Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Characterization of a Large Outbreak of Legionella pneumophila Serogroup 1 Strains in Quebec City, 2012

During the summer of 2012, a major Legionella pneumophila serogroup 1 outbreak occurred in Quebec City, Canada, which caused 182 declared cases of Legionnaire's disease and included 13 fatalities. Legionella pneumophila serogroup 1 isolates from 23 patients as well as from 32 cooling towers located in the vicinity of the outbreak were recovered for analysis. In addition, 6 isolates from the 1996 Quebec City outbreak and 4 isolates from patients unrelated to both outbreaks were added to allow comparison. We characterized the isolates using pulsed-field gel electrophoresis, sequence-based typing, and whole genome sequencing. The comparison of patients-isolated strains to cooling tower isolates allowed the identification of the tower that was the source of the outbreak. Legionella pneumophila strain Quebec 2012 was identified as a ST-62 by sequence-based typing methodology. Two new Legionellaceae plasmids were found only in the epidemic strain. The LVH type IV secretion system was found in the 2012 outbreak isolates but not in the ones from the 1996 outbreak and only in half of the contemporary human isolates. The epidemic strains replicated more efficiently and were more cytotoxic to human macrophages than the environmental strains tested. At least four Icm/Dot effectors in the epidemic strains were absent in the environmental strains suggesting that some effectors could impact the intracellular replication in human macrophages. Sequence-based typing and pulsed-field gel electrophoresis combined with whole genome sequencing allowed the identification and the analysis of the causative strain including its likely environmental source.
Determination of redundancies in a set of patterns

A set of black-and-white patterns can be identified by successive sampling of the individual "cells" which constitute these patterns. If the number of patterns is P and the number of cells is C , it is possible to find, for any specified sampling sequence at least C - P + 1 cells which may be omitted without obstructing unique identification. Such redundant cells can be found by two methods: Construction of a "code mobile," and compilation of a "code schedule. " The "mobile" is useful inasmuch as its topological characteristics can be correlated with the information capabilities and the inherent redundancy of the given identification process. The "schedule," on the other hand, is the numerical means by which practical cases can be rapidly and systematically solved. Besides revealing the redundancies in a given set, both the "mobile" and the "schedule" may serve as useful tools in evaluating and designing sampling programs.
Newly characterized Golgi-localized family of proteins is involved in calcium and pH homeostasis in yeast and human cells

Defects in the human protein TMEM165 are known to cause a subtype of Congenital Disorders of Glycosylation. Transmembrane protein 165 (TMEM165) belongs to an uncharacterized family of membrane proteins called Uncharacterized Protein Family 0016, which are well conserved throughout evolution and share characteristics reminiscent of the cation/Ca2+ exchanger superfamily. Gcr1 dependent translation factor 1 (Gdt1p), the budding yeast member of this family, contributes to Ca2+ homeostasis via an uncharacterized Ca2+ transport pathway localized in the Golgi apparatus. The gdt1Δ mutant was found to be sensitive to high concentrations of Ca2+, and interestingly, this sensitivity was suppressed by expression of TMEM165, the human ortholog of Gdt1p, indicating conservation of function among the members of this family. Patch-clamp analyses on human cells indicated that TMEM165 expression is linked to Ca2+ ion transport. Furthermore, defects in TMEM165 affected both Ca2+ and pH homeostasis. Based on these results, we propose that Gdt1p and TMEM165 could be members of a unique family of Golgi-localized Ca2+/H+ antiporters and that modification of the Golgi Ca2+ and pH balance could explain the glycosylation defects observed in TMEM165-deficient patients.
A Search for Tonal Pattern Perception in Cebus Monkeys: Why Monkeys Can't Hum a Tune

This article reviews a series of experiments aimed at assessing the capacity of cebus monkeys and rats for tonal pattern perception (sensitivity to frequency contour). The animals9 ability to differentiate between two tunes (structured sequences of tones) that shared several component notes and were similar in their average frequency suggested tonal pattern perception in both species. Detailed analysis of the basis of their discriminative behavior revealed, however, that the latter was completely controlled by local cues. Additional studies confirmed this finding and showed that the cognitive limitation was not, in the case of the monkeys, due to a generally impoverished capacity for processing acoustic stimuli or to an unduly truncated auditory short- term store. Many species of songbirds also seem remarkably deficient in their ability to perceive the tonal patterns of non-species-specific acoustic stimuli, which may be widespread among animals. Some implications of this striking difference in the auditory processing capacities of animals and humans are briefly discussed.
What is it like to be conscious? The ontogenesis of consciousness

In recent years, numerous studies have tried to highlight, from a naturalistic point of view, the apparent mysteries of consciousness. Many authors concentrated their efforts on explaining the phylogenetic origins of consciousness. Paradoxically, comments on the ontogenesis of consciousness are almost nonexistent. By crossing the results of psychology of development with a philosophical analysis, this paper aims to make up for this omission. After having characterized the different conceptual aspects of consciousness, we combine these, with observations made by developmental psychologists, to trace the empirical development of consciousness during the first months of life. This combination leads to a theoretical proposal: the intentional characteristics of consciousness, namely, aboutness and purposefulness, depend on the phenomenal properties of conscious states. From this perspective, the phenomenal aspect of conscious states (the "what it is like" effect) is therefore far from being an epiphenomenon.
Mathematical Model for Low-Rate DoS Attacks Against Application Servers

In recent years, variants of denial of service (DoS) attacks that use low-rate traffic have been proposed, including the Shrew attack, reduction of quality attacks, and low-rate DoS attacks against application servers (LoRDAS). All of these are flooding attacks that take advantage of vulnerability in the victims for reducing the rate of the traffic. Although their implications and impact have been comprehensively studied, mainly by means of simulation, there is a need for mathematical models by which the behaviour of these sometimes complex processes can be described. In this paper, we propose a mathematical model for the LoRDAS attack. This model allows us to evaluate its performance by relating it to the configuration parameters of the attack and the dynamics of network and victim. The model is validated by comparing the performance values given against those obtained from a simulated environment. In addition, some applicability issues for the model are contributed, together with interpretation guidelines to the model's behaviour. Finally, experience of the model enables us to make some recommendations for the challenging task of building defense techniques against this attack.
Global Identification of Myc Target Genes Reveals Its Direct Role in Mitochondrial Biogenesis and Its E-Box Usage In Vivo

The Myc oncoprotein is a transcription factor involved in a variety of human cancers. Overexpression of Myc is associated with malignant transformation. In normal cells, Myc is induced by mitotic signals, and in turn, it regulates the expression of downstream target genes. Although diverse roles of Myc have been predicted from many previous studies, detailed functions of Myc targets are still unclear. By combining chromatin immunoprecipitation (ChIP) and promoter microarrays, we identified a total of 1469 Myc direct target genes, the majority of which are novel, in HeLa cells and human primary fibroblasts. We observed dramatic changes of Myc occupancy at its target promoters in foreskin fibroblasts in response to serum stimulation. Among the targets of Myc, 107 were nuclear encoded genes involved in mitochondrial biogenesis. Genes with important roles in mitochondrial replication and biogenesis, such as POLG, POLG2, and NRF1 were identified as direct targets of Myc, confirming a direct role for Myc in regulating mitochondrial biogenesis. Analysis of target promoter sequences revealed a strong preference for Myc occupancy at promoters containing one of several described consensus sequences, CACGTG, in vivo. This study thus sheds light on the transcriptional regulatory networks mediated by Myc in vivo.
Error performance bounds for routing algorithms in wireless cooperative networks

Cooperative diversity has emerged as a promising approach to improving reception reliability by realizing spatial diversity gains for nodes with single antenna. We consider here cooperative ad-hoc wireless networks where communications between two nodes can be assisted by a single relay using two time slots. This paper continues our investigation of PHY techniques and cross-layer routing algorithms in such networks. Specifically, we investigate here the optimal relay location for cooperative link in networks with infinite node density. By using this result, we analyze the error performance bound for routing algorithms in infinitely dense networks. Furthermore, we study the performance bounds for regularly dense networks with linear topology. Theoretical analysis shows that the proposed routing algorithm performs close to the optimal error performance.
Fundamental frequency fluctuation in continuous vowel utterance and its perception

= 30 ms, Hamming, and frame period = 5 ms. The figure shows that the F0 contour estimated from the EGG wave (a) had finer fluctuations than (b). F0s with fine fluctuations estimated from the EGG waves; they were sections 2 s long manually cut out from stable portions of vowels. The number of the data was 45 (5 vowels x 9 speakers). The means ( M ) of F0 in time were distributed between about 125 Hz and 135 Hz, even though the speakers monitored a 130-Hz pure-tone. The standard deviations ( SD ) were 0.5 to 3 Hz, independent of speakers and vowels. In order to classify F0 fluctuations into groups, we calculated power spectra of F0s by a 96,000-point Fourier transform (FT) (48-kHz sampling, 2-s duration). Figures 2(a), (b), and (c) show log power spectra of three typical F0 waves shown in Fig. 3(a), (b), and (c), respectively. The panels in Fig. 2 show interest-ABSTRACT This paper reports how rapid fluctuations of fundamental frequencies in continuously uttered vowels influence vowel quality and shows that vowel qualities with various fundamental frequency fluctuations can be discriminated perceptually. For this purpose, electroglottographs (EGGs) of vowels uttered by nine males were obtained using Laryngograph, and fundamental frequencies with rapid fluctuations were estimated from them. Analyzing forty-five estimated fundamental frequencies, they can be classified into four groups. Moreover, psychoacoustic experiments, with five subjects, evaluating voice quality by multidimensional scaling (MDS) showed that voice quality of the synthesized speech using the fundamental frequencies of the groups was completely discriminable and there was a distinctive frequency band of fundamental frequency fluctuation for specifying each group perceptually.
Analytical approach for simultaneous optimal sizing and placement of multiple Distributed Generators in primary distribution networks

This paper presents a novel analytical expression for finding optimum sizes of multiple Distributed Generators (DGs) simultaneously in order to minimize the power loss reduction ratio. The optimal power factor based on active and reactive power demands by the load is considered for sizing multiple DGs. The generalized analytical expressions for finding optimum sizes of two DGs simultaneously are presented considering mutual coupling factor to reduce the computation time. A brief description of both Exhaustive Load Flow (ELF) method and Improved Analytical (IA) methods are also presented. Systems with varying size and complexity were used for testing and validating the proposed analytical expressions for simultaneous optimal sizing and placement of DGs for active power loss reduction. The test results of IEEE 14 and 30 bus systems using the proposed methodology were compared with ELF and IA methods. Results proved the effectiveness of the proposed method in comparison to the ELF and IA methods.
Promoter selective transcriptional synergy mediated by sterol regulatory element binding protein and Sp1: a critical role for the Btd domain of Sp1

Cellular cholesterol and fatty acid levels are coordinately regulated by a family of transcriptional regulatory proteins designated sterol regulatory element binding proteins (SREBPs). SREBP-dependent transcriptional activation from all promoters examined thus far is dependent on the presence of an additional binding site for a ubiquitous coactivator. In the low-density lipoprotein (LDL) receptor, acetyl coenzyme A carboxylase (ACC), and fatty acid synthase (FAS) promoters, which are all regulated by SREBP, the coactivator is the transcription factor Sp1. In this report, we demonstrate that Sp3, another member of the Sp1 family, is capable of substituting for Sp1 in coactivating transcription from all three of these promoters. Results of an earlier study showed that efficient activation of transcription from the LDL receptor promoter required domain C of Sp1; however, this domain is not crucial for activation of the simian virus 40 promoter, where synergistic activation occurs through multiple Sp1 binding sites and does not require SREBP. Also in the present report, we further localize the critical determinant of the C domain required for activation of the LDL receptor to a small region that is highly conserved between Sp1 and Sp3. This crucial domain encompasses the buttonhead box, which is a 10-amino-acid stretch that is present in several Sp1 family members, including the Drosophila buttonhead gene product. Interestingly, neither the buttonhead box nor the entire C domain is required for the activation of the FAS and ACC promoters even though both SREBP and Sp1 are critical players. ACC and FAS each contain two critical SREBP sites, whereas there is only one in the LDL receptor promoter. This finding suggested that buttonhead-dependent activation by SREBP and Sp1 may be limited to promoters that naturally contain a single SREBP recognition site. Consistent with this model, a synthetic construct containing three tandem copies of the native LDL receptor SREBP site linked to a single Sp1 site was also significantly activated in a buttonhead-independent fashion. Taken together, these studies indicate that transcriptional activation through the concerted action of SREBP and Sp1 can occur by at least two different mechanisms, and promoters that are activated by each one can potentially be identified by the number of critical SREBP binding sites that they contain.
Orthopaedic surgeons and the medical device industry: the threat to scientific integrity and the public trust.

The purpose of this article is to relate recent actions by the United States Department of Justice, the Institute of Medicine, the Association of American Medical Colleges (AAMC), and others to the specific challenges confronting the specialty of orthopaedic surgery. Further, it strives to reconcile the duty and value propositions associated with the orthopaedic surgeon-medical device company relationship, with the persistent risks that are attendant to that relationship, and to develop a new path—one that strives to restore the integrity of scientific investigation and day-to-day clinical decision making, while providing justification for future physician-industry interaction. To consider the topic in perspective, it is interesting to assess the origins of the current model of physician-industry interaction as they relate specifically to the issues currently confronting the specialty of orthopaedic surgery. In 1980, novel legislation in the field of intellectual property, the Bayh-Dole Act, for the first time allowed universities and nonprofit organizations to replace the government as the principal beneficiaries of commercial development resulting from basic-science and clinical research. In essence, the act transferred the ownership of discoveries made with the help of federal research grants to the universities and small businesses where those discoveries were made. On the face of it, the Bayh-Dole Act made sense. Convinced that government ownership had deterred the development of incentives necessary to promote innovation and had severely inhibited productivity, supporters saw the act as a remedy for the depressed American economy in the 1970s. The goal of the act was specific—to address the concern that American firms were not using academic research efficiently for commercialization—and it intended to remedy that shortcoming by facilitating patenting and licensing by U.S. universities of inventions from federally funded research. If successful, it could help to usher in a new era of innovation in America. It was an interesting …
Overexpression of transmembrane protein 168 in the mouse nucleus accumbens induces anxiety and sensorimotor gating deficit

Transmembrane protein 168 (TMEM168) comprises 697 amino acid residues, including some putative transmembrane domains. It is reported that TMEM168 controls methamphetamine (METH) dependence in the nucleus accumbens (NAc) of mice. Moreover, a strong link between METH dependence-induced adaptive changes in the brain and mood disorders has been evaluated. In the present study, we investigated the effects of accumbal TMEM168 in a battery of behavioral paradigms. The adeno-associated virus (AAV) Tmem168 vector was injected into the NAc of C57BL/6J mice (NAc-TMEM mice). Subsequently, the accumbal TMEM168 mRNA was increased approximately by seven-fold when compared with the NAc-Mock mice (controls). The NAc-TMEM mice reported no change in the locomotor activity, cognitive ability, social interaction, and depression-like behaviors; however, TMEM168 overexpression enhanced anxiety in the elevated-plus maze and light/dark box test. The increased anxiety was reversed by pretreatment with the antianxiety drug diazepam (0.3 mg/kg i.p.). Moreover, the NAc-TMEM mice exhibited decreased prepulse inhibition (PPI) in the startle response test, and the induced schizophrenia-like behavior was reversed by pretreatment with the antipsychotic drug risperidone (0.01 mg/kg i.p.). Furthermore, accumbal TMEM168 overexpression decreased the basal levels of extracellular GABA in the NAc and the high K+ (100 mM)-stimulated GABA elevation; however, the total contents of GABA in the NAc remained unaffected. These results suggest that the TMEM168-regulated GABAergic neuronal system in the NAc might become a novel target while studying the etiology of anxiety and sensorimotor gating deficits.
Matching aspect ratio of digital photo via complementing

In this paper a new approach for matching aspect ratio of a digital photo for borderless printing by complementing it with fragments extracted from the same photo is proposed. This approach comprises analysis of side strips of the source photo in order to estimate the possibility to complement it without visible artifacts; complementing one or both opposite sides of the photo, matching the desired aspect ratio; additional processing of complements to make resulting photo look more natural.
Working through grief and loss: oncology nurses' perspectives on professional bereavement.

PURPOSE/OBJECTIVES To determine facilitators and barriers to managing patient loss from the combined perspectives of oncology nurses and to extract essential components of a supportive intervention. RESEARCH APPROACH Qualitative, descriptive. SETTING The comprehensive National Cancer Institute-designated cancer center of a mid-Atlantic university teaching hospital. PARTICIPANTS 34 nurses from inpatient and outpatient adult and pediatric oncology units. METHODOLOGIC APPROACH Focus groups were held with oncology staff nurses to identify challenges regarding work-related bereavement, current support for managing grief and loss, and how to support interpersonal functioning and resiliency. MAIN RESEARCH VARIABLES Work-related bereavement, bereavement support, and interventions and management strategies for bereavement and loss. FINDINGS Two primary themes emerged: dimensions of work-related loss and working through bereavement. Participants also provided many concrete suggestions for the creation of a supportive self-care environment. CONCLUSIONS Support issues were numerous, multilevel, and varied. However, addressing those concerns can improve job satisfaction and decrease compassion fatigue. The findings lay the foundation for appropriate interventions to assist nurses in managing those situations. INTERPRETATION Administrators, managers, and individuals interested in furthering the multifaceted goals of oncology care, including nurses themselves, are challenged to create and maintain mutually supportive environments for providing optimal care to patients and families.
Partition Aware Connected Component Computation in Distributed Systems

How can we find all connected components in an enormous graph with billions of nodes and edges? Finding connected components is a fundamental operation for various graph computation tasks such as pattern recognition, reachability, graph compression, etc. Many algorithms have been proposed for decades, but most of them are not scalable enough to process recent web scale graphs. Recently, a MapReduce algorithm was proposed to handle such large graphs. However, the algorithm repeatedly reads and writes numerous intermediate data that cause network overload and prolong the running time. In this paper, we propose PACC (Partition-Aware Connected Components), a new distributed algorithm based on graph partitioning for load-balancing and edge-filtering. Experimental results show that PACC significantly reduces the intermediate data, and provides up to 10 times faster performance than the current state-of-the-art MapReduce algorithm on real world graphs.
Caregiver Stress Among Grandparents Raising Grandchildren: The Functional Role of Social Support

Abstract Drawing from family stress theory, this study examined the associations among caregiver stress, social support, and stress outcomes measured by life satisfaction and generativity among grandparents raising grandchildren. Social support was hypothesized to moderate the association between caregiver stress and stress outcome indicators. Using survey data from a non-probability sample of 133 grandparent caregivers with full-time responsibility of raising at least one grandchild, regression analysis demonstrated that caregiver stress is associated negatively with life satisfaction and generativity. Informal and formal social support was found to have a beneficial influence on stress outcomes that generalizes to grandparent caregiver participants regardless of the amount of stress they experience. Contrary to predictions, social support did not buffer the association between caregiver stress and life satisfaction nor the association between caregiver stress and generativity. A high degree of perceived informal support was found to function as a detriment to grandparents under conditions of high stress through lowered generativity. Results suggest the need to examine the functional role of social support in the caregiving context.