Miracle-dz/UniFAR-FTUs huggingface dataset:
Weakly- and Semi-Supervised Learning of a DCNN for Semantic Image Segmentation

Deep convolutional neural networks (DCNNs) trained on a large number of images with strong pixel-level annotations have recently significantly pushed the state-of-art in semantic image segmentation. We study the more challenging problem of learning DCNNs for semantic image segmentation from either (1) weakly annotated training data such as bounding boxes or image-level labels or (2) a combination of few strongly labeled and many weakly labeled images, sourced from one or multiple datasets. We develop Expectation-Maximization (EM) methods for semantic image segmentation model training under these weakly supervised and semi-supervised settings. Extensive experimental evaluation shows that the proposed techniques can learn models delivering competitive results on the challenging PASCAL VOC 2012 image segmentation benchmark, while requiring significantly less annotation effort. We share source code implementing the proposed system at this https URL
Use and abuse of dendritic cells by Toxoplasma gondii

The ubiquitous apicomplexan parasite Toxoplasma gondii stimulates its host’s immune response to achieve quiescent chronic infection. Central to this goal are host dendritic cells. The parasite exploits dendritic cells to disseminate through the body, produce pro-inflammatory cytokines, present its antigens to the immune system and yet at the same time subvert their signaling pathways in order to evade detection. This carefully struck balance by Toxoplasma makes it the most successful parasite on this planet. Recent progress has highlighted specific parasite and host molecules that mediate some of these processes particularly in dendritic cells and in other cells of the innate immune system. Critically, there are several important factors that need to be taken into consideration when concluding how the dendritic cells and the immune system deal with a Toxoplasma infection, including the route of administration, parasite strain and host genotype.
Parallel Improvement of Sodium and Chloride Transport Defects by Miglustat (n-Butyldeoxynojyrimicin) in Cystic Fibrosis Epithelial Cells

Cystic fibrosis, an autosomal recessive disease frequently diagnosed in the Caucasian population, is characterized by deficient Cl- transport due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. A second major hall-mark of the disease is Na+ hyperabsorption by the airways, mediated by the epithelial Na+ channel (ENaC). In this study, we report that in human airway epithelial CF15 cells treated with the CFTR corrector miglustat (n-butyldeoxynojyrimicin), whole-cell patch-clamp experiments showed reduced amiloride-sensitive ENaC current in parallel with a rescue of defective CFTR Cl- channel activity activated by forskolin and genistein. Similar results were obtained with cells maintained in culture at 27°C for 24 h before electrophysiology experiments. With monolayers of polarized CF15 cells, short-circuit current (Isc) measurements also show normalization of Na+ and Cl- currents. In excised nasal epithelium of cftrF508del/F508del mice, like with CF15 cells, we found normalization of amiloride-sensitive Isc. Moreover, oral administration of miglustat (6 days) decreased the amiloride-sensitive Isc in cftrF508del/F508del mice but had no effect on cftr-/- mice. Our results thus show that rescuing the trafficking-deficient F508del-CFTR by miglustat down-regulates Na+ absorption. A miglustat-based treatment of CF patients may thus have a beneficial effect both on Cl- and Na+ transports.
Signaling of Cell Death and Cell Survival Following Focal Cerebral Ischemia: Life and Death Struggle in the Penumbra

Focal ischemia by middle cerebral artery occlusion (MCAO) results in necrosis at the infarct core and activation of complex signal pathways for cell death and cell survival in the penumbra. Recent studies have shown activation of the extrinsic and intrinsic pathways of caspase-mediated cell death, as well as activation of the caspase-independent signaling pathway of apoptosis in several paradigms of focal cerebral ischemia by transient MCAO to adult rats and mice. The extrinsic pathway (cell-death receptor pathway) is initiated by activation of the Fas receptor after binding to the Fas ligand (Fas-L); increased Fas and Fas-L expression has been shown following focal ischemia. Moreover, focal ischemia is greatly reduced in mice expressing mutated (nonfunctional) Fas. Increased expression of caspase-1, -3, -8, and -9, and of cleaved caspase-8, has been observed in the penumbra. Activation of the intrinsic (mitochondrial) pathway following focal ischemia is triggered by Bax translocation to and competition with Bcl-2 and other members of the Bcl-2 family in the mitochondria membrane that is followed by cytochrome c release to the cytosol. Bcl-2 over-expression reduces infarct size. Cytochrome c binds to Apaf-1 and dATP and recruits and cleaves pro-caspase-9 in the apoptosome. Both caspase-8 and caspase-9 activate caspase-3, among other caspases, which in turn cleave several crucial substrates, including the DNA-repairing enzyme poly(ADP-ribose) polymerase (PARP), into fragments of 89 and 28 kDa. Inhibition of caspase-3 reduces the infarct size, further supporting caspase-3 activation following transient MCAO. In addition, caspase-8 cleaves Bid, the truncated form of which has the capacity to translocate to the mitochondria and induce cytochrome c release. The volume of brain infarct is greatly reduced in Bid-deficient mice, thus indicating activation of the mitochondrial pathway by cell-death receptors following focal ischemia. Recent studies have shown the mitochondrial release of other factors; Smac/DIABLO (Smac: second mitochondrial activator of caspases; DIABLO: direct IAP binding protein with low pI) binds to and neutralizes the effects of the X-linked inhibitor of apoptosis (XIAP). Finally, apoptosis-inducing factor (AIF) translocates to the mitochondria and the nucleus following focal ischemia and produces peripheral chromatin condensation and large-scale DNA strands, thus leading to the caspase-independent cell death pathway of apoptosis. Delineation of the pro-apoptotic and pro-survival signals in the penumbra may not only increase understanding of the process but also help to rationalize strategies geared to reducing brain damage targeted at the periphery of the infarct core.
Low Overhead Software Wear Leveling for Hybrid PCM + DRAM Main Memory on Embedded Systems

Phase change memory (PCM) is a promising DRAM replacement in embedded systems due to its attractive characteristics, such as low-cost, shock-resistivity, nonvolatility, high density, and low leakage power. However, relatively low endurance has limited its practical applications. In this paper, in addition to existing hardware level optimizations, we propose software enabled wear-leveling techniques to further extend PCMs lifetime when it is adopted in embedded systems. Most existing software optimization techniques focus on reducing the total number of writes to PCM, but none of them consider wear leveling, in which the writes are distributed more evenly over the PCM. An integer linear programming formulation and a polynomial-time algorithm, the software wear-leveling algorithm, are proposed in this paper to achieve wear leveling without hardware overhead. According to the experimental results, the proposed techniques can reduce the number of writes on the most-written addresses by more than 80% when compared with a greedy algorithm, and by more than 60% when compared with the existing optimal data allocation algorithm with under 6% memory access overhead.
Anticipatory and reactive responses to chocolate restriction in frequent chocolate consumers

Many individuals have difficulty adhering to a weight loss diet. One possible explanation could be that dietary restriction paradoxically contributes to overconsumption. The objective of this study was to examine ingestive behavior under a forced chocolate restriction with a focus on the anticipatory restriction period and the post‐restriction period in frequent chocolate consumers.
Violence in the accident and emergency department.

Sir Violence is endemic in present day society. A recent report by the National Union of Public Employees showed that 87% of respondents to a questionnaire were worried about violence in their work. We conducted a questionnaire survey of the Royal College of Nursing Accident and Emergency Association, Essex Branch Conference on 1.6.91 to ascertain current observations and procedures on violence within A&E departments around the country. Demographic details were asked for and the frequencies of physical and verbal violence. Types of verbal violence were identified. The characteristics of assailants associated with physical and verbal violence and of features of the department e.g. waiting time, time of day, staffing level, department under pressure, medication and substance abuse relating to violence. Questions on property and on the police were included. The opportunity to discuss incidents and the presence of a staff support group and training on physical and verbal violence was ascertained. Fifty-eight questionnaires were returned (j ). The average age was 32 years and there were a majority of women, a majority of Caucasians and they were mostly grade E. A total of 17.3% had never experienced physical violence; 44.8% had rarely experienced physical violence; 32.8% had sometimes and 5.2% had often experienced physical violence. No-one said they had never experienced violence and only 1.7% rarely experienced verbal violence. A total of 55.1% had sometimes and 43.2% often experienced verbal violence. A total of 1.7% had received many injuries; 31% some injuries 67.3% no injuries. Of these only 6.9% required treatments and none needed time off work. The verbal violence most frequently encountered was obscenities 45.4%; nonspecific threats 35%; threats to person 24.8%; and sexual harassment 9.4%. The majority thought physical assailants were men (n = 45) and between the ages of 15-40 years. Their status was variable: medical patients, 34%; psychiatric patients, 51%; relatives, 34%; and others, 17%. Verbal violence was attributed to both men (n = 50) and women (n = 32) i.e. there was some overlap. The age range was most commonly 15-40 years. The majority of verbal abuse came from relatives then medical and then psychiatric patients. Factors thought to be related to physical violence were as follows: waiting time, definitely (58.4%) and maybe (33.9%); time of day, maybe (50.9%) and definitely (32%); staffing levels, maybe (62%) and definitely (26%); department under pressure, maybe (56%) and definitely (44%); medication, maybe (70.5%); and
Association of CYP3A4/5, ABCB1 and ABCC2 polymorphisms and clinical outcomes of Thai breast cancer patients treated with tamoxifen

Background Pharmacogenetic study of cytochrome P450 (CYP) gene CYP2D6 and tamoxifen outcomes remain controversial. Apart from CYP2D6, other drug-metabolizing enzymes and transporters also play a role in tamoxifen metabolic pathways. The aim of this study is to investigate the impact of CYP3A4/5, ABCB1, and ABCC2 polymorphisms on the risk of recurrence in Thai patients who received tamoxifen adjuvant therapy. Methods Patients with early-stage breast cancer who received tamoxifen adjuvant therapy were recruited in this study. All six single-nucleotide polymorphisms (SNPs), including CYP3A4*1B (−392 A>G)/*18(878 T>C), CYP3A5*3(6986 G>A), ABCB1 3435 C>T, ABCC2*1C(−24 C>T), and ABCC2 68231 A>G, were genotyped using real-time polymerase chain reaction assays. The impacts of genetic variants on disease-free survival (DFS) were analyzed using the Kaplan–Meier method and Cox regression analysis. Results The ABCB1 3435 C>T was found to have the highest allele frequency among other variants; however, CYP3A4*1B/*18 could not be found in this study. Patients with heterozygous ABCB1 3435 CT genotype showed significantly shorter DFS than those with homozygous 3435 CC genotype (P = 0.041). In contrast, patients who carried homozygous 3435 TT genotype showed no difference in DFS from wild-type 3435 CC patients. Cox regression analysis showed that the relative risk of recurrence was increased by five times (P = 0.043; hazard ratio = 5.11; 95% confidence interval: 1.05–24.74) in those patients carrying ABCB1 3435 CT genotype compared to those with ABCB1 3435 CC. Conclusion ABCB1 3435 C>T is likely to have a clinically significant impact on recurrence risk in Thai patients with breast cancer who receive tamoxifen adjuvant therapy.
Rapid and Accurate Approach for Screening of Microsatellite Unstable Tumours Using Quasimonomorphic Mononucleotide Repeats and Denaturating High Performance Liquid Chromatography (DHPLC)

MSI analysis is becoming increasingly important for the detection of both hereditary non-polyposis colorectal cancer and sporadic primary colorectal tumours with MSI high phenotype. The Bethesda panel of five microsatellite markers has been proposed to provide uniform criteria for MSI analysis. Here we report on an MSI analysis approach using quasimonomorphic mononucleotide repeats and denaturating high performance liquid chromatography (DHPLC). We analysed 595 newly diagnosed colorectal tumours and 145 normal samples. Microsatellite markers BAT-25, BAT-26, NR-21, NR-22, and NR-27 were amplified in multiplex reaction and analysed using DHPLC and capillary electrophoresis (CE). DHPLC conditions for analysis of MSI multiplex assay were evaluated and tested. Analysis and cross-examination of the results obtained from 96 samples using DHPLC and capillary electrophoresis showed the same sensitivity and specificity of the two approaches for detecting MSI-H tumours. Using our new approach we showed that the tested markers are quasimonomorphic in a Slovenian population, with frequencies of polymorphisms 0.07%, 1.4%, 2.1%, 1.4%, and 1.4% for BAT-25, BAT-26, NR-21, NR-22, and NR-27, respectively. Forty-three (7.2%) new MSI-H tumours were identified, of which 84% showed instability in all 5 tested markers. Overall, we developed a high-throughput, robust, accurate and cost-effective approach for the detection of MSI-H tumours.
Insulin Resistance of Normal Weight Central Obese Adolescents in Korea Stratified by Waist to Height Ratio: Results from the Korea National Health and Nutrition Examination Surveys 2008–2010

Background. To evaluate insulin resistance of normal weight central obese 13–18-year-old male and female adolescents stratified by waist to height ratio (WHR). Methods. Data were obtained from the Korea National Health and Nutrition Examination Survey (K-NHANES) conducted during 2008–2010. Central obesity was defined as that in the upper quartile of age and sex specific WHR. Subjects were classified into no central obesity normal weight (NW), central obesity normal weight (CONW), no central obesity overweight (OW), and central obesity overweight (COOW). Results. The prevalence of CONW was 9.6% (83/832) in female and 7.0% (61/909) in male. CONW showed higher levels of insulin (P < 0.006), HOMA-IR (P < 0.006), and ALT (P < 0.001) than NW in female. CONW had higher levels of insulin (P < 0.0001), HOMA-IR (P < 0.0001), and WBC count (P < 0.021) and lower level of HDL (P < 0.0001) than NW in male. WHR and BMI had similar significant correlations with MS components. CONW showed 2.5 times (95% confidence interval, 1.21–5.00) more likelihood to have high insulin resistance than NW in male. Conclusions. Screening for central obesity using WHR in clinical setting is recommended.
Validation of the NITI Endoluminal Compression Anastomosis Ring (EndoCAR) Device and Comparison to the Traditional Circular Stapled Colorectal Anastomosis in a Porcine Model

The purpose of this study was to determine whether the characteristics of compression anastomoses created by a new device are comparable to existing stapler technology. A total of 18 pigs were studied, and each served as its own control using a 27-mm compression device and a 29-mm stapler. Anastomoses were randomized to proximal and distal positions along the rectum and were separated by 10 cm. Six nonsurvival pigs were sacrificed at zero time to failure test the anastomoses. Twelve pigs were sacrificed at 14 days. Failure pressures, circumferences, and radiographic leak rates were determined. Anastomotic tissue was processed for matrix metalloproteinase, collagen, and elastin levels. The compression anastomoses had higher mean failure pressures than stapled anastomoses at zero time (103 vs 29.9 mm Hg). At 2 weeks, there was no difference between failure pressures (256 vs 250 mm Hg). During burst testing, 3 of the compression anastomoses failed at the anastomosis at 2 weeks, whereas none of the stapled anastomoses failed. The mean anastomotic circumference of the compression anastomoses was narrower than the stapled anastomoses (9.63 vs 11.25 cm, P = .001). There were no clinical leaks or radiographic leaks by barium enema at 2 weeks. There was no difference between matrix metalloproteinase, collagen, or elastin content based on tissue analysis. There were dense adhesions to 7 of 12 (58.3%) of the stapled anastomoses, whereas only 1 of 12 (8.3%) of the compression anastomoses had flimsy adhesions. A new compression anastomosis technique using a nickel-titanium alloy may be an advance in technology by reducing leaks and eliminating foreign material in the anastomosis.
Lanreotide autogel in acromegaly – a decade on

Introduction: The novel formulation of lanreotide, lanreotide (LAN) autogel (ATG), has been available in Europe since 2001 and USA from 2006 for the treatment of acromegaly. It is one of only two clinically available somatostatin analogs available for use in acromegaly. Data relating to the use of ATG in acromegaly, specifically relating to comparison to octreotide (OCT) LAR and patient acceptability and preference, have been slow to accumulate. Areas covered: We performed a comprehensive review of the original literature relating to development, pharmacokinetics, acceptability and clinical efficacy of ATG. Expert opinion: LAN ATG is a novel formulation of LAN consequent on self-assembly of nanotubules in water. Diffusion between molecules within the nanotubules and surrounding tissue fluid in vivo leads to pseudo first-order pharmacokinetics. Efficacy is equivalent to the alternate long-acting somatostatin analog, OCT LAR, normalizing growth hormone and IGF-I levels in around 60 and 50% respectively. Control of tumor growth is observed in over 95% of patients, with 64% seeing a clinically significant reduction in tumor size. ATG is provided in a prefilled syringe for deep subcutaneous injection, allowing self-injection, and may be administered up to 8 weeks greatly improving convenience for the patient. The data strongly support consideration of ATG as the medical therapy of choice for patients with acromegaly.
Gene Expression Profile of Adipocyte Differentiation and Its Regulation by Peroxisome Proliferator-Activated Receptor-γ Agonists.

PPARγ is an adipocyte-specific nuclear hormone receptor. Agonists of PPARγ, such as thiazolidinediones (TZDs), promote adipocyte differentiation and have insulin-sensitizing effects in animals and diabetic patients. Affymetrix oligonucleotide arrays representing 6347 genes were employed to profile the gene expression responses of mature 3T3-L1 adipocytes and differentiating preadipocytes to a TZD PPARγ agonist in vitro. The expression of 579 genes was significantly up- or down-regulated by more than 1.5-fold during differentiation and/or by treatment with TZD, and these genes were organized into 32 clusters that demonstrated concerted changes in expression of genes controlling cell growth or lipid metabolism. Quantitative PCR was employed to further characterize gene expression and led to the identification of β-catenin as a new PPARγ target gene. Both mRNA and protein levels for β-catenin were down-regulated in 3T3-L1 adipocytes compared with fibroblasts and were further decreased by treatment of adipocy.
Effects of hemoglobin C and S traits on seven glycohemoglobin methods.

Glycohemoglobin (gHb) is a marker of long-term glycemic control that has been shown to correlate with complications of diabetes mellitus (1). The National Glycohemoglobin Standardization Program (NGSP) was established to standardize gHb results so that clinical laboratory results are comparable to those reported by the Diabetes Control and Complications Trial (2)(3). Previous studies have shown that some gHb methods yield inaccurate results with samples heterozygous for hemoglobin (Hb) C or Hb S (4)(5)(6). At least 10% of black Americans have either Hb C or S trait, and there were 19 million black Americans over age 19 in 1990 (7)(8)(9)(10). The prevalence of diabetes is estimated to be 5.1% of the adult population, with the rate for non-Hispanic blacks being 1.6-fold higher than that of non-Hispanic whites (11). It is therefore probable that at least 150 000 Americans with diabetes have Hb C or S trait. Here, we investigate the measurement of gHb in specimens containing Hb C or S trait using eight gHb methods currently in clinical use. Whole blood samples from individuals homozygous for Hb A (n = 43) and heterozygous for Hb C or S (n = 43 and 61, respectively) were collected in EDTA tubes. Hb variants were identified by their characteristic Variant A1c HPLC chromatograms (Bio-Rad Laboratories). Aliquots of these samples containing between 4% and 14% Hb A1c (NGSP Hb A1c evaluation range) were stored refrigerated (2–8 °C) and analyzed within 10 days of collection. This study was approved by the Institutional Review Board of the University of Utah. The CLC 330 gHb analyzer (Primus Corporation) was operated at the University of Missouri. This method was chosen as the comparison method for this study because results from boronate affinity chromatography should not …
Visual Mobility Analysis using T-Warehouse

Technological advances in sensing technologies and wireless telecommunication devices enable research fields related to the management of trajectory data. The challenge after storing the data is the implementation of appropriate analytics for extracting useful knowledge. However, traditional data warehousing systems and techniques were not designed for analyzing trajectory data. In this paper, the authors demonstrate a framework that transforms the traditional data cube model into a trajectory warehouse. As a proof-of-concept, the authors implement T-Warehouse, a system that incorporates all the required steps for Visual Trajectory Data Warehousing, from trajectory reconstruction and ETL processing to Visual OLAP analysis on mobility data.