Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary fat intake and relationship to serum lipid levels in HIV-infected patients with metabolic abnormalities in the HAART era

Objective:To evaluate dietary intake and its relationship to lipid parameters in HIV-infected patients with metabolic abnormalities. Method:We prospectively determined dietary intake (4-day food records or 24-h recall) in 356 HIV-infected patients and 162 community-derived HIV-negative controls evaluated for metabolic studies between 1998–2005. Differences in dietary intake between HIV-infected patients and non-HIV-infected controls, in relation to the established 2005 USDA (United States Department of Agriculture) Recommended Dietary Guidelines, were determined. The relationship between dietary fat intake and serum lipid levels among HIV-infected individuals was also evaluated. Results:Assessment of dietary intake in this group of HIV-infected patients demonstrated increased intake of total dietary fat (P < 0.05), saturated fat (P = 0.006), and cholesterol (P = 0.006) as well as a greater percentage of calories from saturated fat (P = 0.002) and from trans fat (P = 0.02), despite similar caloric intake to the control individuals. A significantly higher percentage of HIV-infected patients were above the 2005 USDA Recommended Dietary Guidelines for saturated fat (> 10%/day) (76.0% HIV vs. 60.9% controls, P = 0.003), and cholesterol (> 300 mg/day) (49.7% HIV vs. 37.9% controls, P = 0.04). Saturated fat intake was strongly associated with triglyceride level [triglyceride level increased 8.7 mg/dl (parameter estimate) per gram of increased saturated fat intake, P = 0.005] whereas total fat was inversely associated with triglyceride level [triglyceride level decreased 3.0 mg/dl (parameter estimate) per gram of increased total fat intake, P = 0.02] among HIV-infected individuals. Conclusions:Increased intake of saturated fat is seen and contributes to hypertriglyceridemia among HIV-infected patients who have developed metabolic abnormalities. Increased saturated fat intake should be targeted for dietary modification in this population.
The Feasibility of Using Internet Support for the Maintenance of Weight Loss

This pilot study examined the acceptability and feasibility of conducting a weight loss maintenance intervention over the Internet. Obese adults participated in a 15-week behavioral weight control intervention and were then randomly assigned to one of the following three maintenance conditions: (a) in-person, therapist-led (TL); (b) Internet, therapist-led (I); and (c) control (C). Both maintenance interventions met biweekly for 22 weeks using the same program content. Results showed that TL participants were more likely to attend their meetings and feel more satisfied with their group assignment. Ho wever, there were no differences between the TL and I groups in overall attrition or number of peer support contacts made. There was also no significant difference in weight loss between the groups. Thus, the Internet may hold promise as a method for maintaining contact with patients to facilitate long-term behavior change.
Residual image coding using a SPIHT-based video coder

This paper describes the design and implementation of a block-based set partitioning in hierarchical trees (SPIHT) coder which is capable of encoding residual images in low bit-rate video coding. Unlike the SPIHT coder which encodes an entire image frame, the new algorithm encodes the subdivided image regions (16times16 blocks) differentially based on an optimization bit allocation strategy. Instead of applying DWT to the whole image, it is applied separately on each partitioned block of the original image and, depending on the statistics of each image region, the number of wavelet coefficients to be retained is determined. Our experiments show that the proposed block-based SPIHT coder (BSC) performs better than SPIHT in terms of PSNR (objective criteria) & visual perception quality (subjective criteria)
Single molecule RNA sequencing uncovers trans‐splicing and improves annotations in Anopheles stephensi

Single molecule real‐time (SMRT) sequencing has recently been used to obtain full‐length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full‐length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction. We found that error correction using Illumina RNA sequencing (RNA‐seq) generated more data than using the default SMRT pipeline. The full‐length error‐corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively spliced isoforms were added to the annotation. In addition, six trans‐splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans‐splicing events appear to be conserved in Culicidae, as they are also found in Anopheles gambiae and Aedes aegypti. The proteins encoded by trans‐splicing events are also highly conserved and the orthologues of these proteins are cis‐spliced in outgroup species, indicating that trans‐splicing may arise as a mechanism to rescue genes that broke up during evolution.
Development of organised conjunctival leucocyte aggregates after corneal transplantation in rats

Aim: To investigate the development of lymphoid aggregates in the conjunctiva after corneal transplantation in rats. Methods: LEW or PVG strain corneas were transplanted orthotopically to PVG rats. Cornea and conjunctiva were examined clinically for up to 42 days. Eyes were removed with attached conjunctiva on days 10 and 15 after transplantation (before and during rejection), together with normal eyes, fixed, paraffin embedded, and examined immunohistochemically. Results: Clinically, the temporal half of the upper palpebral conjunctiva of recipients of 10/19 allografts and 1/10 isografts developed pronounced swelling, correlating with inflammation and rejection. Histologically, the swelling comprised leucocytic aggregates with an altered overlying epithelium. Aggregates contained granulocytes, macrophages, and cells expressing major histocompatibility complex (MHC) class II, CD4, and CD8, all more numerous in allograft associated conjunctiva. Class II+ cells were more abundant at the surface, whereas macrophages and T cells were more numerous in the deeper stroma. There were few B cells. There was greater CD54 expression by vascular endothelium in allograft associated aggregates. Cells expressing TNFα and IFNγ but not IL1β were present in stromal and superficial areas. Conclusions: Corneal transplantation in rats induces the development of organised conjunctival leucocytic aggregates in a fixed location that are significantly more pronounced in recipients of allografts compared with isografts and show characteristics of a Th1 type immune response. These aggregates have characteristics of conjunctiva associated lymphoid tissue and may be sites of presentation of graft antigens and lymphocyte proliferation at the ocular surface.
Reproducibility of single-beam acoustic seabed classification

Single-beam acoustic seabed classification continues to be a popular method for mapping seabeds and their sediments. Modern methods can generate maps of acoustic classes that are useful and reasonably accurate. Research toward improved methods continues. A continuing impediment to this research is ranking the accuracy of maps produced by new methods. Non-acoustic data, or ground truth, is usually sparse compared to the detail of the acoustic survey, which can mean that ranking maps for accuracy can be inconclusive. Here we present a new tool for ranking classification maps, namely the reproducibility of acoustic classes from repeated surveys of the same area on different days. Methods that have high reproducibility achieve that by capturing echo characteristics that are strongly influenced by seabed type while suppressing details that are driven by sea state or the water column. Six surveys, done with a 50 kHz sounder over a pair of transects near Miami, FL, USA, between 1 May and 13 August 2007, were used to evaluate two questions. First, how reproducible were classifications of this dataset using QTC IMPACT™ (Quester Tangent Corporation)? Second, can classification be improved with adjustments to the standard IMPACT processing? Reproducibility was quantified with the overall accuracy and Kappa statistics, which are both derived from the confusion matrix whose rows and columns are numbers of sites with particular class assignments under distinct circumstances.
A Credit Card Usage Behaviour Analysis Framework - A Data Mining Approach

Credit card is one of the most popular e-payment approaches in current online e-commerce. To consolidate valuable customers, card issuers invest a lot of money to maintain good relationship with their customers. Although several efforts have been done in studying card usage motivation, few researches emphasize on credit card usage behaviour analysis when time periods change from t to t+1. To address this issue, an integrated data mining approach is proposed in this paper. First, the customer profile and their transaction data at time period t are retrieved from databases. Second, a LabelSOM neural network groups customers into segments and identify critical characteristics for each group. Third, a fuzzy decision tree algorithm is used to construct usage behaviour rules of interesting customer groups. Finally, these rules are used to analysis the behaviour changes between time periods t and t+1. An implementation case using a practical credit card database provided by a commercial bank in Taiwan is illustrated to show the benefits of the proposed framework.
Stable Carbon Isotope Fractionation by Methanosarcina barkeri during Methanogenesis from Acetate, Methanol, or Carbon Dioxide-Hydrogen

Methanosarcina barkeri was cultured on methanol, H2-CO2, and acetate, and the 13C/12C ratios of the substrates and the methane produced from them were determined. The discrimination against 13C in methane relative to substrate decreased in the order methanol > CO2 > acetate. The isotopic fractionation for methane derived from acetate was only one-third of that observed with methanol as the substrate. The data presented indicate that the last enzyme of methanogenesis, methylreductase, is not the primary site of isotopic discrimination during methanogenesis from methanol or CO2. These results also support biogeochemical interpretations that gas produced in environments in which acetate is the primary methane precursor will have higher 13C/12C ratios than those from environments where other substrates predominate.
Primary GH insensitivity '(Laron syndrome) caused by a novel 4 kb deletion encompassing exon 5 of the GH receptor gene: effect of intermittent long-term treatment with recombinant human IGF-I.

OBJECTIVE GH insensitivity syndrome (GHIS; Laron syndrome) is clinically characterized by severe postnatal growth failure and very low serum levels of IGF-I despite increased secretion of GH. This mainly autosomal recessive syndrome is clinically indistinguishable from isolated GH deficiency (IGHD). Fifty-one different mutations in the GH receptor (GHR) gene have been discovered, whereas only three deletions causing the disorder have been reported so far. In this report, we describe a consanguineous family from Sri Lanka with a novel deletion of 4097 bp in length encompassing exon 5. SUBJECTS AND METHODS Parents of normal phenotype presented their second child (boy) to our clinic at the age of 7 months with severe growth retardation and the clinical features of IGHD (58 cm, -6.1 standard deviation score (SDS); 5.7 kg, -3.4 SDS). Assessment, however, revealed GHIS with absent GH-binding protein. Thereafter, the patient received intermittent recombinant human IGF-I (rhIGF-I; 80 microg/kg twice daily) treatment prepubertally for 5.5 years. Genomic DNA was extracted for genetic analysis and each exon was PCR amplified individually. Further, in order to amplify the GHR gene from exon 4 to 6, Expand Long Template PCR (Roche) was carried out. In addition, RNA isolation and RT-PCR were performed. RESULTS Separate PCRs of each of the exons of the GHR gene revealed that exon 5 in the patient was missing. Thereafter, "Long PCR" from exons 4 to 6 revealed a 4097 bp deletion encompassing exon 5, in a homozygous state in the patient and in a heterozygous state in both parents. RT-PCR analysis revealed an exact absence of exon 5 resulting in a frameshift, leading to a stop codon in exon 6, which predicts a truncated, non-functional GHR protein. CONCLUSION Fifty-one different mutations within the GHR gene causing GHIS have been reported so far. In contrast, only three deletions within the GHR gene are known. We describe a patient suffering from GHIS caused by a novel 4 kb deletion of the GHR gene encompassing exon 5 and, additionally, we focus on the effect of intermittent rhIGF-I treatment during prepuberty.
Prophages of Staphylococcus aureus Newman and their contribution to virulence

Four prophages (φNM1–4) were identified in the genome of Staphylococcus aureus Newman, a human clinical isolate. φNM1, φNM2 and φNM4, members of the siphoviridae family, insert at different sites (poiA, downstream of isdB and geh) in the staphylococcal chromosome. φNM3, a β‐haemolysin (hlb) converting phage, encodes modulators of innate immune responses (sea, sak, chp and scn) in addition to other virulence genes. Replication of φNM1, φNM2 and φNM4 occurs in culture and during animal infection, whereas φNM3 prophage replication was not observed. Prophages were excised from the chromosome and S. aureus variants lacking φNM3 or φNM1, φNM2 and φNM4 displayed organ specific virulence defects in a murine model of abscess formation. S. aureus Newman lacking all four prophages was unable to cause disease, thereby revealing essential contributions of prophages to the pathogenesis of staphylococcal infections.
Association of maternal endothelial dysfunction with preeclampsia.

CONTEXT Preeclampsia is believed to result from release of placental factors that damage maternal vascular endothelium. However, because most studies have been conducted during pregnancy, it has not been possible to separate maternal from placental mechanisms underlying endothelial dysfunction in preeclampsia. OBJECTIVE To determine whether endothelial function is impaired in nonpregnant women with previous preeclampsia and whether endothelial dysfunction is mediated by oxidative stress. DESIGN AND SETTING Case-control study conducted at 3 hospital maternity units in London, England, between July 1997 and June 2000. PARTICIPANTS A total of 113 women with previous preeclampsia (n = 35 with recurrent episodes; n = 78 with a single episode) and 48 women with previous uncomplicated pregnancies, all of whom were at least 3 months (median, 3 years) postpartum. MAIN OUTCOME MEASURES Brachial artery flow-mediated (endothelium-dependent) and glyceryl trinitrate-induced (endothelium-independent) dilatation were compared between previously preeclamptic women and controls. To investigate oxidative stress, these measurements were repeated after administration of ascorbic acid, 1 g intravenously, in 15 cases and 15 controls. RESULTS Mean (SD) flow-mediated dilatation was lower in women with previous preeclampsia compared with controls (recurrent group, 0.9% [4.1%]; single-episode group, 2.7% [3.5%]; and control group, 4.7% [4.3%]; P<.001). In contrast, glyceryl trinitrate-induced dilatation was similar in the 3 groups (recurrent, 19.5% [5.9%]; single-episode, 21.0% [8.0%]; and control, 21.0% [8.3%]; P =.65). Impaired flow-mediated dilatation in previously preeclamptic women was not accounted for by recognized vascular risk factors. Ascorbic acid administration increased flow-mediated dilatation in previously preeclamptic women (baseline, 2.6% [3.3%]; after administration, 5.6% [3.0%]; P =.001) but not in controls (baseline, 6.2% [3.3%]; after administration, 6.7% [5.0%]; P =.72). CONCLUSIONS Our results indicate that endothelial function is impaired in women with previous preeclampsia and is not explained by established maternal risk factors but is reversed by antioxidant ascorbic acid administration.
Factors associated with mortality in critically injured trauma patients who require simultaneous cultures.

BACKGROUND In trauma patients surviving their initial injuries, infectious complications and multiple organ failure represent the major causes of death after the first 72 hours. Critically injured trauma patients frequently have bacteria recoverable simultaneously from multiple culture sites; the clinical significance of this event is unknown. The objective of this study was to identify the association between growth patterns of multiple site cultures and mortality among critically injured trauma patients. METHODS We performed a retrospective chart review collecting demographic and medical data on admissions to a state-designated Level I trauma center from April 2000 to December 2002. The inclusion criteria were age >17 years, admission to the trauma intensive care unit (TICU), and simultaneous sampling of blood, sputum, and urine in the setting of fever of undetermined origin or alteration in the white blood cell count. Four mutually exclusive groups were developed according to the number of positive culture sites. We used standard statistical analysis and multivariate logistic regression. RESULTS During the study period, 3,402 patients were admitted to the trauma service of whom 124 met the inclusion criteria. Eighty percent of these (99) were male, and the average age was 41 years. The median TICU stay was 17 days. The mortality rate was 24.2% (30 nonsurvivors). The survivors and non-survivors were comparable in injury severity score (ISS), initial base deficit, initial hematocrit, initial blood pressure, and hospital length of stay (p > 0.05), whereas age (p = 0.03), female sex (p = 0.04), and TICU stay (p < 0.01) were higher among non-survivors. More non-survivors showed growth of microorganisms in simultaneous blood, sputum, and urine cultures (p = 0.02). By multivariate analysis, adjusting for age, sex, and TICU length of stay, patients with growth of microorganisms in simultaneous cultures (blood, sputum, and urine) had a 3-fold greater mortality rate (OR, 3.20; 95% CI 1.05, 9.73). CONCLUSIONS In this group of patients, growth of bacteria in simultaneous cultures was associated with higher mortality-a factor that may be considered a poor prognostic indicator. This factor requires further studies to explore the relation with survival in critically injured patients.
NCXplore: a design space exploration framework of temporal encoding for on-chip serial interconnects

Multi-processor systems-on-chip (MPSoC) seek for high performance, scalable and power efficient communication infrastructures. Recent research considers on-chip serial links for communication fabrics as a solution to reduce routing congestion and design complexity. This paper describes a methodology and a tool-chain for design space exploration of temporal encoding schemes, thereafter referred to as NCXplore. NCXplore assists the designer to achieve the best fit as regards both switching activity combined with reduction of crosstalk effects, and performance. A novel class of temporal encoding schemes is also presented to manage switching activity and crosstalk induced delays. NCXplore accepts any encoding technique as a mapping function to investigate crosstalk effects.
Generation of effective referring expressions in situated context

In task-oriented communication, references often need to be effective in their distinctive function, that is, help the hearer identify the referent correctly and as effortlessly as possible. However, it can be challenging for computational or empirical studies to capture referential effectiveness. Empirical findings indicate that human-produced references are not always optimally effective, and that their effectiveness may depend on different aspects of the situational context that can evolve dynamically over the course of an interaction. On this basis, we propose a computational model of effective reference generation which distinguishes speaker behaviour according to its helpfulness to the hearer in a certain situation, and explicitly aims at modelling highly helpful speaker behaviour rather than speaker behaviour invariably. Our model, which extends the planning-based paradigm of sentence generation with a statistical account of effectiveness, can adapt to the situational context by making this distinction newly for each new reference. We find that the generated references resemble those of effective human speakers more closely than references of baseline models, and that they are resolved correctly more often than those of other models participating in a shared-task evaluation with human hearers. Finally, we argue that the model could serve as a methodological framework for computational and empirical research on referential effectiveness.
Severe neutropenia: a diagnostic approach.

Normal levels of neutrophils are essential to prevent infections. Neutropenia is a relatively common disorder most often due to chemotherapy treatments, adverse drug reactions, or autoimmune disorders. The differential diagnosis of neutropenia is broad and encompasses congenital, infectious, rheumatologic, and iatrogenic causes. Severe neutropenia or agranulocytosis, defined as an absolute neutrophil count of less than 0.5 × 10/L (<500/μL), is uncommon but can cause morbidity and mortality from infections. Epidemiologic studies show a wide variation in the incidence of neutropenia among geographic regions, with an average annual incidence of 56.4 cases of neutropenia and 9.0 cases of agranulocytosis per million people in the United States. Data from the International Agranulocytosis and Aplastic Anemia Study in Europe show an annual incidence of 6.2 cases of agranulocytosis per million people. Both studies assessed only hospitalized patients with severe neutropenia due primarily to noncytotoxic drugs, infections, or immune disorders and excluded those patients who were treated with cytotoxic drugs. Male and nonwhite patients had an increased risk, and patients between 50 and 59 years of age had the highest risk. No epidemiologic studies adequately address the relative severity, frequency, and mortality of the different causes of neutropenia. In this review, we present the case of a patient with apparently acute severe neutropenia.