Miracle-dz/UniFAR-FTUs huggingface dataset:
Recommendations for the Evaluation for Autoimmune Liver Disease in Nonalcoholic Fatty Liver Disease

We read with interest the article published by Chalisani et al.(1) These Guidelines provide clarity for the diagnosis and management of NAFLD. However, we feel that routine diagnosis of nonalcoholic fatty liver disease (NAFLD) can be simplified. As highlighted by the Guidelines, clinicians must explore common alternative causes when evaluating a patient with mild liver function abnormalities and risk factors for metabolic syndrome. (1) These include excessive alcohol intake, hepatitis B and C viral infection, medications, hemochromatosis, and Wilson’s disease. (1) Workup often involves evaluation for autoantibodies to exclude autoimmune hepatitis (AIH). Current evidence demonstrates that autoantibodies, including ANA and anti-SMA, can be detected in up to one third of patients with NAFLD. (2) Of note, the presence or absence of autoantibodies is not related to the degree of fibrosis found on liver biopsy. (3,4) Ravi et al. have shown that autoimmune markers in NAFLD do not influence the natural history or disease course. (5) In Adams’ study, 225 patients with suspected NAFLD underwent liver biopsy. (4) Only 1 patient met diagnostic criteria for AIH according to the criteria of the International Autoimmune Hepatitis Group. It therefore seems that ordering autoantibody studies is not helpful for diagnosing NAFLD. Imaging studies, such as ultrasound, are part of the workup of patients with liver function tests less than 2-3 times the upper limit of normal (ULN). However, the role of imaging is not explored in the literature discussing the role of autoimmune markers in NAFLD. We propose that the workup of suspected NAFLD include hepatitis B antigen, hepatitis C antibody, iron studies, total iron-binding capacity, and abdominal ultrasound. Antimitochondrial antibodies may be added when alkaline phosphatase is elevated. These tests are likely to support or refute the diagnosis of NAFLD in virtually every case. Patients with suspected AIH requiring treatment will likely have symptoms and/or liver function tests several times above the ULN. A request for autoimmune markers can be limited to patients with these more specific findings.
Microsaccades Are Coupled to Heartbeat

During visual fixation, the eye generates microsaccades and slower components of fixational eye movements that are part of the visual processing strategy in humans. Here, we show that ongoing heartbeat is coupled to temporal rate variations in the generation of microsaccades. Using coregistration of eye recording and ECG in humans, we tested the hypothesis that microsaccade onsets are coupled to the relative phase of the R-R intervals in heartbeats. We observed significantly more microsaccades during the early phase after the R peak in the ECG. This form of coupling between heartbeat and eye movements was substantiated by the additional finding of a coupling between heart phase and motion activity in slow fixational eye movements; i.e., retinal image slip caused by physiological drift. Our findings therefore demonstrate a coupling of the oculomotor system and ongoing heartbeat, which provides further evidence for bodily influences on visuomotor functioning. SIGNIFICANCE STATEMENT In the present study, we show that microsaccades are coupled to heartbeat. Moreover, we revealed a strong modulation of slow eye movements around the R peak in the ECG. These results suggest that heartbeat as a basic physiological signal is related to statistical modulations of fixational eye movements, in particular, the generation of microsaccades. Therefore, our findings add a new perspective on the principles underlying the generation of fixational eye movements. Importantly, our study highlights the need to record eye movements when studying the influence of heartbeat in neuroscience to avoid misinterpretation of eye-movement-related artifacts as heart-evoked modulations of neural processing.
Prevalence and Genotyping of Cryptosporidium spp. in Farm Animals in Egypt

ABSTRACT In this study, we examined the prevalence and molecular characteristics of Cryptosporidium in buffalo, dairy cattle and sheep in different farms at Kafr El Sheikh Province, Egypt. Rectal fecal samples, including 466 samples from buffalo, 1697 from cattle and 120 from sheep, were collected from different ages and screened by modified Ziehl-Neelsen acid-fast microscopy for detection of Cryptosporidium oocysts. All studied farms were positives with an overall prevalence of 1.29% in buffalo (4.17% in claves versus 0.48% in adults), 7.07% in cattle (6.90% in calves versus 10.20% and 6.10% in heifers and adults, respectively) and 2.50% in sheep (4.40% in lambs versus 1.30% in adults). PCR-RFLP analyses of small-subunit rRNA genes from positive specimens revealed the occurrence of C. parvum and C. ryanae in buffalo; C. parvum, C. ryanae, C. bovis and C. andersoni in cattle and only C. xiaoi in sheep. Genotypes distribution showed that C. ryanae was the dominant species (60.0%) followed by C. parvum (40.0%) in buffalo calves. Meanwhile, in cattle calves, C. parvum was the commonest species (74.23%) followed by C. ryanae (16.10%) and C. bovis (9.70%). Subtyping of C. parvum based on sequence analysis of the polymorphic 60 kDa glycoprotein gene locus showed the presence of subtypes IIdA20G1 and IIaA15G1R1 in both buffalo and cattle calves, addressing the potential role of calves in zoonotic cryptosporidiosis in Egypt.
Dynamic Modeling to Assess the Business Value of Electronic Commerce

Before adopting electronic commerce (E-Comm), organizations need to assess its real business value, and to compare its costs with those of the associated investments. The intangible nature of most E-Comm benefits may make it difficult to develop an actual business case. This paper presents a case study of E-Comm investment evaluation. Computer-based models of the business processes affected by E-Comm were developed and dynamically simulated to assist in obtaining insight on the real benefits and dangers associated with the planned business change. The potential of Dynamic Process Modeling to support assessment of E-Comm business value is discussed in light of the results of the case study.
Rank acquisition in rhesus macaque yearlings following permanent maternal separation: The importance of the social and physical environment

Rank acquisition is a developmental milestone for young primates, but the processes by which primate yearlings attain social rank in the absence of the mother remain unclear. We studied 18 maternally reared yearling rhesus macaques (Macaca mulatta) that differed in their social and physical rearing environments. We found that early social experience and maternal rank, but not individual traits (weight, sex, age), predicted dominance acquisition in the new peer-only social group. Yearlings also used coalitions to reinforce the hierarchy, and social affiliation (play and grooming) was likely a product, rather than a determinant, of rank acquisition. Following relocation to a familiar environment, significant rank changes occurred indicating that familiarity with a physical environment was salient in rank acquisition. Our results add to the growing body of literature emphasizing the role of the social and physical environment on behavioral development, namely social asymmetries among peers.
A prospective study of holiday weight gain.

BACKGROUND It is commonly asserted that the average American gains 5 lb (2.3 kg) or more over the holiday period between Thanksgiving and New Year's Day, yet few data support this statement. METHODS To estimate actual holiday-related weight variation, we measured body weight in a convenience sample of 195 adults. The subjects were weighed four times at intervals of six to eight weeks, so that weight change was determined for three periods: preholiday (from late September or early October to mid-November), holiday (from mid-November to early or mid-January), and postholiday (from early or mid-January to late February or early March). A final measurement of body weight was obtained in 165 subjects the following September or October. Data on other vital signs and self-reported health measures were obtained from the patients in order to mask the main outcome of interest. RESULTS The mean (+/-SD) weight increased significantly during the holiday period (gain, 0.37+/-1.52 kg; P<0.001), but not during the preholiday period (gain, 0.18+/-1.49 kg; P=0.09) or the postholiday period (loss, 0.07+/-1.14 kg; P=0.36). As compared with their weight in late September or early October, the study subjects had an average net weight gain of 0.48+/-2.22 kg in late February or March (P=0.003). Between February or March and the next September or early October, there was no significant additional change in weight (gain, 0.21 kg+/-2.3 kg; P=0.13) for the 165 participants who returned for follow-up. CONCLUSIONS The average holiday weight gain is less than commonly asserted. Since this gain is not reversed during the spring or summer months, the net 0.48-kg weight gain in the fall and winter probably contributes to the increase in body weight that frequently occurs during adulthood.
ImplementingQuestion and Answer Technique to Enhance Students’ Speaking Ability at SMP Islam Paramitha Malang

Speaking is one of language skills which has to be mastered by the students. By being able to speak, students will be able to transfer their thought to others. Unfortunately, sometimes students, at SMP Islam Paramitha especially, failed to utter their idea in spoken manner due to several factors as lack of vocabulary, not knowing what and how to say the ideas, and mostly feeling unconfident. This problem cannot be neglected; therefore, the researcher decided to carry out a two-cycle Classroom Action Research (CAR). In This CAR the researcher implemented question and answer technique to improve students’ speaking ability on expressing their daily activities. By using observation sheets, interview guide, and test, it was found that 70% of the students had been successfully improving their speaking ability. As a result, the intended spoken communication, either between students and students or teacher and students, did take place.
Cigarette Smoking and Prostate Cancer in a Prospective US Cohort Study

Smoking is an important risk factor for many cancers, yet the relationship between smoking and prostate cancer remains uncertain. We investigated whether smoking affected the risk of prostate cancers within a large prospective cohort study of dietary and environmental cancer risk factors among men ages 50 to 71 upon enrollment in 1995-1996 (n = 283,312). Cox proportional hazards regression models with hazard ratios (HR) and 95% confidence intervals (95% CI) were adjusted for age, race, education, height, body mass index, physical activity, family history of prostate cancer, diabetes, self-reported health status, prostate-specific antigen testing, digital rectal exam, total energy, α-tocopherol, calcium, α-linolenic acid, selenium, red meat, fish, and tomato intake. There were 14,810 nonadvanced and 1,830 advanced incident prostate cancers identified through 2003, and 394 men died of their disease through 2005. Current smokers had a decreased risk of nonadvanced prostate cancer (HR, 0.82; 95% CI, 0.77-0.88), but an increased risk of fatal prostate cancer (HR, 1.69; 95% CI, 1.25-2.27). Former smoking was also associated with decreased risk of nonadvanced prostate cancers (HR, 0.89; 95% CI, 0.86-0.92), but not fatal prostate cancers (HR, 1.03; 95% CI, 0.83-1.27). There was no apparent association between smoking and advanced prostate cancer. A number of biologically plausible mechanisms could explain these results, including the direct effects of carcinogens in tobacco smoke and the resulting changes in sex hormone or growth factor profiles. These findings suggest that current and former smokers may be at decreased risk of being diagnosed with prostate cancer and current smokers are at an increased risk of dying from prostate cancer. (Cancer Epidemiol Biomarkers Prev 2009;18(9):2427–35)
Antecedents of preschool children's internalizing problems: a longitudinal study of low-income families.

OBJECTIVE To examine antecedents of young children's internalizing problems using research related to emotion regulation to guide prediction. METHOD Longitudinal data were collected on 86 low-income mother-child dyads to examine risk factors related to early internalizing problems as measured by the Child Behavior Checklist (CBCL). RESULTS The following risk factors, assessed during infancy, were related to the development of preschool-age internalizing problems: negative emotionality, disorganized attachment classification, negative life events, exposure to child-rearing disagreements, and parenting hassles. In addition, the interaction of high negative emotionality and exposure to parental conflict added unique variance to the prediction of scores on the CBCL Withdrawal and Depression/Anxiety subscales. CONCLUSIONS Children's preschool-age internalizing problems can be identified during infancy from multiple domains related to the development of emotion regulation. Further longitudinal work is encouraged that incorporates direct measurement of children's negative emotionality, parenting, and family factors that influence both parenting and children's emotion regulation.
The Biosynthesis of Cyclopropanated Mycolic Acids in Mycobacterium tuberculosis

The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. The gene whose product cyclopropanates the proximal double bond was cloned by homology to a putative cyclopropane synthase identified from the Mycobacterium leprae genome sequencing project. This gene, named cma2, was sequenced and found to be 52% identical to cma1 (which cyclopropanates the distal double bond) and 73% identical to the gene from M. leprae. Both cma genes were found to be restricted in distribution to pathogenic species of mycobacteria. Expression of cma2 in Mycobacterium smegmatis resulted in the cyclopropanation of the proximal double bond in the α series of mycolic acids. Coexpression of both cyclopropane synthases resulted in cyclopropanation of both centers, producing a molecule structurally similar to the M. tuberculosis α-dicyclopropyl mycolates. Differential scanning calorimetry of purified cell walls and mycolic acids demonstrated that cyclopropanation of the proximal position raised the observed transition temperature by 3°C. These results suggest that cyclopropanation contributes to the structural integrity of the cell wall complex.
Using a Model Incorporating Initial Oxygen Concentration and Blood Flow Increase

Type II photodynamic therapy (PDT) is an experimental modality for cancer treatment based on the combined action of a photosensitizer, a special wavelength of light and singlet oxygen (O2) generation. The cell killing is caused by the reaction of cellular acceptors with O2. A mathematical model has been previously developed to incorporate the macroscopic kinetic equations for O2 generation, photosensitizers in ground and triplet states, oxygen (O2), and tissue acceptors along with the diffusion equation for the light transport in tissue. Accurate estimation of the tissue oxygen changes during PDT is influenced by initial oxygen concentration ([O2]0) and blood flow, so that incorporation of different [O2]0 and blood flow changes in our model allows a better calculation of the O2 generation. In this study, the effects of [O2]0, as well as the changes of the blood flow during PDT, on the magnitude of O2 generation is studied.
Perceiving Commerial Activeness Over Satellite Images

Different urban regions usually have different commercial hotness due to the different social contexts inside. As satellite imagery promises high-resolution, low-cost, real-time, and ubiquitous data acquisition, this study aims to solve commercial hotness prediction as well as the correlated social contexts mining problem via visual pattern analysis on satellite images. The goal is to reveal the underlying law correlating visual patterns of satellite images with commercial hotness so as to infer the commercial hotness map of a whole city for government regulation and business planning. We propose a novel deep learning-based model, which learns semantic information from raw satellite images to enable predicting regional commercial hotness. First, we collect satellite images from Google Map and label such images with POI categories according to the annotations from OpenStreetMap. Then, we train a model of deep convolutional networks that leverage raw images to infer the social attributes of the region of interest. Finally, we use three classical regression methods to predict regional commercial hotness from the corresponding social contexts reflected in satellite images in Shanghai, where the applied deep features are learned from the examples of Beijing to guarantee the generality. The result shows that the proposed model is robust enough to reach 82% precision at average. To the best of our knowledge, it is the first work focused on discovering relations between commercial hotness and satellite images. A web service is developed to demonstrate how business planning can be done in reference to the predicted commercial hotness of a given region.
HELIOSEISMOLOGY OF PRE-EMERGING ACTIVE REGIONS. II. AVERAGE EMERGENCE PROPERTIES

We report on average subsurface properties of pre-emerging active regions as compared to areas where no active region emergence was detected. Helioseismic holography is applied to samples of the two populations (pre-emergence and without emergence), each sample having over 100 members, which were selected to minimize systematic bias, as described in Leka et al. We find that there are statistically significant signatures (i.e., difference in the means of more than a few standard errors) in the average subsurface flows and the apparent wave speed that precede the formation of an active region. The measurements here rule out spatially extended flows of more than about 15 m s−1 in the top 20 Mm below the photosphere over the course of the day preceding the start of visible emergence. These measurements place strong constraints on models of active region formation.
TRIAD I-The Realistic Interpretation of Advanced Directives

Rationale: Living wills often accompany patients who present for emergent care. Despite evidence suggesting that misunderstanding could lead to inappropriate care, few studies have assessed underlying assumptions about these instructions and how care may be affected. Objectives: To determine if the living will implies a code status before clinical interaction and to assess how the term "do-not-resuscitate" is defined in terms of patient care. Methods: An intranet survey was administered to clinical departments at a 350-bed acute care and level II trauma center. There were 585 potential respondents including physicians, nurses, and first-responders. No age or experience restrictions or exclusions were applied, given that emergent care presumes neither minimum age nor previous experience. The survey presented a fictitious living will refusing lifesaving interventions and prompted respondents to assign a code status (do-not-resuscitate or full code) and define the level of care associated with the former. Clinical information was withheld to isolate responses to the advance directive. Results: Between 440 and 452 responses were made. Most were female (64%) and nurses (62%) with an average age of 38.2 years (range 18-68) and an average duration of employment of 13.3 years (range 0.3-40.9). Seventy-nine percent (347/440) indicated do-not-resuscitate and 70% (317/452) construed do-not-resuscitate with "comfort care/end-of-life care. " Occupation hierarchy (pre-hospital, nurse, physician) was related to the likelihood of choosing full code or full care (P ≤ 0.001, odds ratios: 4.03 [95% bounds 1.70, 9.55]; 2.19 [95% bounds: 1.04, 4.65], respectively). Conclusions: A majority of caregivers at a level II trauma center construed a living will with a do-not-resuscitate order which, in turn, was equated with end-of-life care. Such understandings may unnecessarily put patients at risk when presenting for emergent care.
The Pseudomonas aeruginosa type III secretion translocator PopB assists the insertion of the PopD translocator into host cell membranes

Many Gram-negative bacterial pathogens use a type III secretion system to infect eukaryotic cells. The injection of bacterial toxins or protein effectors via this system is accomplished through a plasma membrane channel formed by two bacterial proteins, termed translocators, whose assembly and membrane-insertion mechanisms are currently unclear. Here, using purified proteins we demonstrate that the translocators PopB and PopD in Pseudomonas aeruginosa assemble heterodimers in membranes, leading to stably inserted hetero-complexes. Using site-directed fluorescence labeling with an environment-sensitive probe, we found that hydrophobic segments in PopD anchor the translocator to the membrane, but without adopting a typical transmembrane orientation. A fluorescence dual-quenching assay revealed that the presence of PopB changes the conformation adopted by PopD segments in membranes. Furthermore, analysis of PopD's interaction with human cell membranes revealed that PopD adopts a distinctive conformation when PopB is present. An N-terminal region of PopD is only exposed to the host cytosol when PopB is present. We conclude that PopB assists with the proper insertion of PopD in cell membranes, required for the formation of a functional translocon and host infection.
Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing

ABSTRACT HIV superinfection, which occurs when a previously infected individual acquires a new distinct HIV strain, has been described in a number of populations. Previous methods to detect superinfection have involved a combination of labor-intensive assays with various rates of success. We designed and tested a next-generation sequencing (NGS) protocol to identify HIV superinfection by targeting two regions of the HIV viral genome, p24 and gp41. The method was validated by mixing control samples infected with HIV subtype A or D at different ratios to determine the inter- and intrasubtype sensitivity by NGS. This amplicon-based NGS protocol was able to consistently identify distinct intersubtype strains at ratios of 1% and intrasubtype variants at ratios of 5%. By using stored samples from the Rakai Community Cohort Study (RCCS) in Uganda, 11 individuals who were HIV seroconcordant but virally unlinked from their spouses were then tested by this method to detect superinfection between 2002 and 2005. Two female cases of HIV intersubtype superinfection (18.2%) were identified. These results are consistent with other African studies and support the hypothesis that HIV superinfection occurs at a relatively high rate. Our results indicate that NGS can be used for detection of HIV superinfection within large cohorts, which could assist in determining the incidence and the epidemiologic, virologic, and immunological correlates of this phenomenon.
A Vector Space Model for Syntactic Distances Between Dialects

Syntactic comparison across languages is essential in the research field of linguistics, e.g. when investigating the relationship among closely related languages. In IR and NLP, the syntactic information is used to understand the meaning of word occurrences according to the context in which their appear. In this paper, we discuss a mathematical framework to compute the distance between languages based on the data available in current state-of-the-art linguistic databases. This framework is inspired by approaches presented in IR and NLP.