Miracle-dz/UniFAR-FTUs huggingface dataset:
The GATC-Binding Protein SeqA Is Required for Bile Resistance and Virulence in Salmonella enterica Serovar Typhimurium

ABSTRACT Disruption of the seqA gene of Salmonella enterica serovar Typhimurium causes defects similar to those described in E. coli: filament formation, aberrant nucleoid segregation, induction of the SOS response, envelope instability, and increased sensitivity to membrane-damaging agents. Differences between SeqA− mutants of E. coli and S. enterica, however, are found. SeqA− mutants of S. enterica form normal colonies and do not exhibit alterations in phage plaquing morphology. Lack of SeqA causes attenuation of S. enterica virulence by the oral route but not by the intraperitoneal route, suggesting a virulence defect in the intestinal stage of infection. However, SeqA− mutants are fully proficient in the invasion of epithelial cells. We hypothesize that attenuation of SeqA− mutants by the oral route may be caused by bile sensitivity, which in turn may be a consequence of envelope instability.
Upper mantle seismic anisotropy at a strike‐slip boundary: South Island, New Zealand

New shear wave splitting measurements made from stations onshore and offshore the South Island of New Zealand show a zone of anisotropy 100–200 km wide. Measurements in central South Island and up to approximately 100 km offshore from the west coast yield orientations of the fast quasi‐shear wave nearly parallel to relative plate motion, with increased obliquity to this orientation observed farther from shore. On the eastern side of the island, fast orientations rotate counterclockwise to become nearly perpendicular to the orientation of relative plate motion approximately 200 km off the east coast. Uniform delay times between the fast and slow quasi‐shear waves of nearly 2.0 s onshore continue to stations approximately 100 km off the west coast, after which they decrease to ~1 s at 200 km. Stations more than ~300 km from the west coast show little to no splitting. East coast stations have delay times around 1 s. Simple strain fields calculated from a thin viscous sheet model (representing distributed lithospheric deformation) with strain rates decreasing exponentially to both the northwest and southeast with e‐folding dimensions of 25–35 km (approximately 75% of the deformation within a zone 100–140 km wide) match orientations and amounts of observed splitting. A model of deformation localized in the lithosphere and then spreading out in the asthenosphere also yields predictions consistent with observed splitting if, at depths of 100–130 km below the lithosphere, typical grain sizes are ~ 6–7 mm.
U.S. State Resident Big Five Personality and Work Satisfaction: The Importance of Neuroticism

Two studies determined relations between state resident Big Five personality scores and state work satisfaction for the 50 states in the United States. Study 1 and 2 personality profiles were based on responses of 619,397 residents to the 44-item Big Five Inventory. For Studies 1 and 2, state work satisfaction scores were respectively taken from the Gallup-Healthways Well-Being Index based on 353,039 phone interviews in 2008 and on 353,564 in 2012. Higher neuroticism was associated with lower work satisfaction (r = −.49, p < .001) in both studies despite negative recession impacts in Study 2. In Study 1, the robust relation persisted with state socioeconomic status, percent of White population identified in the census, urban population percent, unemployment rate, economic conservatism, income inequality, and political conservatism controlled. In Study 2, the relation persisted while controlling for peak-recession and end-of-recession unemployment rates, 2010-2011 GDP growth, and the other corresponding control variables of Study 1.
Sex Acculturation and Risk Perceptions: Information Seeking and Processing Among Chinese Students in the U.S.

SEX ACCULTURATION AND RISK PERCEPTIONS: INFORMATION SEEKING AND PROCESSING AMONG CHINESE STUDENTS IN THE U.S. Jieyu Ding, B.A Marquette University, 2017 The number of Chinese students studying in the United States is increasing each year and studying in the U.S. provides them with more access to risk information of sexual activities than that of their counterparts in China. Chinese students in the U.S. have shown higher knowledge level about HIV/STI than Chinese students in China. However, their risk perceptions about HIV/STI are relatively low compared to American students due to a lack of formal sex education and a sex-conservative society. Method: this study collected 385 online surveys via Survey Monkey from Chinese students studying in the U.S. The questionnaire was designed to examine Chinese students’ risk perceptions and their information seeking and processing behaviors about HIV/STI. Results: the study showed that Chinese students were most motivated by their perceived informational gathering capacity to seek more information about HIV/STI (beta = .38, p ≤ .001) and process it in depth (beta = .30, p ≤ .001). Both informational subjective norms (beta = .16, p ≤ .001) and informational insufficiency (beta = .19, p ≤ .001) predicted information seeking behaviors but only informational subjective norms predicted significant systematic processing (beta = .17, p ≤ .001). However, current knowledge was very high and did not motivate processing behaviors. Future studies should explore motivations for information seeking and processing when current knowledge level is high and unable to motivate seeking and processing behaviors.
Puerperal Sepsis in a Rural Hospital in Sudan

Background: Increasingly, women in rural areas in Sudan reported to hospital with puerperal infections. Aims: This study was design to identify the common pathogens causing puerperal infections and their susceptibility to current antibiotics. Subjects and methods: We prospectively studied 170 women from January, 2011 through January 2012 attended Hussein Mustafa Hospital for Obstetrics and Gynecology at Gadarif State, Sudan. We included patients if they met the criteria proposed by the WHO for definition of maternal sepsis. Blood was collected on existing infection guidelines for clean practice and equipments. Results: Out of the 170 samples, 124 (72.9%) were pathogen-positive samples. Out the 124 positive cases, aerobes were the predominant isolates 77 (62.1 %%) which included Staph.aureus 49 (39.5%), Staph. epidemics 7 (5.6%) and Listeria monocytogenes 21 (16.9%). The anaerobes isolates were Clostridium perfringens 34 (27.4 %) and Entrobactor cloacae 13 (10.5%). Standard biochemical test were for bacterial isolation. Higher rate of infections followed vaginal delivery compared to Cesarean section 121 (97.6%), 3 (2.5%) respectively. All strains of Staph were sensitive to Vancomycin, Gentamicin and Ceftriaxone. C. perfringens were sensitive to Ceftriaxone, Penicillins, Vancomycin and Metronidazole, while E. cloacae were sensitive to Gentamicin and Ceftriaxone. Conclusion: Despite the limited resources in the developing countries, treatment based on cultures remains the only solution to reduce maternal morbidity and mortality rates following puerperal infections.
Statistical Mechanics of Dissipative Particle Dynamics.

The stochastic differential equations corresponding to the updating algorithm of Dissipative Particle Dynamics (DPD), and the corresponding Fokker-Planck equation are derived. It is shown that a slight modification to the algorithm is required before the Gibbs distribution is recovered as the stationary solution to the Fokker-Planck equation. The temperature of the system is then directly related to the noise amplitude by means of a fluctuation-dissipation theorem. However, the correspondingly modified, discrete DPD algorithm is only found to obey these predictions if the length of the time step is sufficiently reduced. This indicates the importance of time discretisation in DPD.
Survey, Culture, and Genome Analysis of Ocular Chlamydia trachomatis in Tibetan Boarding Primary Schools in Qinghai Province, China

Trachoma, the leading infectious cause of blindness worldwide, is an ancient human disease. Its existence in China can be traced back to as early as the twenty-seventh century BC. In modern China, the overall prevalence of trachoma has dramatically reduced, but trachoma is still endemic in many areas of the country. Here, we report that 26 (8%) of 322 students from two rural boarding schools of Qinghai province, west China, were identified as having ocular C. trachomatis infection; and 15 ocular C. trachomatis strains were isolated from these trachoma patients. Chlamydiae in 37 clinical samples were genotyped as type B based on ompA gene analyses. Three ompA variants with one or two in-between SNP differences in the second or fourth variable domain were found. C. trachomatis strains QH111L and QH111R were from the same patient's left and right conjunctival swabs, respectively, but their ompA genes have a non-synonymous base difference in the second variable domain. Moreover, this SNP only exists in this single sample, suggesting QH111L is a newly emerged ompA variant. Interestingly, chromosomal phylogeny analysis found QH111L clusters between a branch of two type B strains and a branch of both A and C strains, but is significantly divergent from both branches. Comparative chromosome analysis found that compared to sequences of reference B/TZ1A828/OT strain, 12 of 22 QH111L's chromosomal genes exhibiting more than nine SNPs have the best homology with reciprocal genes of UGT strains while 9 of 22 genes are closest to those of type C strains. Consistent with findings of UGT-type genetic features in the chromosome, the QH111L plasmid appears to be intermediate between UGT and classical ocular plasmids due to the existence of UGT-type SNPs in the QH111L plasmid. Moreover, the QH111L strain has a unique evolutionarily older cytotoxin region compared to cytotoxin regions of other C. trachomatis strains. The genome analyses suggest that the QH111L strain is derived from recombinations between UGT and classical ocular ancestors. This is the first study of culture and characterization of ocular C. trachomatis in Qinghai Tibetan areas.
Cementless anatomical prosthesis for the treatment of 3-part and 4-part proximal humerus fractures: cadaver study and prospective clinical study with minimum 2 years followup

Introduction: The purpose of this study was to evaluate the functional and radiological outcomes of a cementless, trauma-specific locked stem for 3- and 4-part proximal humeral fractures. Materials and methods: This study consisted of two parts: a cadaver study with 22 shoulders and a multicenter prospective clinical study of 23 fracture patients evaluated at least 2 years after treatment. In the cadaver study, the locked stem (HumelockTM, FX Solutions) and its instrumentation were evaluated. In the clinical study, five senior surgeons at four different hospitals performed the surgical procedures. An independent surgeon evaluated the patients using clinical (Constant score, QuickDASH) and radiological (X-rays, CT scans) outcome measures. Results: The cadaver study allowed us to validate the height landmarks relative to the pectoralis major tendon. In the clinical study, at the review, abduction was 95° (60–160), forward flexion was 108° (70–160), external rotation (elbow at body) was 34° (0–55), the QuickDASH was 31 (4.5–59), the overall Constant score was 54 (27–75), and the weighted Constant score was 76 (31.5–109). Discussion: This preliminary study of hemiarthroplasty (HA) with a locked stem found results that were at least equivalent to published series. As all patients had at least a 2-year follow-up, integration of the locked stem did not cause any specific complications. These results suggest that it is possible to avoid using cement when hemiarthroplasty is performed for the humeral stem. This implant makes height adjustment and transosseous suturing of the tuberosities more reproducible.
Streaming Anomaly Detection Using Randomized Matrix Sketching

Data is continuously being generated from sources such as machines, network traffic, application logs, etc. Timely and accurate detection of anomalies in massive data streams has important applications such as in preventing machine failures, intrusion detection, and dynamic load balancing. In this paper, we introduce a novel (unsupervised) anomaly detection framework which can be used to detect anomalies in a streaming fashion by making only one pass over the data while utilizing limited storage. We adapt ideas from matrix sketching to maintain, in a streaming model, a set of few orthogonal vectors that form a good approximate basis for all the observed data. Using this constructed orthogonal basis, anomalies in new incoming data are detected based on a simple reconstruction error test. We theoretically prove that our algorithm compares favorably with an offline approach based on expensive global singular value decomposition (SVD) updates. Additionally, we apply ideas from randomized low-rank matrix approximations to further speedup the algorithm. The experimental results show the effectiveness and efficiency of our approach over other popular scalable anomaly detection approaches.
Structure theorem and isomorphism test for graphs with excluded topological subgraphs

We generalize the structure theorem of Robertson and Seymour for graphs excluding a fixed graph H as a minor to graphs excluding H as a topological subgraph. We prove that for a fixed H, every graph excluding H as a topological subgraph has a tree decomposition where each part is either "almost embeddable" to a fixed surface or has bounded degree with the exception of a bounded number of vertices. Furthermore, such a decomposition is computable by an algorithm that is fixed-parameter tractable with parameter |H|. We present two algorithmic applications of our structure theorem. To illustrate the mechanics of a "typical" application of the structure theorem, we show that on graphs excluding H as a topological subgraph, Partial Dominating Set (find k vertices whose closed neighborhood has maximum size) can be solved in time f(H,k) • nO(1) time. More significantly, we show that on graphs excluding H as a topological subgraph, Graph Isomorphism can be solved in time nf(H). This result unifies and generalizes two previously known important polynomial-time solvable cases of Graph Isomorphism: bounded-degree graphs and H-minor free graphs. The proof of this result needs a generalization of our structure theorem to the context of invariant treelike decomposition.
Childhood musical murmur classification with Support Vector Machine technique

Musical murmur, a typical occurrence of heart sound, frequently found in the pediatric population reflects no harm compared to murmur. 8 out of 10 children are then by nature prone to this physiological phenomenon. Correctly distinguishing musical murmur from pathological one is a critical assessment to avoid unnecessary treatment at vain cost disbursement and ease parents' concern. This research investigates the algorithm development for automated high-yield classification with less time on analysis. 493 recorded heart sounds (HSs), comprised of 144 normal HSs, 141 musical murmurs, and 208 pathological murmurs, are first undergone through Preprocessing stage to form consistency of each incoming HSs. Derived HSs are extracted with Wavelet Packet (WP), as to form significant characteristics as a feature vector set. Then, Principal Component Analysis (PCA) is applied to the compactness of feature set in which the dimensionality reduction is attained through data-driven retrieval as to signify the most relevant features of HS record. Support Vector Machine (SVM) classifier trained by Radial Basis Function (RBF) kernel is constructed to detect and discriminate musical murmur from other murmur types by cross-validation process. Finally, classifier performance is evaluated by Confusion Matrix where an accuracy rate of 90.26% is ensured for the potential classification of model.
Multistage methods for freight train classification

In this article, we study the train classification problem. Train classification basically is the process of rearranging the cars of a train in a specified order, which can be regarded as a special sorting problem. This sorting is done in a special railway installation called a classification yard, and a classification process is described by a classification schedule. In this article, we develop a novel encoding of classification schedules, which allows characterizing train classification methods simply as classes of schedules. Applying this efficient encoding, we achieve a simpler, more precise analysis of well‐known classification methods. Furthermore, we elaborate a valuable optimality condition inherent in our encoding, which we succesfully apply to obtain tight lower bounds for the length of schedules in general and to develop new classification methods. Finally, we present complexity results and algorithms to derive optimal schedules for several real‐world settings. Together, our theoretical results provide a solid foundation for improving train classification in practice. © 2010 Wiley Periodicals, Inc. NETWORKS, 2011
NRD1, which encodes nardilysin protein, promotes esophageal cancer cell invasion through induction of MMP2 and MMP3 expression

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies worldwide. In the present study, to identify novel prognostic markers or therapeutic targets for ESCC, we reviewed a list of genes with upregulated expression in ESCC compared with normal esophagus, as identified by our serial analysis of gene expression (SAGE) analysis. We focused on the NRD1 gene, which encodes the nardilysin protein. Quantitative reverse transcription–polymerase chain reaction (qRT‐PCR) in 34 ESCC tissue samples revealed that mRNA expression of NRD1 was upregulated in 56% of ESCC tissue samples. Immunohistochemical analysis of nardilysin in 109 ESCC tissue samples demonstrated that 43 (39%) ESCC cases were positive for nardilysin. Nardilysin‐positive ESCC cases were more advanced in terms of T classification (P = 0.0007), N classification (P = 0.0164), and tumor stage (P < 0.0001) than nardilysin‐negative ESCC cases. Furthermore, nardilysin expression was significantly associated with poorer prognosis (P = 0.0258). Univariate and multivariate analyses revealed that nardilysin expression is an independent prognostic classifier of patients with ESCC. The invasiveness of NRD1‐knockdown TE1 and TE5 esophageal cancer cell lines was less than that of the negative control siRNA‐transfected cell lines. Expression of MMP2 and MMP3 mRNA was significantly lower in NRD1‐knockdown TE5 cells than in negative control siRNA‐transfected cells. These results suggest that nardilysin is involved in tumor progression, and is an independent prognostic classifier in patients with ESCC.
Probabilistic broadcast for flooding in wireless mobile ad hoc networks

Although far from the optimal, flooding is an indispensable message dissemination technique for network-wide broadcast within mobile ad hoc networks (MANETs). As such, the plain flooding algorithm provokes a high number of unnecessary packet rebroadcasts, causing contention, packet collisions and ultimately wasting precious limited bandwidth. We explore the phase transition phenomenon observed in percolation theory and random graphs as a basis for defining probabilistic flooding algorithm. By considering ideal and realistic models, we acquire a better understanding of the factors that determine phase transition, the consequences of the passage to realistic MANET conditions and to what extent we may benefit from probabilistic flooding in real MANET networks.
Skins of Morality: Bio-borders, Ephemeral Citizenship and Policing Women in Indonesia

Abstract Indonesia’s policewomen were rarely in public (or even police) consciousness prior to 2013. Yet the succeeding five years saw an explosion in visibility. Public furore concerning forced virginity testing of recruits, national debate over permitting women to veil on duty, and social media sites consumed with beauty concomitantly propelled policewomen into the limelight. I draw on these three examples to illustrate how various forms of power are levelled precisely at the borders of a woman’s body, what I frame as bio-borders. I focus on three bio-borders: hymens, veils and beauty. Drawing on Franck Billé’s (2017) work on skin and geopolitical boundaries, I analyse these bio-borders as sites where Indonesia’s neoliberal moral authority is asserted and contested. As an enforcer of state law, a policewoman’s virginity, purity and appearance signify Indonesia’s moral standing and mandate overt surveillance and control. Policewomen thus undergo intense daily moral labour to conform to expectations. As good moral ephemeral citizens showcasing Indonesia’s public face, policewomen: feel unable/unwilling to contest forced virginity testing; are empowered to demand the right to wear the veil on duty; and are complicit in accepting (and enjoying) beauty as a recruitment requirement while simultaneously expressing regret that they are judged on appearance.
Reducing web latency: the virtue of gentle aggression

To serve users quickly, Web service providers build infrastructure closer to clients and use multi-stage transport connections. Although these changes reduce client-perceived round-trip times, TCP's current mechanisms fundamentally limit latency improvements. We performed a measurement study of a large Web service provider and found that, while connections with no loss complete close to the ideal latency of one round-trip time, TCP's timeout-driven recovery causes transfers with loss to take five times longer on average. In this paper, we present the design of novel loss recovery mechanisms for TCP that judiciously use redundant transmissions to minimize timeout-driven recovery. Proactive, Reactive, and Corrective are three qualitatively-different, easily-deployable mechanisms that (1) proactively recover from losses, (2) recover from them as quickly as possible, and (3) reconstruct packets to mask loss. Crucially, the mechanisms are compatible both with middleboxes and with TCP's existing congestion control and loss recovery. Our large-scale experiments on Google's production network that serves billions of flows demonstrate a 23% decrease in the mean and 47% in 99th percentile latency over today's TCP.