Miracle-dz/UniFAR-FTUs huggingface dataset:
Combination antibiotic therapy improves survival in patients with community-acquired pneumonia and shock*

Objective:To assess whether combination antibiotic therapy improves outcome of severe community-acquired pneumonia in the subset of patients with shock. Design:Secondary analysis of a prospective observational, cohort study. Setting:Thirty-three intensive care units (ICUs) in Spain. Patients:Patients were 529 adults with community-acquired pneumonia requiring ICU admission. Interventions:None. Measurement and Main Results:Two hundred and seventy (51%) patients required vasoactive drugs and were categorized as having shock. The effects of combination antibiotic therapy and monotherapy on survival were compared using univariate analysis and a Cox regression model. The adjusted 28-day in-ICU mortality was similar (p = .99) for combination antibiotic therapy and monotherapy in the absence of shock. However, in patients with shock, combination antibiotic therapy was associated with significantly higher adjusted 28-day in-ICU survival (hazard ratio, 1.69; 95% confidence interval, 1.09–2.60; p = .01) in a Cox hazard regression model. Even when monotherapy was appropriate, it achieved a lower 28-day in-ICU survival than an adequate antibiotic combination (hazard ratio, 1.64; 95% confidence interval, 1.01–2.64). Conclusions:Combination antibiotic therapy does not seem to increase ICU survival in all patients with severe community-acquired pneumonia. However, in the subset of patients with shock, combination antibiotic therapy improves survival rates.
Peroxisome Proliferator–Activated Receptor &ggr; Level Contributes to Structural Integrity and Component Production of Elastic Fibers in the Aorta

Loss of integrity and massive disruption of elastic fibers are key features of abdominal aortic aneurysm (AAA). Peroxisome proliferator–activated receptor &ggr; (PPAR&ggr;) has been shown to attenuate AAA through inhibition of inflammation and proteolytic degradation. However, its involvement in elastogenesis during AAA remains unclear. PPAR&ggr; was highly expressed in human AAA within all vascular cells, including inflammatory cells and fibroblasts. In the aortas of transgenic mice expressing PPAR&ggr; at 25% normal levels (PpargC/− mice), we observed the fragmentation of elastic fibers and reduced expression of vital elastic fiber components of elastin and fibulin-5. These were not observed in mice with 50% normal PPAR&ggr; expression (Pparg+/− mice). Infusion of a moderate dose of angiotensin II (500 ng/kg per minute) did not induce AAA but Pparg+/− aorta developed flattened elastic lamellae, whereas PpargC/− aorta showed severe destruction of elastic fibers. After infusion of angiotensin II at 1000 ng/kg per minute, 73% of PpargC/− mice developed atypical suprarenal aortic aneurysms: superior mesenteric arteries were dilated with extensive collagen deposition in adventitia and infiltrations of inflammatory cells. Although matrix metalloproteinase inhibition by doxycycline somewhat attenuated the dilation of aneurysm, it did not reduce the incidence nor elastic lamella deterioration in angiotensin II–infused PpargC/− mice. Furthermore, PPAR&ggr; antagonism downregulated elastin and fibulin-5 in fibroblasts, but not in vascular smooth muscle cells. Chromatin immunoprecipitation assay demonstrated PPAR&ggr; binding in the genomic sequence of fibulin-5 in fibroblasts. Our results underscore the importance of PPAR&ggr; in AAA development though orchestrating proper elastogenesis and preserving elastic fiber integrity.
Cellular Interactions of the Cytolethal Distending Toxins from Escherichia coli and Haemophilus ducreyi*

Background: Cytolethal distending toxins (CDTs) produced by pathogenic bacteria are genotoxic. Results: CDTs exploit two different endocytic pathways to reach the nucleus. Conclusion: Individual members of the CDT superfamily interact with host cells by distinct mechanisms. Significance: Learning how CDTs interact with and modulate host cells and tissues is critical for understanding the strategies used by pathogenic bacteria during infection. The cytolethal distending toxins (CDTs) compose a subclass of intracellularly acting genotoxins produced by many Gram-negative pathogenic bacteria that disrupt the normal progression of the eukaryotic cell cycle. Here, the intoxication mechanisms of CDTs from Escherichia coli (Ec-CDT) and Haemophilus ducreyi (Hd-CDT), which share limited amino acid sequence homology, were directly compared. Ec-CDT and Hd-CDT shared comparable in vitro DNase activities of the CdtB subunits, saturable cell surface binding with comparable affinities, and the requirement for an intact Golgi complex to induce cell cycle arrest. In contrast, disruption of endosome acidification blocked Hd-CDT-mediated cell cycle arrest and toxin transport to the endoplasmic reticulum and nucleus, while having no effects on Ec-CDT. Phosphorylation of the histone protein H2AX, as well as nuclear localization, was inhibited for Hd-CdtB, but not Ec-CdtB, in cells expressing dominant negative Rab7 (T22N), suggesting that Hd-CDT, but not Ec-CDT, is trafficked through late endosomal vesicles. In support of this idea, significantly more Hd-CdtB than Ec-CdtB co-localized with Rab9, which is enriched in late endosomal compartments. Competitive binding studies suggested that Ec-CDT and Hd-CDT bind to discrete cell surface determinants. These results suggest that Ec-CDT and Hd-CDT are transported within cells by distinct pathways, possibly mediated by their interaction with different receptors at the cell surface.
An Electronic Nose Based on Coated Piezoelectric Quartz Crystals to Certify Ewes’ Cheese and to Discriminate between Cheese Varieties

An electronic nose based on coated piezoelectric quartz crystals was used to distinguish cheese made from ewes’ milk, and to distinguish cheese varieties. Two sensors coated with Nafion and Carbowax could certify half the ewes’ cheese samples, exclude 32 cheeses made from cow’s milk and to classify half of the ewes’ cheese samples as possibly authentic. Two other sensors, coated with polyvinylpyrrolidone and triethanolamine clearly distinguished between Flamengo, Brie, Gruyère and Mozzarella cheeses. Brie cheeses were further separated according to their origin, and Mozzarella grated cheese also appeared clearly separated from non-grated Mozzarella.
Social cognition and the cerebellum: A meta‐analytic connectivity analysis

This meta‐analytic connectivity modeling (MACM) study explores the functional connectivity of the cerebellum with the cerebrum in social cognitive processes. In a recent meta‐analysis, Van Overwalle, Baetens, Mariën, and Vandekerckhove ( ) documented that the cerebellum is implicated in social processes of “body” reading (mirroring; e.g., understanding other persons' intentions from observing their movements) and “mind” reading (mentalizing, e.g., inferring other persons' beliefs, intentions or personality traits, reconstructing persons' past, future, or hypothetical events). In a recent functional connectivity study, Buckner et al. ( ) offered a novel parcellation of cerebellar topography that substantially overlaps with the cerebellar meta‐analytic findings of Van Overwalle et al. ( ). This overlap suggests that the involvement of the cerebellum in social reasoning depends on its functional connectivity with the cerebrum. To test this hypothesis, we explored the meta‐analytic co‐activations as indices of functional connectivity between the cerebellum and the cerebrum during social cognition. The MACM results confirm substantial and distinct connectivity with respect to the functions of (a) action understanding (“body” reading) and (b) mentalizing (“mind” reading). The consistent and strong connectivity findings of this analysis suggest that cerebellar activity during social judgments reflects distinct mirroring and mentalizing functionality, and that these cerebellar functions are connected with corresponding functional networks in the cerebrum. Hum Brain Mapp 36:5137–5154, 2015. © 2015 Wiley Periodicals, Inc.
Knockdown of Oncogenic KRAS in Non–Small Cell Lung Cancers Suppresses Tumor Growth and Sensitizes Tumor Cells to Targeted Therapy

Oncogenic KRAS is found in more than 25% of lung adenocarcinomas, the major histologic subtype of non–small cell lung cancer (NSCLC), and is an important target for drug development. To this end, we generated four NSCLC lines with stable knockdown selective for oncogenic KRAS. As expected, stable knockdown of oncogenic KRAS led to inhibition of in vitro and in vivo tumor growth in the KRAS-mutant NSCLC cells, but not in NSCLC cells that have wild-type KRAS (but mutant NRAS). Surprisingly, we did not see large-scale induction of cell death and the growth inhibitory effect was not complete. To further understand the ability of NSCLCs to grow despite selective removal of mutant KRAS expression, we conducted microarray expression profiling of NSCLC cell lines with or without mutant KRAS knockdown and isogenic human bronchial epithelial cell lines with and without oncogenic KRAS. We found that although the mitogen-activated protein kinase pathway is significantly downregulated after mutant KRAS knockdown, these NSCLCs showed increased levels of phospho-STAT3 and phospho–epidermal growth factor receptor, and variable changes in phospho-Akt. In addition, mutant KRAS knockdown sensitized the NSCLCs to p38 and EGFR inhibitors. Our findings suggest that targeting oncogenic KRAS by itself will not be sufficient treatment, but may offer possibilities of combining anti-KRAS strategies with other targeted drugs. Mol Cancer Ther; 10(2); 336–46. ©2011 AACR.
Automatic Evaluation of Intrusion Detection Systems

An intrusion detection system (IDS) is a crucial element of a network security posture. Although there are many IDS products available, it is rather difficult to find information about their accuracy. Only a few organizations evaluate these products. Furthermore, the data used to test and evaluate these IDS is usually proprietary. Thus, the research community cannot easily evaluate the next generation of IDS. Toward this end, DARPA provided in 1998, 1999 and 2000 an intrusion detection evaluation data set. However, no new data set has been released by DARPA since 2000, in part because of the cumbersomeness of the task. In this paper, we propose a strategy to address certain aspects of generating a publicly available documented data set for testing and evaluating intrusion detection systems. We also present a tool that automatically analyzes and evaluates IDS using our proposed data set
Assisting software architects in architectural decision-making using Quark

Non-Functional Requirements (NFRs) and constraints are among the principal drivers of architectural decision-making. NFRs are improved or damaged by architectural decisions (ADs), while constraints directly include or exclude parts of the architecture (e.g., logical components or technologies). We may determine the impact of an AD, or which parts of the architecture are aected by a constraint, but at the end it is hard to know if we are respecting the NFRs and the imposed constraints with all the ADs made. In the usual approach, architects use their own experience to produce software architectures that comply with the NFRs and imposed constraints, but at the end, especially for crucial decisions, the architect has to deal with complex trade-os between NFRs and juggle with possible incompatibilities raised by the imposed constraints. In this paper we present Quark, a method to assist software architects in architectural decision-making, and the conceptualization of the relationship between NFRs and ADs defined in Arteon, an ontology to represent and manage architectural knowledge. Finally, we provide an overview of the Quark and Arteon implementation, the ArchiTech tool.
A prototype molecular interactive collaborative environment (MICE).

Illustrations of macromolecular structure in the scientific literature contain a high level of semantic content through which the authors convey, among other features, the biological function of that macromolecule. We refer to these illustrations as molecular scenes. Such scenes, if available electronically, are not readily accessible for further interactive interrogation. The basic PDB format does not retain features of the scene; formats like PostScript retain the scene but are not interactive; and the many formats used by individual graphics programs, while capable of reproducing the scene, are neither interchangeable nor can they be stored in a database and queried for features of the scene. MICE defines a Molecular Scene Description Language (MSDL) which allows scenes to be stored in a relational database (a molecular scene gallery) and queried. Scenes retrieved from the gallery are rendered in Virtual Reality Modeling Language (VRML) and currently displayed in WebView, a VRML browser modified to support the Virtual Reality Behavior System (VRBS) protocol. VRBS provides communication between multiple client browsers, each capable of manipulating the scene. This level of collaboration works well over standard Internet connections and holds promise for collaborative research at a distance and distance learning. Further, via VRBS, the VRML world can be used as a visual cue to trigger an application such as a remote MEME search. MICE is very much work in progress. Current work seeks to replace WebView with Netscape, Cosmoplayer, a standard VRML plug-in, and a Java-based console. The console consists of a generic kernel suitable for multiple collaborative applications and additional application-specific controls. Further details of the MICE project are available at http:/(/)mice.sdsc. edu.
Modeling gender dependency in the Subspace GMM framework

The Subspace GMM acoustic model has both globally shared parameters and parameters specific to acoustic states, and this makes it possible to do various kinds of tying. In the past we have investigated sharing the global parameters among systems with distinct acoustic states; this can be useful in a multilingual setting. In the current paper we investigate the reverse idea: to have different global parameters for different acoustic conditions (gender, in this case) while sharing the acoustic-state-specific parameters. We experiment with modeling gender dependency in this way, and show Word Error Rate improvements on a range of tasks and comparable results to the Vocal Tract Length Normalization (VTLN)-like technique Exponential Transform (ET).
Adullam at SemEval-2017 Task 4: Sentiment Analyzer Using Lexicon Integrated Convolutional Neural Networks with Attention

We propose a sentiment analyzer for the prediction of document-level sentiments of English micro-blog messages from Twitter. The proposed method is based on lexicon integrated convolutional neural networks with attention (LCA). Its performance was evaluated using the datasets provided by SemEval competition (Task 4). The proposed sentiment analyzer obtained an average F1 of 55.2%, an average recall of 58.9% and an accuracy of 61.4%.
Novel mutations in CYP11B1 gene leading to 11 beta-hydroxylase deficiency in Brazilian patients.

BACKGROUND Deficiency of 11 beta-hydroxylase results in the impairment of the last step of cortisol synthesis. In females, the phenotype of this disorder includes different degrees of genital ambiguity and arterial hypertension. Mutations in the CYP11B1 gene are responsible for this disease. OBJECTIVE The objective of the study was to screen the CYP11B1 gene for mutations in two unrelated Brazilian females with congenital adrenal hyperplasia due to 11 beta-hydroxylase deficiency. DESIGN The coding and intron-exon junction regions of CYP11B1 were totally sequenced. A putative splice mutation was further investigated by minigene transcription. RESULTS We report two novel CYP11B1 mutations in these Brazilian patients. An Arabian Lebanese descendent female was found to be homozygous for a cytosine insertion at the beginning of exon 8, changing the 404 arginine to proline. It alters the open reading frame, creating a putative truncated protein at 421 residue, which eliminates the domain necessary for the association of heme prosthetic group. A severely virilized female was homozygous for the g.2791G>A transition in the last position of exon 4. This nucleotide is also part of 5' intron 4 donor splice site consensus sequence. Minigene experiments demonstrated that g.2791G>A activated an alternative splice site within exon 4, leading to a 45-bp deletion in the transcript. The putative translation of such modified mRNA indicates a truncated protein at residue 280. CONCLUSIONS We describe two novel mutations, g. 4671_4672insC and g.2791G>A, that drastically affects normal protein structure. These mutations abolish normal enzyme activity, leading to a severe phenotype of congenital adrenal hyperplasia due to 11 beta-hydroxylase deficiency.
An Analysis of Phytochrome-mediated Anthocyanin Synthesis.

Phytochrome (far red form) alone can mediate anthocyanin synthesis in the mustard seedling (Sinapis alba L.). Complete photoreversibility and reciprocity, for both red and far red light exposures over a period of at least 5 minutes, demonstrate this phytochrome involvement.The duration of the initial lag-phase is constant (about 3 hours at 25 C) for seedlings more than 30 hours old and is specific for the system, being independent of the dose or quality of light. Since a complete reversal by far red of a red light induction is possible only during a 5 minute period, phytochrome (far red form) obviously mediates anthocyanin synthesis during the lag-phase although the actual synthesis of pigment can proceed only after the lag-phase is overcome. We suggest that phytochrome (far red form) exerts a double function during the initial lag-phase. It mediates both the build up of a biosynthetic potential ("capacity") and anthocyanin synthesis. However, the sequence of events leading to anthocyanin is arrested at some intermediate stage until this "capacity" is built up after 3 hours. Once "capacity" is achieved it does not decay readily. Therefore, no significant "secondary lag-phase" occurs if the seedling, under appropriate conditions, is reirradiated after an intervening dark period. The rate or extent of synthesis for both anthocyanin and lipoxygenase, previously reported (32), are functions of the amount of phytochrome (far red form). No "phytochrome paradoxes," i.e., nonrational relationships between the amount of phytochrome (far red form) and rate or extent of response, were detected. This fact suggests that the mustard seedling is especially well suited for investigating the biophysical and molecular mechanisms of phytochrome action.
Attitudes Toward Lesbians and Gays Among American and Dutch Adolescents

Attitudes toward lesbians and gays vary across national populations, and previous research has found relatively more accepting attitudes in the Netherlands as compared to the United States. In this study, we compared beliefs about and attitudes toward lesbians and gays in samples of Dutch and American heterosexual adolescents, utilizing survey data from 1,080 American adolescents (mean age = 15.86 years) attending two schools and from 1,391 Dutch adolescents (mean age = 16.27 years) attending eight schools. Findings indicated the Dutch participants were more tolerant of lesbians and gays, after adjusting for the gender, age, and racial/ethnic minority status of the participants. However, between-country differences were attenuated by accounting for the beliefs about lesbians and gays that participants used to justify their attitudes. American participants were more likely to justify their attitudes using beliefs related to social norms and religious opposition, while the Dutch participants were more likely to justify their attitudes using beliefs related to individual rights and the biological/genetic basis of homosexuality. The results suggest that the relative importance of particular beliefs about lesbians and gays to attitudes at the group level may be context dependent but also that certain beliefs are salient to attitudes across national contexts.
Collaborators awareness for user cohabitation in co-located collaborative virtual environments

In a co-located collaborative virtual environment, multiple users share the same physical tracked space and the same virtual workspace. When the virtual workspace is larger than the real workspace, navigation interaction techniques must be deployed to let the users explore the entire virtual environment. When a user navigates in the virtual space while remaining static in the real space, his/her position in the physical workspace and in the virtual workspace are no longer the same. Thus, in the context where each user is immersed in the virtual environment with a Head-Mounted-Display, a user can still perceive where his/her collaborators are in the virtual environment but not where they are in real world. In this paper, we propose and compare three methods to warn users about the position of collaborators in the shared physical workspace to ensure a proper cohabitation and safety of the collaborators. The frst one is based on a virtual grid shaped as a cylinder, the second one is based on a ghost representation of the user and the last one displays the physical safe-navigation space on the foor of the virtual environment. We conducted a user-study with two users wearing a Head-Mounted-Display in the context of a collaborative First-Person-Shooter game. Our three methods were compared with a condition where the physical tracked space was separated into two zones, one per user, to evaluate the impact of each condition on safety, displacement freedom and global satisfaction of users. Results suggest that the ghost avatar and the cylinder grid can be good alternatives to the separation of the tracked space.
Impaired Sensory-Emotional Integration in a Violent Adolescent Sex Offender

ABSTRACT Social risk factors, executive neuropsychological functioning, and emotional numbing were examined as potential risk factors for violent sexual assaults by an adolescent male. The subject had been exposed to at least four previously identified social risk factors, including neglect, early separation from both parents, sexual abuse, and low socio-economic status. At the time of assessment, executive neuropsychological functioning was intact. While impaired emotional responsiveness was an important factor in the assaults, the construct of emotional numbing is too broad to identify the specific neuropsychological impairment involved in the subject's assault behavior. The authors suggest that failures in sensory-emotional integration contributed to the likelihood of violent behavior. Implications for further research and clinical practice are discussed.
Cystic Hygroma of the Neck: Ultrasound Findings

This is a report of a case of cystic hygroma of the neck in a female child. Cystic hygroma is a rare congenital malformation of the lymphatic system, most frequently detected in the head and neck region. Ultrasound is considered as being the first level study to investigate a suspected mass suggestive of cystic hygroma. The Authors describe the main diagnostic ultrasound features for this type of lymphatic lesion.