Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites

Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.
Depressive Symptoms in Adolescents.

BACKGROUND In this study, we determined the current prevalence of depressive symptoms in adolescents in Germany. METHODS A sample of 1001 adolescents aged 12 to 17 that was representative for Germany was surveyed in August and September 2017 through telephone interviews about depressive symptoms in the two weeks leading up to the interview and about the subjects' psychosocial features. The instrument that was used, called DesTeen, includes questions about depressed mood, loss of interest, loss of energy, feelings of worthlessness, guilt feelings, and cognitive symptoms. RESULTS Prevalences could be estimated and associated factors could be determined in a subset comprising 988 of the original 1001 subjects (mean age 14.58 years, 48.4% female). The estimated point prevalence of depressive symptoms (summated DesTeen score ≥ 14) in adolescents aged 12 to 17 was 8.2% (95% confidence interval [6.5; 9.9]). Girls (11.6% [95% CI 8.8; 14.4]) were more commonly affected than boys (5.0% [95% CI 3.1; 6.9]), and this difference was statistically significant (p<0.001). Depressive symptoms were more common with female sex, older age, poorer scholastic performance, lower interpersonal trust, more negative body image, more problematic use of social media or computer games, and lower family functioning. A multivariable regression model explained approximately one-third of the variation among groups (Nagelkerke's R2 = 0.35). CONCLUSION A substantial percentage of German adolescents suffers from depres - sive symptoms. This study was the first to show certain associations, such as that between depressive symptoms in adolescence and the problematic use of social media in German youth.
Sample-Efficient Imitation Learning via Generative Adversarial Nets

GAIL is a recent successful imitation learning architecture that exploits the adversarial training procedure introduced in GANs. Albeit successful at generating behaviours similar to those demonstrated to the agent, GAIL suffers from a high sample complexity in the number of interactions it has to carry out in the environment in order to achieve satisfactory performance. We dramatically shrink the amount of interactions with the environment necessary to learn well-behaved imitation policies, by up to several orders of magnitude. Our framework, operating in the model-free regime, exhibits a significant increase in sample-efficiency over previous methods by simultaneously a) learning a self-tuned adversarially-trained surrogate reward and b) leveraging an off-policy actor-critic architecture. We show that our approach is simple to implement and that the learned agents remain remarkably stable, as shown in our experiments that span a variety of continuous control tasks. Video visualisations available at: \url{this https URL}.
Brief Synopsis: Review of Renal Tubule and Interstitial Anatomy and Physiology and Renal INHAND, SEND, and DIKI Nomenclature

This article provides a synopsis of the first two presentations from the second scientific session of the 37th Annual Symposium of the Society of Toxicologic Pathology in Indianapolis, Indiana, on June 18, 2018; the session focused on acute kidney injury. The first presentation, given by Dr. Kevin McDorman, focused on “Fundamentals of Renal Tubule and Interstitial Anatomy and Physiology. ” Several common background findings from toxicity studies were additionally discussed. Lastly, factors that impact the relevance and usefulness of historical control data, such as quality and consistency of histopathology, were discussed. The second presentation, given by Dr. Torrie Crabbs, provided a review of International Harmonization of Nomenclature and Diagnostic Criteria (INHAND), Standard for Exchange of Nonclinical Data (SEND), and drug-induced kidney injury (DIKI) nomenclature. INHAND is a global collaborative project that provides internationally accepted standardized nomenclature and diagnostic criteria for proliferative and nonproliferative changes in laboratory animals in toxicity and carcinogenicity studies. SEND is currently a required standard for data submission to the Food and Drug Administration (FDA). Since the FDA has indicated its preference for INHAND nomenclature, SEND will predominately use INHAND terminology; thus, familiarity with INHAND terminology is critical for toxicologic pathologists. The diagnostic features of three common DIKI findings, in addition to several complicated INHAND terminologies, were reviewed.
High frequency electrical stimulation induces a long-lasting enhancement of event-related potentials but does not change the perception elicited by intra-epidermal electrical stimuli delivered to the area of increased mechanical pinprick sensitivity

High frequency electrical stimulation (HFS) of the skin induces increased pinprick sensitivity in the surrounding unconditioned skin. The aim of the present study was to investigate the contribution of A-fiber nociceptors to this increased pinprick sensitivity. For this we assessed if the perception and brain responses elicited by low-intensity intra-epidermal electrical stimulation (IES), a method preferentially activating Aδ-fiber nociceptors, are increased in the area of HFS-induced increased pinprick sensitivity. HFS was delivered to one of the two forearms of seventeen healthy volunteers. Mechanical pinprick stimulation and IES were delivered at both arms before HFS (T0), 20 minutes after HFS (T1) and 45 minutes after HFS (T2). In all participants, HFS induced an increase in pinprick perception at the HFS-treated arm, adjacent to the site of HFS. This increase was significant at both T1 and T2. HFS did not affect the percept elicited by IES, but did enhance the magnitude of the N2 wave of IES-evoked brain potentials, both at T1 and at T2. Our results show that HFS induces a long-lasting enhancement of the N2 wave elicited by IES in the area of secondary hyperalgesia, indicating that HFS enhances the responsiveness of the central nervous system to nociceptive A-fiber input. However, we found no evidence that HFS affects the perception elicited by IES, which may suggest that the population of nociceptors that mediate the perception elicited by IES do not contribute to HFS-induced increased pinprick sensitivity.
Spectral Analysis and Parameter Identification of Textile-Based Dye-Sensitized Solar Cells

Linearized equivalent electrical-circuit representation of dye-sensitized solar cells is helpful both for the better understanding of the physical processes in the cell as well as for various optimizations of the cells. White-box and grey-box modelling approaches are well-known and they are widely used for standard cell types. However, in the case of new cell types or the lack of deep knowledge of the cell’s physic such approaches may not be applicable immediately. In this article a black-box approach for such cases is presented applied together with spectral analysis. The spectral analysis and the black-box approach were as first validated with a standard glass-based dye-sensitized solar cell and thereafter applied for the characterization of a new type of textile-based dye-sensitized solar cells. Although there are still improvement potentials, the results are encouraging and the authors believe that the black-box method with spectral analysis may be used particularly for new types of dye-sensitized solar cells.
A Phase II and Biomarker Study of Sorafenib Combined with Modified FOLFOX in Patients with Advanced Hepatocellular Carcinoma

Purpose: Sorafenib is a standard first-line treatment for advanced hepatocellular carcinoma (HCC). The phase III SHARP trial showed a median time-to-progression (mTTP) of 5.5 months, overall response rate (ORR) of 2%, and median overall survival (mOS) of 10.7 months with sorafenib. FOLFOX4 has shown modest activity in advanced HCC. We evaluated the combination of sorafenib and modified (m)FOLFOX in a single-arm, multicenter phase II study. Patients and Methods: The study included Child–Pugh A patients with advanced HCC and no prior systemic therapies. Patients received sorafenib 400 mg twice a day for 2 weeks, followed by concurrent mFOLFOX [5-fluorouracil (5-FU) 1,200 mg/m2/day for 46 hours, leucovorin 200 mg/m2, and oxaliplatin 85 mg/m2 biweekly]. The primary endpoint was mTTP with an alternative hypothesis of 7 months, and secondary endpoints included ORR, mOS, and circulating biomarkers. Results: The study enrolled 40 patients: HCV/EtOH/HBV, 43%/28%/13%; Child–Pugh A5, 70%. Notable grade 3/4 adverse events (AE) included AST/ALT elevation (28%/15%), diarrhea (13%), hyperbilirubinemia (10%), hand–foot syndrome (8%), and bleeding (8%). mTTP was 7.7 months [95% confidence interval (CI): 4.4–8.9], ORR 18%, and mOS 15.1 months (7.9–16.9). Sorafenib + mFOLFOX increased plasma PlGF, VEGF-D, sVEGFR1, IL12p70, and CAIX and CD4+ and CD8+ effector T lymphocytes and decreased plasma sVEGFR2 and s-c-KIT and regulatory T cells (Tregs). Shorter TTP was associated with high baseline sVEGFR1. Shorter TTP and OS were associated with increases in Tregs and CD56Dim natural killer (NK) cells after sorafenib alone and plasma sMET after combination treatment (all P < 0.05). Conclusions: Sorafenib + mFOLFOX met the prespecified endpoint with encouraging efficacy but moderate hepatotoxicity. Thus, this regimen may be effective in select patients with adequate liver reserve. Biomarker evaluations suggested a correlation between time-to-progression (TTP) and angiogenic biomarkers and circulating Tregs.
Simple Unsupervised Keyphrase Extraction using Sentence Embeddings

Keyphrase extraction is the task of automatically selecting a small set of phrases that best describe a given free text document. Supervised keyphrase extraction requires large amounts of labeled training data and generalizes very poorly outside the domain of the training data. At the same time, unsupervised systems have poor accuracy, and often do not generalize well, as they require the input document to belong to a larger corpus also given as input. Addressing these drawbacks, in this paper, we tackle keyphrase extraction from single documents with EmbedRank: a novel unsupervised method, that leverages sentence embeddings. EmbedRank achieves higher F-scores than graph-based state of the art systems on standard datasets and is suitable for real-time processing of large amounts of Web data. With EmbedRank, we also explicitly increase coverage and diversity among the selected keyphrases by introducing an embedding-based maximal marginal relevance (MMR) for new phrases. A user study including over 200 votes showed that, although reducing the phrases’ semantic overlap leads to no gains in F-score, our high diversity selection is preferred by humans.
Regulation of Regional Cerebral Blood Flow During Graded Reflex-Mediated Sympathetic Activation via Lower Body Negative Pressure.

The role of the sympathetic nervous system in cerebral blood flow (CBF) regulation remains unclear. Previous studies have primarily measured middle cerebral artery blood velocity to assess CBF. Recently, there has been a transition towards measuring internal carotid artery (ICA) and vertebral artery (VA) blood flow using duplex Doppler ultrasound. Given that the VA supplies autonomic control centers in the brainstem, we hypothesized that graded sympathetic activation via lower body negative pressure (LBNP) would reduce ICA but not VA blood flow. ICA and VA blood flow were measured during two protocols: Protocol-1, low-to-moderate LBNP (-10, -20, -30, -40 Torr) and Protocol-2, moderate-to-high LBNP (-30, -50, -70 Torr). ICA and VA blood flow, diameter, and blood velocity were unaffected up to -40 LBNP. However, -50 and -70 LBNP evoked reductions in ICA and VA blood flow (e.g., -70 LBNP: %∆VA-baseline= -27.6±3.0) that were mediated by decreases in both diameter and velocity (e.g., -70 LBNP: %∆VA-baseline diameter= -7.5±1.9 and %∆VA-baseline velocity= -13.6±1.7), which were comparable between vessels. Since hyperventilation during -70 LBNP reduced PETCO2, this decrease in PETCO2 was matched via voluntary hyperventilation. Reductions in ICA and VA blood flow during hyperventilation alone were significantly smaller than during -70 LBNP and were primarily mediated by decreases in velocity (%∆VA-baseline velocity= -8.6±2.4; %∆VA-baseline diameter= -0.05±0.56). These data demonstrate that both ICA and VA were unaffected by low-to-moderate sympathetic activation, whereas robust reflex-mediated sympatho-excitation caused similar magnitudes of vasoconstriction in both arteries. Thus, contrary to our hypothesis, the ICA was not preferentially vasoconstricted by sympathetic activation.
Revisiting Trends in Augmented Reality Research: A Review of the 2nd Decade of ISMAR (2008–2017)

In 2008, Zhou et al. presented a survey paper summarizing the previous ten years of ISMAR publications, which provided invaluable insights into the research challenges and trends associated with that time period. Ten years later, we review the research that has been presented at ISMAR conferences since the survey of Zhou et al., at a time when both academia and the AR industry are enjoying dramatic technological changes. Here we consider the research results and trends of the last decade of ISMAR by carefully reviewing the ISMAR publications from the period of 2008–2017, in the context of the first ten years. The numbers of papers for different research topics and their impacts by citations were analyzed while reviewing them—which reveals that there is a sharp increase in AR evaluation and rendering research. Based on this review we offer some observations related to potential future research areas or trends, which could be helpful to AR researchers and industry members looking ahead.
Prevalence and Perceived Acceptability of Nongenital Sexually Transmitted Infection Testing in a Cohort of Young Transgender Women.

PURPOSE This study documents the prevalence and acceptability of self-reported nongenital sexually transmitted infection (STI) testing among young transgender women (n = 72). METHODS Bivariate analyses assessed differences in outcomes by demographic and behavioral characteristics. RESULTS Less than half of participants self-reported nongenital STI testing (43% rectal; 44% pharyngeal). More than half of the sample reported that they would not find self-collection of specimens uncomfortable/unpleasant (53% rectal; 62% pharyngeal). No differences were found between demographics and prevalence of nongenital STI testing; those reporting condomless receptive anal sex were more likely to report previous pharyngeal testing. CONCLUSION Future studies should document prevalence of nongenital STIs among transgender women.
Mesenteric Panniculitis (MP): A Frequent Coincidental CT Finding of Debatable Clinical Significance

Abstract Background Mesenteric panniculitis (MP) is histologically characterized by chronic nonspecific inflammation of the adipose tissue of the intestinal mesentery with unclear etiology. MP occurs predominantly in men, mostly in mid to late adulthood. MP is typically found as an incidental diagnosis on abdominal CT. Methods A comprehensive review of the literature including case reports and cohort studies was performed. Therefore, a global search in PubMed was carried out. Search terms were (and/or) “mesenteric panniculitis”, “panniculitis mesenterialis”, “mesenteric lymph nodes”, “CT”, “imaging”, “sclerosing mesenteritis”, “case report”, “therapy”. Results and Conclusion MP is a relatively common CT finding. The true prevalence seems to be higher than the reported 0.6 % to 2.4 % due to underreporting. The most important differential diagnosis is malignant lymphoma, which may be difficult to distinguish from MP. The majority of patients with MP are clinically asymptomatic and do not require therapy. In rare symptomatic cases, non-specific symptoms like abdominal pain, fever, nausea or vomiting occur. For therapy, glucocorticoids and tamoxifen have been suggested. Several studies suggested that MP is associated with other diseases and might be a paraneoplastic phenomenon, but four recently published case-control studies suggest that MP is an independent non-specific benign age-related phenomenon. However, two further studies show a possible association of MP with malignant lymphoma. The clinical relevance of MP remains the subject of scientific debate. Key Points: Mesenteric panniculitis (MP) is a non-specific, chronic inflammation of the mesenteric adipose tissue with characteristic CT signs MP is a relatively common incidental finding on abdominal CT Malignant lymphoma is the main differential diagnosis An association of MP with other diseases including malignancy has been discussed but cannot be confirmed unequivocally MP is rarely symptomatic with fever, nausea, vomiting, abdominal pain, or diarrhea Citation Format Gögebakan Ö, Osterhoff MA, Albrecht T. Mesenteric Panniculitis (MP): A Frequent Coincidental CT Finding of Debatable Clinical Significance. Fortschr Röntgenstr 2018; 190: 1044 – 1052
Activity and outcomes of a cardio‐oncology service in the United Kingdom—a five‐year experience

Cardio‐oncology clinics optimise the cardiovascular status of cancer patients but there is a limited description of their structure, case mix, activity and results. The purpose of this paper is to describe the activity and outcomes of a cardio‐oncology service, particularly with respect to supporting optimal cancer treatment and survival.
Longitudinal Variation of Amino Acid Levels in Human Milk and Their Associations with Infant Gender

It is discussed that specific amino acids (AAs) have functional roles in early life. Understanding the AA composition in human milk (HM) during lactation assists in specifying these roles. To this end we assessed the levels of free AAs (FAAs), total AAs (free and bound, TAAs) and protein levels in HM in the first 6 months of lactation, and evaluated possible associations with infant gender. HM samples of 25 healthy Dutch mothers participating in the PreventCD study were collected monthly during the first 6 months of lactation. Of the participating mothers, 12 gave birth to a boy and 13 gave birth to a girl. Analyses of the HM samples revealed that levels of free glutamate, glutamine, aspartate, glycine, and serine significantly increased during months 1–3 of lactation, both in absolute sense and relative to TAA levels. Evaluation of gender differences by mixed model analyses revealed an association between female infant gender and higher protein content (p = 0.0465) and TAA content (p = 0.0362) in HM during the first 3 months of lactation. Furthermore, there was a tendency for an association of male infant gender with higher levels of free glutamine (p = 0.0948) in HM during the first 3 months of lactation. These results show that FAA, TAA and protein levels in HM display a time-specific occurrence during lactation. Moreover, although confirmation is necessary in view of the small sample size, this study indicates that the AA composition in HM shows differential effects of the infant’s sex.
Dynamic In Vivo Chest X-ray Dark-Field Imaging in Mice

X-ray grating interferometry is a powerful emerging tool in biomedical imaging, providing access to three complementary image modalities. In addition to the conventional attenuation modality, interferometry provides a phase modality, which visualizes soft tissue structures, and a dark-field modality, which relates to the number and size of sub-resolution scattering objects. A particularly strong dark-field signal originates from the alveoli or air sacs in the lung. Dark-field lung radiographs in animal models have already shown increased sensitivity in diagnosing lung diseases, such as lung cancer or emphysema, compared to conventional X-ray chest radiography. However, to date, X-ray dark-field lung imaging has either averaged information over several breaths or has been captured during a breath hold. In this paper, we demonstrate the first time-resolved dark-field imaging of a breath cycle in a mechanically ventilated mouse, in vivo, which was obtained using a grating interferometer. We achieved a time resolution of 0.1 s, visualizing the changes in the dark-field, phase, and attenuation images during inhalation and exhalation. These measurements show that the dark-field signal depends on the air volume and, hence, the alveolar dimensions of the lung. Conducting this type of scan with animal disease models would help to locate the optimum breath point for single-image diagnostic dark-field imaging and could indicate if the changes in the dark-field signal during breath provide a diagnostically useful complementary measure.