Miracle-dz/UniFAR-FTUs huggingface dataset:
TEMP: a computational method for analyzing transposable element polymorphism in populations

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git.
Clustering Syntactic Positions with Similar Semantic Requirements

This article describes an unsupervised strategy to acquire syntactico-semantic requirements of nouns, verbs, and adjectives from partially parsed text corpora. The linguistic notion of requirement underlying this strategy is based on two specific assumptions. First, it is assumed that two words in a dependency are mutually required. This phenomenon is called here corequirement. Second, it is also claimed that the set of words occurring in similar positions defines extensionally the requirements associated with these positions. The main aim of the learning strategy presented in this article is to identify clusters of similar positions by identifying the words that define their requirements extensionally. This strategy allows us to learn the syntactic and semantic requirements of words in different positions. This information is used to solve attachment ambiguities. Results of this particular task are evaluated at the end of the article. Extensive experimentation was performed on Portuguese text corpora.
Association Rules Mining: A Recent Overview

In this paper, we provide the preliminaries of basic concepts about association rule mining and survey the list of existing association rule mining techniques. Of course, a single article cannot be a complete review of all the al- gorithms, yet we hope that the references cited will cover the major theoretical issues, guiding the researcher in interesting research directions that have yet to be explored.
Decreased Overall Virulence in Coinfected Hosts Leads to the Persistence of Virulent Parasites

Multiple infections are known to affect virulence evolution. Some studies even show that coinfections may decrease the overall virulence (the disease‐induced mortality of a coinfected host). Yet, epidemiological studies tend to overlook the overall virulence, and within‐host models tend to ignore epidemiological processes. Here, I develop an epidemiological model where overall virulence is an explicit function of the virulence of the coinfecting strains. I show that in most cases, a unique strain is evolutionarily stable (in accordance with the model I use here). However, when the overall virulence is lower than the virulence of each of the coinfecting strains (i.e., when coinfections decrease virulence), the evolutionary equilibrium may be invaded by highly virulent strains, leading to the coexistence of two strains on an evolutionary timescale. This model has theoretical and experimental implications: it underlines the importance of overall virulence and of epidemiological feedbacks on virulence evolution.
Socioeconomic Disparities in Breast Cancer Screening in Hawaii

Introduction Despite evidence that breast cancer screening reduces morbidity and mortality, many women do not obtain mammograms. Our objective was to analyze the relationship between income and mammography screening for members enrolled in a large health plan in Hawaii. Methods We analyzed claims data for women (N = 46,328) aged 50 to 70 years during 2003 and 2004. We used parametric and nonparametric regression techniques. We used probit estimation to conduct multivariate analysis. Results At the 5th percentile of the earnings distribution, the probability of mammography is 57.1%, and at the 95th percentile, it is 67.7%. Movement from the 5th percentile to the 35th percentile of the earnings distribution increases the probability of mammography by 0.0378 percentage points. A similar movement from the 65th percentile to the 95th percentile increases the probability by 0.0394 percentage points. Also, we observed an income gradient within narrowly defined geographic regions where physical access to medical care providers is not an issue. Conclusion We observed a steep income gradient in mammography screening in Hawaii. Because of the prevalence of measurement error, this gradient is probably far greater than our estimate. We cannot plausibly attribute our findings to disparities in coverage because 100% of our sample had health insurance coverage. The gradient also does not appear to result from poorer people residing in areas that are geographically isolated from providers of medical care.
Herd Behavior in Financial Markets: An Experiment with Financial Market Professionals

We study herd behavior in a laboratory financial market with financial market professionals. We compare two treatments, one in which the price adjusts to the order flow so that herding should never occur, and one in which event uncertainty makes herding possible. In the first treatment, subjects herd seldom, in accordance with both the theory and previous experimental evidence on student subjects. A proportion of subjects, however, engage in contrarianism, something not accounted for by the theory. In the second treatment, the proportion of herding decisions increases, but not as much as theory suggests; moreover, contrarianism disappears altogether.
Investigation of the relationship between personality characteristics and vasomotor symptoms in menopausal women

Background: Research demonstrates that most of the menopausal symptoms and problems are the reflection of individual and social circumstances rather than the endocrine events of the menopause. As majority of women live 30 years or more through postmenopausal period, treatment and following up their problems during this period is among the main duties of a midwife. The aim of this study is to determine the relationship between personality traits and vasomotor symptoms in postmenopausal women. Materials and Methods: This correlation study was conducted on 400 postmenopausal women referring to the training maternity centers of Mashhad, Iran. Subjects were selected through simple sampling method and filled NEO Five-Factor Inventory (NEO-FFI (questionnaire. Their daily records of hot flashes and night sweats were also collected. NEO-FFI questionnaire assesses the five personality aspects of neuroticism, extraversion, openness to experience, conscientiousness, and agreeableness. After the data were collected, they were analyzed by Pearson and Spearman correlation coefficients, Mann-Whitney, Kruskal-Wallis, and linear regression statistical tests. P < 0.05 was considered as a statistically significant value. Results: Most of the women were in average level of personality traits. Among the aspects of personality traits, there was a significant correlation between intensity of hot flashes (P = 0.041) and night sweats (P = 0.028), and conscientiousness. Conclusions: According to the results of the study, during treatment of the vasomotor symptoms, a midwife should pay close attention to the personality of postmenopausal women to achieve an effective treatment. These women should also be referred to a psychologist, if needed.
Erasing Sensorimotor Memories via PKMζ Inhibition

Sensorimotor cortex has a role in procedural learning. Previous studies suggested that this learning is subserved by long-term potentiation (LTP), which is in turn maintained by the persistently active kinase, protein kinase Mzeta (PKMζ). Whereas the role of PKMζ in animal models of declarative knowledge is established, its effect on procedural knowledge is not well understood. Here we show that PKMζ inhibition, via injection of zeta inhibitory peptide (ZIP) into the rat sensorimotor cortex, disrupts sensorimotor memories for a skilled reaching task even after several weeks of training. The rate of relearning the task after the memory disruption by ZIP was indistinguishable from the rate of initial learning, suggesting no significant savings after the memory loss. These results indicate a shared molecular mechanism of storage for declarative and procedural forms of memory.
A Variance Explanation Paradox : When a Little is a Lot

Concerning a single major league at bat, the percentage of variance in batting performance attributable to skill differentials among major league baseball players can be calculated statistically. The statistically appropriate calculation is seriously discrepant with intuitions about the influence of skill in batting performance. This paradoxical discrepancy is discussed in terms of habits of thought about the concept of variance explanation. It is argued that percent variance explanation is a misleading index of the influence of systematic factors in cases where there are processes by which individually tiny influences cumulate to produce meaningful outcomes.
Heart Rate Variability Characteristics in a Large Group of Active-Duty Marines and Relationship to Posttraumatic Stress

Objective Heart rate variability (HRV), thought to reflect autonomic nervous system function, is lowered under conditions such as posttraumatic stress disorder (PTSD). The potential confounding effects of traumatic brain injury (TBI) and depression in the relationship between HRV and PTSD have not been elucidated in a large cohort of military service members. Here we describe HRV associations with stress disorder symptoms in a large study of Marines while accounting for well-known covariates of HRV and PTSD including TBI and depression. Methods Four battalions of male active-duty Marines (n = 2430) were assessed 1 to 2 months before a combat deployment. HRV was measured during a 5-minute rest. Depression and PTSD were assessed using the Beck Depression Inventory and Clinician-Administered PTSD Scale, respectively. Results When adjusting for covariates, including TBI, regression analyses showed that lower levels of high-frequency HRV were associated with a diagnosis of PTSD (&bgr; = −0.20, p = .035). Depression and PTSD severity were correlated (r = 0.49, p < .001); however, participants with PTSD but relatively low depression scores exhibited reduced high frequency compared with controls (p = .012). Marines with deployment experience (n = 1254) had lower HRV than did those with no experience (p = .033). Conclusions This cross-sectional analysis of a large cohort supports associations between PTSD and reduced HRV when accounting for TBI and depression symptoms. Future postdeployment assessments will be used to determine whether predeployment HRV can predict vulnerability and resilience to the serious psychological and physiological consequences of combat exposure.
From Korotkoff and Marey to automatic non-invasive oscillometric blood pressure measurement: does easiness come with reliability?

ABSTRACT The auscultatory technique remains the point of reference for the validation of non-invasive blood pressure measurement devices, although the exact origin of the Korotkoff sounds is still debated and comparison with intra-arterial measurement shows limits and pitfalls. Automatic oscillometric devices are now widely used by nurses, physicians, and patients. However, many available devices have not been duly validated. Moreover, they calculate systolic and diastolic blood pressures using undisclosed algorithms. Therefore, these devices are not interchangeable, and their reliability may be questionable in some clinical situations. Nevertheless, oscillometry is increasingly used, beside NIBP, for the assessment of central blood pressure and systemic arterial wall stiffness. Awareness of its limits and causes of error is all the more necessary.
Biofilms: Microbial Life on Surfaces

Microorganisms attach to surfaces and develop biofilms. Biofilm-associated cells can be differentiated from their suspended counterparts by generation of an extracellular polymeric substance (EPS) matrix, reduced growth rates, and the up- and down- regulation of specific genes. Attachment is a complex process regulated by diverse characteristics of the growth medium, substratum, and cell surface. An established biofilm structure comprises microbial cells and EPS, has a defined architecture, and provides an optimal environment for the exchange of genetic material between cells. Cells may also communicate via quorum sensing, which may in turn affect biofilm processes such as detachment. Biofilms have great importance for public health because of their role in certain infectious diseases and importance in a variety of device-related infections. A greater understanding of biofilm processes should lead to novel, effective control strategies for biofilm control and a resulting improvement in patient management.
Characterization of TsaR, an Oxygen-Sensitive LysR-Type Regulator for the Degradation of p-Toluenesulfonate in Comamonas testosteroni T-2

ABSTRACT TsaR is the putative LysR-type regulator of the tsa operon (tsaMBCD) which encodes the first steps in the degradation of p-toluenesulfonate (TSA) in Comamonas testosteroni T-2. Transposon mutagenesis was used to knock out tsaR. The resulting mutant lacked the ability to grow with TSA and p-toluenecarboxylate (TCA). Reintroduction of tsaR in trans on an expression vector reconstituted growth with TSA and TCA. The tsaR gene was cloned into Escherichia coli with a C-terminal His tag and overexpressed as TsaRHis. TsaRHis was subject to reversible inactivation by oxygen, which markedly influenced the experimental approaches used. Gel filtration showed TsaRHis to be a monomer in solution. Overexpressed TsaRHis bound specifically to three regions within the promoter between the divergently transcribed tsaR and tsaMBCD. The dissociation constant (KD) for the whole promoter region was about 0.9 μM, and the interaction was a function of the concentration of the ligand TSA. A regulatory model for this LysR-type regulator is proposed on the basis of these data.
New Tetra-Schiff Bases as Efficient Photostabilizers for Poly(vinyl chloride)

Three new tetra-Schiff bases were synthesized and characterized to be used as photostabilizers for poly(vinyl chloride) (PVC) films. The photostability of PVC films (40 μm thickness) in the presence of Schiff bases (0.5 wt %) upon irradiation (300 h) with a UV light (λmax = 365 nm and light intensity = 6.43 × 10−9 ein∙dm−3∙s−1) was examined using various spectroscopic measurements and surface morphology analysis. The changes in various functional groups’ indices, weight and viscosity average molecular weight of PVC films were monitored against irradiation time. The additives used showed photostability for PVC films, with Schiff base 1 being the most effective additive upon irradiation, followed by 2 and 3. The atomic force microscopy (AFM) images for the PVC surface containing Schiff base 1 after irradiation were found to be smooth, with a roughness factor (Rq) of 36.8, compared to 132.2 for the PVC (blank). Several possible mechanisms that explain PVC photostabilization upon irradiation in the presence of tetra-Schiff bases were proposed.
COPD Surveillance—United States, 1999-2011

This report updates surveillance results for COPD in the United States. For 1999 to 2011, data from national data systems for adults aged ≥ 25 years were analyzed. In 2011, 6.5% of adults (approximately 13.7 million) reported having been diagnosed with COPD. From 1999 to 2011, the overall age-adjusted prevalence of having been diagnosed with COPD declined (P = .019). In 2010, there were 10.3 million (494.8 per 10,000) physician office visits, 1.5 million (72.0 per 10,000) ED visits, and 699,000 (32.2 per 10,000) hospital discharges for COPD. From 1999 to 2010, no significant overall trends were noted for physician office visits and ED visits; however, the age-adjusted hospital discharge rate for COPD declined significantly (P = .001). In 2010 there were 312,654 (11.2 per 1,000) Medicare hospital discharge claims submitted for COPD. Medicare claims (1999-2010) declined overall (P = .045), among men (P = .022) and among enrollees aged 65 to 74 years (P = .033). There were 133,575 deaths (63.1 per 100,000) from COPD in 2010. The overall age-adjusted death rate for COPD did not change during 1999 to 2010 (P = .163). Death rates (1999-2010) increased among adults aged 45 to 54 years (P < .001) and among American Indian/Alaska Natives (P = .008) but declined among those aged 55 to 64 years (P = .002) and 65 to 74 years (P < .001), Hispanics (P = .038), Asian/Pacific Islanders (P < .001), and men (P = .001). Geographic clustering of prevalence, Medicare hospitalizations, and deaths were observed. Declines in the age-adjusted prevalence, death rate in men, and hospitalizations for COPD since 1999 suggest progress in the prevention of COPD in the United States.
Cardiac Rehabilitation vs. Home Exercise After Coronary Artery Bypass Graft Surgery: A Comparison of Heart Rate Recovery

Wu S-K, Lin Y-W, Chen C-L, Tsai S-W: Cardiac rehabilitation vs. home exercise after coronary artery bypass graft surgery: a comparison of heart rate recovery. Am J Phys Med Rehabil 2006;85:711–717. Objective:The autonomic dysfunction is known to adversely affect clinical outcome in patients with cardiovascular disease, and exercise training has been shown to modify the sympathovagal control of heart rate. The purposes of this study were to investigate the effect of cardiac rehabilitation on heart rate recovery in patients who received coronary artery bypass grafting (CABG) and compare the effect with that of a home-based exercise program. Design:Fifty-four male patients having undergone CABG were randomly assigned to a cardiac rehabilitation exercise program (n = 18), a home-based exercise program (n = 18), and a control group (n = 18) for 12 wks to evaluate the differences in heart rate recovery among groups. Results:Patients in the cardiac rehabilitation group had significant increases in heart rate recovery (19.1 ± 6.2 vs. 14.0 ± 5.4 beats/min, P = 0.022) compared with those in the control group. There were no significant differences in heart rate recovery between cardiac rehabilitation and home-based exercise groups (16.2 ± 4.8 beats/min) or between home-based exercise and control groups. All three groups had significantly improved heart rate recovery compared with their baseline data (P < 0.001, < 0.001, and 0.007). Conclusion:Our results point out that a cardiac rehabilitation exercise program has a positive effect on heart rate recovery in patients having undergone CABG and is consistent with the autonomic improvement. Although the home-based exercise group did not reveal statistical significances over those in the control group, it had comparable efficacy to that demonstrated in the cardiac rehabilitation group.
"NoW - Network on Wheels" : Project Objectives, Technology and Achievements

NoW – Network on Wheels is a German research project carried out by major car manufacturers, suppliers, research institutes and universities, and supported by the German government. The project develops a vehicular communication system for car-to-car and car-to-infrastructure communication based on ad hoc principles and wireless LAN technology for road safety and infotainment applications. The paper (i) gives a project overview and recalls its motivation, (ii) outlines the developed system and technology, and (iii) summarizes the project achievements.1
Association of fatty acid composition in serum phospholipids with metabolic syndrome and arterial stiffness

0939-4753/$ see front matter a 201 http://dx.doi. org/10.1016/j.numecd. Abstract Background and aim: We examined the association of fatty acid (FA) composition in serum phospholipids with the features of metabolic syndrome (MetS) and arterial stiffness. Methods: Korean men (nZ 593, 30e79yrs) were categorized based on the number of MetS risk factors (RFs) and measured for the markers of MetS, serum phospholipid FA composition and brachial-ankle pulse wave velocity (baPWV), an index for the severity of arterial stiffness. Results: Insulin resistance (HOMA-IR), baPWV, LDL size, and adiponectin were significantly altered corresponding to the number of MetS RFs. The proportions of total monounsaturated FA, palmitoleic acid (16:1), oleic acid (18:1u-9) and dihomo-g-linolenic acid (DGLA, 20:3u-6) in serum phospholipids, and DGLA/linoleic acid (LA) (20:3u-6/18:2u-6), deta9-desaturase activity (D9D-16: 16:1/16:0 and D9D-18: 18:1u-9/18:0) significantly increased corresponding to the number of MetS RFs, but D5D (20:4u-6/20:3u-6) decreased. baPWV positively correlated withHOMA-IR, palmitic acid (16:0), oleic acid, D6D (18:3u-6/18:2u-6), DGLA/LAandD9D-18, and negatively with adiponectin, LDL size, LA, docosahexaenoic acid (DHA, 22:6u-3) and D5D. Multiple stepwise regressionmodels revealed that baPWVwas significantly influenced by systolic blood pressure, age, bodyweight, triglyceride and LA in serumphospholipids (RZ 0.378). Interestingly, baPWV (1419 1 cm/s) andMetS (22%)were highest in individualswith lower proportion of LA (<12.361%) and higher proportion of DGLA ( 1.412%) in serum phospholipid FAs. Conclusion: The features of MetS significantly related to serum phosopholipid FA composition. Particularly, arterial stiffnesswasassociatedwithLAadditively togetherwithDLGA. Itmay suggest a potential benefit of sufficient amounts of LA in serum or in diet can reduce cardiovascular risk. a 2011 Elsevier B.V. All rights reserved.
Immuno-PET for Clinical Theranostic Approaches

Recent advances in molecular characterization of tumors have allowed identification of new molecular targets on tumor cells or biomarkers. In medical practice, the identification of these biomarkers slowly but surely becomes a prerequisite before any treatment decision, leading to the concept of personalized medicine. Immuno-positron emission tomography (PET) fits perfectly with this approach. Indeed, monoclonal antibodies (mAbs) labelled with radionuclides represent promising probes for theranostic approaches, offering a non-invasive solution to assess in vivo target expression and distribution. Immuno-PET can potentially provide useful information for patient risk stratification, diagnosis, selection of targeted therapies, evaluation of response to therapy, prediction of adverse effects or for titrating doses for radioimmunotherapy. This paper reviews some aspects and recent developments in labelling methods, biological targets, and clinical data of some novel PET radiopharmaceuticals.