Miracle-dz/UniFAR-FTUs huggingface dataset:
Mesencephalic Astrocyte-Derived Neurotrophic Factor (MANF) Protects Against Neuronal Apoptosis via Activation of Akt/MDM2/p53 Signaling Pathway in a Rat Model of Intracerebral Hemorrhage

Neuronal apoptosis plays key roles in secondary brain injury caused by intracerebral hemorrhage (ICH). This study first reported the role of mesencephalic astrocyte-derived neurotrophic factor (MANF) in alleviating secondary brain injury through anti-apoptosis in rat model of ICH. The recombinant human-MANF (rh-MANF) and selective Akt inhibitor MK2206 was administrated intracerebroventricularly 1 h after ICH. Brain water content, behavioral assessment, BBB (blood brain barrier) leakage was evaluated 24 h after the induction of ICH. Western blot analysis was used to evaluate the expression level of target proteins (MANF, mouse 3T3 cell double-minute 2 (MDM2), P53, Akt, Bcl-2, Bax, and caspase-3). Terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) was applied to evaluate the neuronal cell death. Besides, whether MANF was expressed in neurons was verified with double immunofluorescence staining. The results suggested that the level of MANF, and its downstream proteins, Akt, MDM2 was upregulated and reached peak at 24 h after ICH. MANF was mainly expressed in neurons. The administration of rh-MANF could significantly increase the level of p-Akt, p-MDM2, Bcl/Bax ratio, but reduce the expression of p53, caspase-3 and neuronal death, thus ameliorate the neurological functions at 24 h after ICH. However, these effects of rh-MANF could be obviously reversed by MK2206. MANF could exert its neuronal anti-apoptotic effects via Akt/MDM2/P53 pathways. Therefore, MANF could be a valuable drug target in the treatment of ICH.
Are Dynamic Capabilities the Missing Link Between the IS Strategy and Performance Relationship?

This study examines two dynamic capabilities which are possible intervening mechanisms by which an information systems strategy relates to information systems performance. It also explores the relevance of the dynamic capabilities absorptive capacity and agility at three different levels of environmental dynamism. Responses from a sample of over 200 CIOs suggest that absorptive capacity and agility are indeed intervening mechanisms by which information systems strategy is linked to performance, particularly for innovative strategies and in environments that are highly dynamic. It suggests that pursuit of the strategy that is able to develop and maintain the highest levels of dynamic capabilities would be the one to likewise gain the most ground on performance. The findings also bring to light the fact that even in relatively stable environments, dynamic capabilities still play major roles in effectuating performance.
Serial passage through resistant and susceptible cucumber cultivars affects the virulence of Fusarium oxysporum f. sp. cucumerinum

Fusarium oxysporum f. sp. cucumerinum (Foc) is the causal pathogen of cucumber Fusarium wilt resulting in losses to cucumber production. To investigate the effects of the selective pressures of host plants on the virulence of Foc, a low virulence isolate, foc‐3b, was successively inoculated on resistant and susceptible cucumber cultivars for five generations. The virulence of the original isolate diverged; virulence was significantly strengthened after serial passage on the resistant cultivar and weakened on the susceptible plants (p ˂ .05). The expression of four virulence‐related genes of F. oxysporum, G‐protein α subunit gene fga1, sucrose nonfermenting 1 gene snf1, F‐box protein gene frp1, and Class V chitin synthase gene chsV, was quantified using real‐time PCR. All genes were significantly upregulated after serial passage on the resistant cultivar, compared to the original strain, and the expression of snf1 was downregulated in strains re‐isolated from the susceptible plants (p ˂ .05). A significant positive correlation was found between the expression levels of gene snf1, frp1, and chsV and disease severity of cucumber Fusarium wilt, suggesting these genes may impact virulence differentiation. This study will improve the management of cucumber Fusarium wilt and provide insight into the mechanisms underlying virulence of F. oxysporum.
Temporomandibular Disorders among Dutch Adolescents: Prevalence and Biological, Psychological, and Social Risk Indicators

Aims To assess the prevalence rates of pain-related temporomandibular disorders (TMDs) and temporomandibular joint (TMJ) sounds in a large group of Dutch adolescents, aged between 12 and 18 years and to determine if the same biological, psychological, and social risk indicators are related to both TMD pain and TMJ sounds. Methods In this cross-sectional questionnaire survey, 4,235 questionnaires were analyzed, with an about equal gender distribution. Results The overall prevalence of pain-related TMDs was 21.6% (26.1% for girls and 17.6% for boys) and that of TMJ sounds was 15.5% (19.3% for girls and 11.7% for boys). Logistic regression analyses revealed that the following variables appeared to be the strongest predictors of TMD pain: female gender, increasing age, sleep bruxism, biting on lips and/or cheeks, stress, and feeling sad. Regarding self-reported TMJ sounds, the multiple regression model revealed that female gender, increasing age, awake bruxism, and biting on lips and/or cheeks were the strongest predictors. Conclusions TMDs are a common finding among Dutch adolescents. Except for the psychological factors that appeared to be associated with TMD pain only, pain-related TMDs and TMJ sounds shared similar biological risk indicators.
Clinical characteristics, classification and surgical treatment of periductal mastitis.

Background This study aimed to describe the clinical characteristics of periductal mastitis (PDM), propose the practical clinical classification system and evaluate the results of different surgical treatments in different type of PDM patients. Methods A retrospective study was carried out at department of breast surgery, Peking Union Medical College Hospital, Beijing, China. A total of 152 patients with the diagnosis of PDM were reviewed from March 2012 to December 2016. All of the patients underwent surgery. Data were collected regarding clinical manifestation, treatment, and outcomes. Results The median age was 36 years. A subareolar breast mass was the most frequent symptom. The most common clinical manifestations were mass (98.0%), rubefaction (41.1%), nipple retraction (36.8%), abscess (36.8%), skin ulceration (25.7%), and mammary duct fistula (19.1%). Fourteen (9.2%) patients were recurrent PDM at first hospitalization. Eight (5.3%) patients had prolactinoma. Five (3.3%) patients were taking antipsychotic medications. Only four (2.6%) patients were smokers. Eight patients were highly suspected to be breast cancer before surgery. A four-type classification system was first proposed according to clinical manifestations. The different surgeries in each category were evaluated. After 3 years median follow-up, 11 (7.2%) patients got recurrence including two initial recurrent PDM. Conclusions Periductal mastitis is a distinct benign breast condition of unknown etiology. Mass, abscess and fistula are most common manifestations of the disease. Wide surgical excision, fistulectomy and extended excision with transfer of a random breast dermo-glandular flap (BDGF) are effective surgical modalities for different type of PDM.
The Response of a Weakly Stratified Layer to Buoyancy Forcing

Abstract The response of a weakly stratified layer of fluid to a surface cooling distribution is investigated with linear theory in an attempt to clarify recent numerical results concerning the sinking of cooled water in polar ocean boundary currents. A channel of fluid is forced at the surface by a cooling distribution that varies in the down-channel as well as the cross-channel directions. The resulting geostrophic flow in the central region of the channel impinges on its boundaries, and regions of strong downwelling are observed. For the parameters of the problem investigated, the downwelling occurs in a classical Stewartson layer but the forcing of the layer leads to an unusual relation with the interior flow, which is forced to satisfy the thermal condition on the boundary while the geostrophic normal flow in the interior is brought to rest in the boundary layer. As a consequence of the layer’s dynamics, the resulting long-channel flow exhibits a nonmonotonic approach to the interior flow, and the st.
Rapid depth perception in hunting archerfish. I. The predictive C-starts use an independent estimate of target height

ABSTRACT Archerfish dislodge aerial prey with water jets and use their predictive C-starts to secure it. Their C-starts turn the fish to the later point of impact and set the speed so that the fish arrive just in time. The starts are adjusted on the basis of information on speed, direction, timing and horizontal start position of prey movement – sampled during less than 100 ms after prey starts falling. Presently, it is unclear whether one essential parameter, the initial height of prey, can also be determined during this brief sampling time. Shooters and probably also observing bystanders already know target height – used to hit and to shape their jets – and would simply have to feed this information into their C-start circuitry. We challenged archerfish by launching initially invisible prey objects either from the expected height level, at which the fish were looking and at which they fired shots, or from more lateral positions and a lower or higher initial height. The arrangement was designed so that an analysis of the direction and the linear speed chosen by the starting fish could determine whether the C-start information is based on the expected height or on the actual height, which can be detected only after hidden prey has begun falling. Our findings demonstrate that the fish quickly estimate initial height during the initial falling phase of prey and do not simply use the expected height level to which they were cued. Editor's Choice: Hunting archerfish use information sampled in less than 100 ms to assess the initial height of ballistically falling prey.
On gradient regularizers for MMD GANs

We propose a principled method for gradient-based regularization of the critic of GAN-like models trained by adversarially optimizing the kernel of a Maximum Mean Discrepancy (MMD). We show that controlling the gradient of the critic is vital to having a sensible loss function, and devise a method to enforce exact, analytical gradient constraints at no additional cost compared to existing approximate techniques based on additive regularizers. The new loss function is provably continuous, and experiments show that it stabilizes and accelerates training, giving image generation models that outperform state-of-the art methods on $160 \times 160$ CelebA and $64 \times 64$ unconditional ImageNet.
Longitudinal Characterization of mGluR5 Using 11C-ABP688 PET Imaging in the Q175 Mouse Model of Huntington Disease

Metabotropic glutamate receptor 5 (mGluR5) represents a potential therapeutic target for Huntington disease. Using 11C-ABP688 (3-(6-methyl-pyridin-2-ylethynyl)-cyclohex-2-enone-O-11C-methyl-oxime), a noncompetitive and highly selective antagonist for mGluR5, we aimed to longitudinally characterize in vivo changes in mGluR5 by means of PET imaging in the Q175 mouse model of Huntington disease. Methods: 11C-ABP688 PET imaging, followed by a CT scan, was performed on 18 heterozygous mice and 18 wild-type (WT) littermates at 3 different time points (6, 9, and 13 mo old). 11C-ABP688 nondisplaceable binding potential (BPND) was calculated for each time point in striatum and cortex using the cerebellum as the reference region. In addition, voxel-based statistical parametric mapping (SPM) analysis was performed on BPND images. Postmortem validation of mGluR5 level and neuronal density was performed on the mice at 6 mo old. Results: The 11C-ABP688 BPND of heterozygous animals was significantly reduced at all time points in the striatum (−13.1%, −13.5%, and −14.2% at 6, 9, and 13 mo, respectively; P < 0.001 for all) and in the cortex (−9.8%, −10.2%, and −10.6%, respectively; P < 0.01 for all), when compared with WT animals. Longitudinal changes in 11C-ABP688 BPND were also found in heterozygous mice, showing a reduction at 13 mo compared with 6 mo (−10.4%, P < 0.05). SPM analysis confirmed reduced BPND in heterozygous compared with WT mice, as well as a time-related decline in 11C-ABP688 binding in the striatum of heterozygous mice. Postmortem analysis confirmed a mGluR5 decrease in both striatum (−36.6%; P < 0.01) and cortex (−16.6%; P < 0.05) in heterozygous mice, whereas no difference in neuronal density was found. Conclusion: In vivo imaging of mGluR5 using 11C-ABP688 PET/CT revealed a marked reduction in ligand binding in the striatum and cortex of heterozygous mice, compared with WT mice, as well as a temporal decline. This study suggests that 11C-ABP688 PET imaging is a potential biomarker to monitor the progression of, and therapeutic strategies for, Huntington disease.
Divergence estimation in the presence of incomplete lineage sorting and migration

This paper focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. We develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the the population size parameters and the migration rates between pairs of species tree branches to be integrated out. We then describe a BEAST2 package DENIM which based on this model, and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leaché et al 2014 showed migration causes problems for species tree inference using the multispecies coalescent when migration is present but ignored. We re-analyze this simulated data to explore DENIM’s performance, and demonstrate substantial improvements over *BEAST. We also re-analyze an empirical data set. [isolation-with-migration; incomplete lineage sorting; multispecies coalescent; species tree; phylogenetic analysis; Bayesian; Markov chain Monte Carlo]
Geometric Understanding of Deep Learning

Deep learning is the mainstream technique for many machine learning tasks, including image recognition, machine translation, speech recognition, and so on. It has outperformed conventional methods in various fields and achieved great successes. Unfortunately, the understanding on how it works remains unclear. It has the central importance to lay down the theoretic foundation for deep learning. In this work, we give a geometric view to understand deep learning: we show that the fundamental principle attributing to the success is the manifold structure in data, namely natural high dimensional data concentrates close to a low-dimensional manifold, deep learning learns the manifold and the probability distribution on it. We further introduce the concepts of rectified linear complexity for deep neural network measuring its learning capability, rectified linear complexity of an embedding manifold describing the difficulty to be learned. Then we show for any deep neural network with fixed architecture, there exists a manifold that cannot be learned by the network. Finally, we propose to apply optimal mass transportation theory to control the probability distribution in the latent space.
Sex and Geographic Differences in the Prevalence of Reported Childhood Motor Disability and Their Trends in Taiwan

Motor disability (MD) is not uncommon in children, but data at the national level are scarce. As the Taiwan government certifies and registers disabled residents for providing services on a routine basis, the registry provides a unique opportunity for studying MD. Using data from the registry, we calculated the prevalence of MD by age, sex, and geographic area and assessed the changes from 2004 to 2010. We excluded cases under 3 years old because the government discourages the certification at this age. We found that cases between 3 and 17 years old decreased from 8187 to 6022 per year from 2004 to 2010 and the prevalence generally decreased every year in all age groups. There were more boy cases than girl cases every year, and the prevalence rate ratios ranged from 1.26 to 1.39 (p < 0.05 in all years), with a decreasing trend over time (p < 0.01). Rural areas had higher prevalence in all the years, and the prevalence rate ratio decreased from 1.31 to 1.23 (p < 0.05 in all years), with a decreasing trend over time (p < 0.05). Further studies identifying the risk factors contributing to the decreases might help in the prevention of MD in the future.
Performance of hybrid quantum/classical variational heuristics for combinatorial optimization

The recent literature on near-term applications for quantum computers contains several examples of the applications of hybrid quantum-classical variational approaches. This methodology can be applied to a variety of optimization problems, but its practical performance is not well studied yet. This paper moves some steps in the direction of characterizing the practical performance of the methodology, in the context of finding solutions to classical combinatorial optimization problems. Our study is based on numerical results obtained applying several classical nonlinear optimization algorithms to Hamiltonians for six combinatorial optimization problems; the experiments are conducted via noise-free classical simulation of the quantum circuits implemented in Qiskit. We empirically verify that: (1) finding the ground state is harder for Hamiltonians with many Pauli terms; (2) classical global optimization methods are more successful than local methods due to their ability of avoiding the numerous local optima; (3) there does not seem to be a clear advantage in introducing entanglement in the variational form.
Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass

Switchgrass is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA‐sequencing (RNA‐seq) reads derived from crown, young shoot, and leaf tissues, we generated sequence data from seven switchgrass cultivars, three lowland and four upland, to enable comparative analyses between switchgrass cultivars and to identify single nucleotide polymorphisms (SNPs) for use in breeding and genetic analysis. We also generated individual transcript assemblies for each of the cultivars. Transcript data indicate that subgenomes of octoploid switchgrass are not substantially different from subgenomes of tetraploids as expected for an autopolyploid origin of switchgrass octoploids. Using RNA‐seq reads aligned to the switchgrass Release 0 AP13 reference genome, we identified 1,305,976 high‐confidence SNPs. Of these SNPs, 438,464 were unique to lowland cultivars, but only 12,002 were found in all lowlands. Conversely, 723,678 SNPs were unique to upland cultivars, with only 34,665 observed in all uplands. Comparison of our high‐confidence transcriptome‐derived SNPs with SNPs previously identified in a genotyping‐by‐sequencing (GBS) study of an association panel revealed limited overlap between the two methods, highlighting the utility of transcriptome‐based SNP discovery in augmenting genome diversity polymorphism datasets. The transcript and SNP data described here provide a useful resource for switchgrass gene annotation and marker‐based analyses of the switchgrass genome.
Decreased Siglec-9 Expression on Natural Killer Cell Subset Associated With Persistent HBV Replication

Siglec-9 is an MHC-independent inhibitory receptor selectively expressed on CD56dim NK cells. Its role in infection diseases has not been investigated yet. Here, we studied the potential regulatory roles of NK Siglec-9 in the pathogenesis of chronic hepatitis B (CHB) infection. Flow cytometry evaluated the expression of Siglec-9 and other receptors on peripheral NK cells. Immunofluorescence staining was used to detect Siglec-9 ligands on liver biopsy tissues and cultured hepatocyte cell lines. Siglec-9 blocking assay was carried out and cytokine synthesis and CD107a degranulation was detected by flow cytometry. Compared to healthy donors, CHB patients had decreased Siglec-9+ NK cells, which reversely correlated with serum hepatitis B e antigen and HBV DNA titer. Siglec-9 expression on NK cells from patients achieving sustained virological response recovered to the level of normal donors. Neutralization of Siglec-9 restored cytokine synthesis and degranulation of NK cells from CHB patients. Immunofluorescence staining showed increased expression of Siglec-9 ligands in liver biopsy tissues from CHB patients and in hepatocyte cell lines infected with HBV or stimulated with inflammatory cytokines (IL-6 or TGF-β). These findings identify Siglec-9 as a negative regulator for NK cells contributing to HBV persistence and the intervention of Siglec-9 signaling might be of potentially translational significance.
Denoising Distant Supervision for Relation Extraction via Instance-Level Adversarial Training

Existing neural relation extraction (NRE) models rely on distant supervision and suffer from wrong labeling problems. In this paper, we propose a novel adversarial training mechanism over instances for relation extraction to alleviate the noise issue. As compared with previous denoising methods, our proposed method can better discriminate those informative instances from noisy ones. Our method is also efficient and flexible to be applied to various NRE architectures. As shown in the experiments on a large-scale benchmark dataset in relation extraction, our denoising method can effectively filter out noisy instances and achieve significant improvements as compared with the state-of-the-art models.
Duration of Contact Precautions for Acute-Care Settings

purpose This expert guidance document (EG) provides recommendations regarding discontinuation of contact precautions (CP) at the individual patient level in acute-care hospitals employing CP for 1 or more of the following organisms: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), Clostridium dif ﬁ cile , and multidrug-resistant Enterobacteriaceae (MDR-E), including carbapenem-resistant Enterobacteriaceae (CRE) and extended-spectrum β -lactamase (ESBL) – producing organisms. This document also provides a review of the role of molecular testing in guiding decisions pertaining to duration of CP for patients with these organisms. The guidance does not address decisions regarding the initiation of CP for any speci ﬁ c organism.