRO) for submodular functions, providing efficient algorithms backed by theoretical guarantees which leverage several novel contributions to the general theory of DRO. We also show compelling empirical evidence that DRO improves generalization to the unknown stochastic submodular function.
Probing Electrophysiological Indices of Perceptual Awareness across Unisensory and Multisensory Modalities

The neural underpinnings of perceptual awareness have been extensively studied using unisensory (e.g., visual alone) stimuli. However, perception is generally multisensory, and it is unclear whether the neural architecture uncovered in these studies directly translates to the multisensory domain. Here, we use EEG to examine brain responses associated with the processing of visual, auditory, and audiovisual stimuli presented near threshold levels of detectability, with the aim of deciphering similarities and differences in the neural signals indexing the transition into perceptual awareness across vision, audition, and combined visual–auditory (multisensory) processing. More specifically, we examine (1) the presence of late evoked potentials (∼>300 msec), (2) the across-trial reproducibility, and (3) the evoked complexity associated with perceived versus nonperceived stimuli. Results reveal that, although perceived stimuli are associated with the presence of late evoked potentials across each of the examined sensory modalities, between-trial variability and EEG complexity differed for unisensory versus multisensory conditions. Whereas across-trial variability and complexity differed for perceived versus nonperceived stimuli in the visual and auditory conditions, this was not the case for the multisensory condition. Taken together, these results suggest that there are fundamental differences in the neural correlates of perceptual awareness for unisensory versus multisensory stimuli. Specifically, the work argues that the presence of late evoked potentials, as opposed to neural reproducibility or complexity, most closely tracks perceptual awareness regardless of the nature of the sensory stimulus. In addition, the current findings suggest a greater similarity between the neural correlates of perceptual awareness of unisensory (visual and auditory) stimuli when compared with multisensory stimuli.