Miracle-dz/UniFAR-FTUs huggingface dataset:
Capsular Polysaccharide Is a Major Complement Resistance Factor in Lipopolysaccharide O Side Chain-DeficientKlebsiella pneumoniae Clinical Isolates

ABSTRACT We have previously demonstrated the existence of Klebsiella pneumoniae clinical isolates deficient in the lipopolysaccharide O side chain, the major factor for resistance to complement-mediated killing in this bacterial species. These isolates are complement resistant, and their mechanisms to resist complement were investigated by selecting transposon-generated complement-sensitive mutants. One mutant with a drastically reduced capacity to grow in nonimmune human serum carried the transposon inserted in an open reading frame of a gene cluster involved in capsule synthesis. This mutant produced less capsule, bound more molecules of the complement component C3, and was more sensitive to complement-mediated and opsonophagocytic killings than was the parent strain. Four additional clinical isolates representing four different K serotypes were studied, and results showed that capsular polysaccharide is a major complement resistance factor in these O side chain-deficient isolates.
Human interpretation of light diffuseness

The light diffuseness (Xia, Pont et al. 2016, Xia, Pont et al. 2016) can strongly influence the appearance of scenes and objects inside it. There are numerous studies investigating how to measure the light diffuseness or modelling index. However, there are few studies about how light diffuseness is interpreted by human observers. We use an appearancematching experiment to investigate observers' visual interpretation of light diffuseness from object appearance and its potential interactions with viewing angles, light probe type, etcetera. The results indicate that, generally, the observers are able to distinguish different diffuseness levels for both the smooth and rough white spherical probes. The “diffuseness-direction ambiguity” (Pont and Koenderink 2007) is obvious especially for the smooth probe and it can be largely corrected for by the “effective vector to scalar ratio” (Cuttle 1971). Moreover, the results showed that the use of a probe with mesorelief can at least partly resolve the “diffuseness-direction ambiguity”.
Prospective study of recreational physical activity and ovarian cancer.

BACKGROUND It has been hypothesized that physical activity may reduce the risk of ovarian cancer by decreasing estrogen levels, reducing body fat, and reducing the frequency of ovulation. Epidemiologic studies of this relationship have obtained inconsistent results. The only prospective study to date reported a positive association between frequent vigorous exercise and ovarian cancer risk. We further evaluated this relationship in the Nurses' Health Study cohort. METHODS Participation in recreational physical activity was assessed by questionnaire in 1980, 1982, 1986, 1988, 1992, and 1994, with questions assessing exercise frequency, duration, and intensity. Results were adjusted for age, parity, oral contraceptive use, tubal ligation, and other risk factors for ovarian cancer. All statistical tests were two-sided. RESULTS During a 16-year follow-up (from 1980 to 1996), 1.2 million person-years were accrued by 92 825 cohort members, and 377 cases of epithelial ovarian cancer were confirmed. The relative risk (RR) of ovarian cancer for women engaging in recreational physical activity for 7 hours or more per week compared with those reporting less than 1 hour per week was 0.80 (95% confidence interval [CI] = 0.49 to 1.32; P(trend) =. 59). When both the frequency and intensity of activity were taken into account, activity level was also not associated with a reduced risk of ovarian cancer. Compared with inactive women, participants reporting high activity in terms of metabolic equivalent task hours (MET hours) were at greater risk of ovarian cancer (RR for 20 to <30 MET hours/week = 1.84 [95% CI = 1.12 to 3.02]; RR for >30 MET hours/week = 1.27 [95% CI = 0.75 to 2.14]). CONCLUSIONS Overall, results did not suggest an inverse association between recreational physical activity and ovarian cancer. The possibility of a modest increase in risk with frequent vigorous activity requires further investigation.
HYBRID PERMUTATION TEST WITH APPLICATION TO SURFACE SHAPE ANALYSIS

This paper presents a new statistical surface analysis framework that aims to accurately and efficiently localize regionally specific shape changes between groups of 3D surfaces. With unknown distribution and small sample size of the data, existing shape morphometry analysis involves testing thousands of hypothe- ses for statistically significant effects through permutation. In this work, we de- velop a novel hybrid permutation test approach to improve the system's efficiency by approximating the permutation distribution of the test statistic with a Pearson distribution series that involves the calculation of the first four moments of the permutation distribution. We propose to derive these moments theoretically and analytically without any permutation. Detailed derivations and experimental re- sults using two different test statistics are demonstrated using simulated data and brain data for shape morphometry analysis. Furthermore, an adaptive procedure is utilized to control the False Discovery Rate (FDR) for increased power of finding significance.
Queue structure and optimal buffer division between ingress/egress ports in crossbar-based switches

The memory used in high-speed switching often needs to be customer designed and is expensive. As the link speed approaches 10-G and 40-G rates, reducing the memory requirement can translate into significant cost saving. In this paper, we study an optimal memory partition scheme between ingress ports and egress ports of a crossbar-based switch. We show how the optimal partition between ingress and egress ports can save memory, and how the partition is affected by the queue structure in the switch. Compared with the 50-50 partition, the optimal partition scheme can reduce buffer requirements by at least 30%.
Detection of recurrence in patients with rectal cancer: PET/CT after abdominoperineal or anterior resection.

PURPOSE To assess diagnostic accuracy of combined positron emission tomography (PET) and computed tomography (CT) in detection of pelvic recurrence in patients with rectal cancer who underwent abdominoperineal or anterior resection. MATERIALS AND METHODS Sixty-two patients were enrolled; 37 were men, and 25 were women. Seventeen patients underwent abdominoperineal resection and 45 underwent anterior resection with an anastomosis in the pelvic region before referral for PET/CT. Pelvic sites of fluorine 18 ((18)F) fluorodeoxyglucose (FDG) uptake were rated separately on PET and PET/CT images as benign or malignant on the basis of shape, location, and intensity of (18)F FDG uptake (1-2 = benign and/or physiologic, 3 = equivocal, 4-5 = malignant). Two readers interpreted images in consensus. Altered pelvic anatomy and presence of presacral abnormalities were assessed with CT. Pelvic recurrence was confirmed with histologic analysis or clinical and imaging follow-up. Sensitivity, specificity, positive and negative predictive values, and accuracy of PET and PET/CT in the detection of pelvic recurrence were compared with lesion- and patient-based analyses by using the chi(2) test. Clinical relevance of PET/CT assessment was determined. RESULTS Of 81 pelvic sites with increased (18)F FDG uptake, 44 were malignant. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy for differentiating malignant from benign (18)F FDG uptake in the pelvis were 98%, 96%, 90%, 97%, and 93% for PET/CT and 82%, 65%, 73%, 75%, and 74% for PET, respectively. The most common cause for false-positive interpretation of PET findings was physiologic (18)F FDG uptake in displaced pelvic organs. Presacral CT abnormalities were present in 30 (48%) of 62 patients, and seven (23%) abnormalities were malignant. PET/CT was used to distinguish benign and malignant presacral abnormalities with a sensitivity, specificity, positive predictive value, and negative predictive value of 100%, 96%, 88%, and 100%, respectively. PET/CT findings were clinically relevant in 29 (47%) of 62 patients. CONCLUSION PET/CT is an accurate technique in the detection of pelvic recurrence after surgical removal of rectal cancer.
Enhancement of Macrophage Stimulation by Lipoteichoic Acid and the Costimulant Hemoglobin Is Dependent on Toll-Like Receptors 2 and 4

ABSTRACT Macrophage stimulation by lipoteichoic acid (LTA) and hemoglobin (Hb) requires Toll-like receptors 2 and 4 (TLR2 and -4). There are two distinct temporal phases of interleukin-6 (IL-6) production. The first results in a slight enhancement of IL-6 secretion in response to LTA plus Hb compared to that with LTA alone and is TLR4 independent. The second requires TLR4 and accounts for most of the additional stimulation seen with LTA plus Hb.
Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection

Human immunodeficiency virus type 1 (HIV-1) has high replication and mutation rates that generate large census populations and high levels of genetic variation. We examined the roles of natural selection, population growth, random genetic drift, and recombination in shaping the variation in 1509 C2-V5 env sequences derived from nine men with chronic HIV-1 infection. These sequences were obtained from clinical visits that reflect the first 6-13.7 years of infection. Pairwise comparisons of nonsynonymous and synonymous distances, Tajima's D test, Fu and Li's D* test, and a test of recurrent mutation revealed evidence for episodes of nonneutral evolution in a total of 22 out of 145 blood samples, representing six of the nine individuals. Using three coalescent-based maximum-likelihood estimators, we found viral effective population sizes in all nine individuals to be ∼103. We also show that a previous estimate of the effective population size of ∼105 based on rare haplotype frequencies decreases to ∼103 upon correcting a biased sampling procedure. We conclude that the genetic variation in these data sets can be explained by a predominance of random genetic drift of neutral mutations with brief episodes of natural selection that were frequently masked by recombination.
Late versus Early Onset Depression in Elderly Patients: Vascular Risk and Cognitive Impairment.

BACKGROUND Three-quarters of patients with major depressive disorder have late-onset depression. Late-onset depression is more often associated with cognitive impairment than earlyonset depression and evidences showed a relationship between vascular factors and late-life depression. OBJECTIVES To compare cognitive functions between late-onset (≥60 years) and early-onset (<60 years) depression in elderly patients and to highlight the effect of vascular risk factors in elderly patients with late and early onset depression. METHODS This was a cross sectional, case control study with consecutive referral done on eighty elderly patients with depression who were recruited from Geriatric Outpatient Clinic of Psychiatry and Addiction Prevention Hospital, Al Kasr Al-Ainy, Cairo University. They were divided into two groups according to the age of onset of depression: Late Onset Depression (LOD) group and Early Onset Depression (EOD) group. They were cognitively assessed using ACE III, Framingham risk score for vascular risk assessment. RESULTS Late onset group had worse performance than early onset group regarding memory, verbal fluency, language, visuospatial abilities and had more vascular risk. CONCLUSION Elderly patients with late onset depression had higher severity of depression as well as they were more cognitively affected regarding memory, verbal fluency, language, and visuospatial abilities. Vascular risk factors especially hypertension and diabetes mellitus were higher elderly patients with late onset depression and affects the severity of depression and degree of cognitive impairment.
Effects of Body Position and Loading Modality on Muscle Activity and Strength in Shoulder Presses

Abstract Saeterbakken, AH and Fimland, MS. Effects of body position and loading modality on muscle activity and strength in shoulder presses. J Strength Cond Res 27(7): 1824–1831, 2013—Little is known about the effect of performing upper-body resistance exercises with dumbbells versus barbells and standing versus seated. Therefore, this study sought to compare electromyogram activity (EMG) and one-repetition maximum (1-RM) in barbell and dumbbell shoulder presses performed seated and standing. Fifteen healthy men volunteered for 1-RM and EMG testing with a load corresponding to 80% of the 1-RM. Electromyogram activity was measured in the anterior, medial, and posterior deltoids and biceps and triceps brachii. The following EMG differences or trends were observed: For deltoid anterior: ∼11% lower for seated barbell versus dumbbell (p = 0.038), ∼15% lower in standing barbell versus dumbbell (p < 0.001), ∼8% lower for seated versus standing dumbbells (p = 0.070); For medial deltoid, ∼7% lower for standing barbell versus dumbbells (p = 0.050), ∼7% lower for seated versus standing barbell (p = 0.062), 15% lower for seated versus standing dumbbell (p = 0.008); For posterior deltoid: ∼25% lower for seated versus standing barbell (p < 0.001), ∼24% lower for seated versus standing dumbbells (p = 0.002); For biceps, ∼33% greater for seated barbell versus dumbbells (p = 0.002), 16% greater for standing barbell versus dumbbell (p = 0.074), ∼23% lower for seated versus standing dumbbells (p < 0.001); For triceps, ∼39% greater for standing barbell versus dumbbells (p < 0.001), ∼20% lower for seated versus standing barbell (p = 0.094). 1-RM strength for standing dumbbells was ∼7% lower than standing barbell (p = 0.002) and ∼10% lower than seated dumbbells (p < 0.001). In conclusion, the exercise with the greatest stability requirement (standing and dumbbells) demonstrated the highest neuromuscular activity of the deltoid muscles, although this was the exercise with the lowest 1-RM strength.
Event detection and summarization in American football broadcast video

We propose a framework for event detection and summary generation in football broadcast video. First, we formulate summarization as a play detection problem, with play being defined as the most basic segment of time during which the ball is being played. Then we propose both deterministic and probabilistic approaches to the detection of the plays. The detected plays are concatenated to generate a compact, time-compressed summary of the original video. Such a summary is complete in the sense that it contains every meaningful action of the underlying game, and it also servers as a much better starting point for higher-level summarization and other analyses than the original video does. Based on the summary, we also propose an audio-based hierarchical summarization method. Experimental results show the proposed methods work very well on consumer grade platforms.
Recognition of Gene/Protein Names using Conditional Random Fields

With the overwhelming amount of publicly available data in the biomedical field, traditional tasks performed by expert database annotators rapidly became hard and very expensive. This situation led to the development of computerized systems to extract information in a structured manner. The first step of such systems requires the identification of named entities (e.g. gene/protein names), a task called Named Entity Recognition (NER). Much of the current research to tackle this problem is based on Machine Learning (ML) techniques, which demand careful and sensitive definition of the several used methods. This article presents a NER system using Conditional Random Fields (CRFs) as the machine learning technique, combining the best techniques recently described in the literature. The proposed system uses biomedical knowledge and a large set of orthographic and morphological features. An F-measure of 0,7936 was obtained on the BioCreative II Gene Mention corpus, achieving a significantly better performance than similar baseline systems.
VerilogA modeling of the memristor for circuit applications

The memristor has attracted great attention in recent years due to the high demand of nano-sized high performance nonvolatile memories. Furthermore, recent breakthrough in nanotechnology makes the fabrication of the memristor a reality. In this work, the switching mechanism and the resistive switching behavior that take place in the memristor are introduced. The ionic transportation mechanism is used to explain the resistive switching process. In addition, a working model for the memristor that based on the existing oxygen vacancy migration mechanism is conducted. A VerilogA model of the memristor that based on this working model is proposed. Simulation results using this VerilogA model compliment existing proposals well. In conclusion, the future of the memristor is promising.
Hierarchical role classification based on social behavior analysis

Role identification is a difficult job for many social network applications. One of the difficulties is to maintain and utilize large amount of distinct roles. In this paper, we attempt to adopt fuzzy classification method and construct a hierarchy for role classification. We believe this approach can encourage the utilization of social roles by considering their identifiable features at different levels.
Optimal and Near-Optimal Detection in Bursty Impulsive Noise

In many practical scenarios, the ambient noise process is known to be impulsive. To combat this, several robust measures have been proposed in the literature. Most of them assume white noise processes, i.e., the noise samples are independent and identically distributed heavy-tailed random variables. However, noise is seldom white in practice and therefore exhibits memory. For impulsive noise, dependency among samples results in outliers clustering together. The process is thus impulsive and bursty. In our work, we employ stationary <inline-formula><tex-math notation="LaTeX"> $\alpha$</tex-math></inline-formula>-sub-Gaussian noise with memory order <inline-formula><tex-math notation="LaTeX"> $m$</tex-math></inline-formula> (<inline-formula><tex-math notation="LaTeX">$\alpha$</tex-math></inline-formula>SGN( <inline-formula><tex-math notation="LaTeX">$m$</tex-math></inline-formula>)) to model bursty impulsive noise. The model is based on the multivariate <inline-formula><tex-math notation="LaTeX">$\alpha$</tex-math></inline-formula> -sub-Gaussian (<inline-formula><tex-math notation="LaTeX">$\alpha$</tex-math></inline-formula>SG) distribution family and statistically characterizes adjacent samples from elliptical distributions. The latter assumption holds well for snapping shrimp noise found in warm shallow underwater channels. We investigate the performance of conventional robust detectors in <inline-formula><tex-math notation="LaTeX">$\alpha$</tex-math></inline-formula>SGN(<inline-formula> <tex-math notation="LaTeX">$m$</tex-math></inline-formula>) and also propose novel near-optimal detectors. The Neyman–Pearson (NP) approach for binary hypothesis testing is considered and extensive simulation results for the aforementioned detectors are offered. For all instances, we employ an <inline-formula><tex-math notation="LaTeX"> $\alpha$</tex-math></inline-formula>SGN(<inline-formula><tex-math notation="LaTeX">$m$</tex-math></inline-formula>) process whose parameters are tuned to snapping shrimp noise data sets. By incorporating good signal design rules, it is shown that there is a large performance gap between the new and conventional detectors in various impulsive regimes. Moreover, it is possible to derive a near-optimal detector if one only has information of the temporal statistics of the noise process.
Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers

Adamantanes (amantadine and rimantadine) are one of the two classes of Food and Drug Administration–approved antiviral drugs used for the prevention and treatment of influenza A virus infections. They inhibit viral replication by blocking the wild-type (WT) M2 proton channel, thus preventing viral uncoating. However, their use was discontinued due to widespread drug resistance. Among a handful of drug-resistant mutants, M2-S31N is the predominant mutation and persists in more than 95% of currently circulating influenza A strains. We recently designed two classes of M2-S31N inhibitors, S31N-specific inhibitors and S31N/WT dual inhibitors, which are represented by N-[(5-cyclopropyl-1,2-oxazol-3-yl)methyl]adamantan-1-amine (WJ379) and N-[(5-bromothiophen-2-yl)methyl]adamantan-1-amine (BC035), respectively. However, their antiviral activities against currently circulating influenza A viruses and their genetic barrier to drug resistance are unknown. In this report, we evaluated the therapeutic potential of these two classes of M2-S31N inhibitors (WJ379 and BC035) by profiling their antiviral efficacy against multidrug-resistant influenza A viruses, in vitro drug resistance barrier, and synergistic effect with oseltamivir. We found that M2-S31N inhibitors were active against several influenza A viruses that are resistant to one or both classes of Food and Drug Administration–approved anti-influenza drugs. In addition, M2-S31N inhibitors display a higher in vitro genetic barrier to drug resistance than amantadine. The antiviral effect of WJ379 was also synergistic with oseltamivir carboxylate. Overall, these results reaffirm that M2-S31N inhibitors are promising antiviral drug candidates that warrant further development.
Two-pass color interpolation for color filter array

How to manufacture a low-cost digital still camera (DSC) that can meanwhile provide a good image quality is always an engineering challenge. For this purpose, the color filter array (CFA) is perhaps the most commonly used structure for modern DSCs. However, since most of the color information is filtered out, a good interpolation process is required to retrieve the original image. Many interpolation methods have thus been proposed. In this work, we propose to perform the edge-preserving signal correlation based (EP-SCB) interpolation [1] as a second pass to those images restored from some other existing interpolation methods such as local polynomial approximation intersection of confidence intervals (LPA-ICI) rule [2]. Experiments show that most of the images' PSNRs can be improved by the second pass. The simplicity of the EP-SCB hence makes it a suitable candidate as an enhancement option for DSCs techniques.