Miracle-dz/UniFAR-FTUs huggingface dataset:
Colorectal Cancer in Ulcerative Colitis: Survival in Patients With and Without Colorectal Cancer Symptoms

&NA; Patients with ulcerative colitis are at increased risk for colorectal adenocarcinoma compared with the general population. Although surveillance for colorectal malignancy and dysplasia (a premalignant lesion) has been recommended, a benefit in reducing mortality from colorectal cancer via surveillance or prophylactic colectomy is still being debated. We reviewed the outcome of 40 consecutive patients with ulcerative colitis with colorectal adenocarcinoma diagnosed between 1956 and 1991 at The Johns Hopkins Hospital. The diagnosis of ulcerative colitis and the tumor, node, metastasis (TNM) stage of colorectal cancer were obtained from clinicopathologic records. Follow‐up information was complete for all patients. Patients were divided into two groups: 18 asymptomatic patients who had colorectal cancer detected by colonoscopy, biopsies for dysplasia, or barium enema, or had undergone “prophylactic” colectomy as part of a colorectal cancer‐prevention strategy (asymptomatic group), whereas 22 patients did not undergo cancer‐prevention testing or prophylactic surgery and had symptoms of colorectal cancer (symptomatic group). Colorectal cancer was diagnosed at a statistically significantly earlier cancer stage in the asymptomatic group [12 (67%) of 18 at stage I or II] compared with those in the symptomatic group [two (9%) of 22 at stage I or II] (Wilcoxon test, p < 0.01). Colorectal cancer 5‐year survival in the asymptomatic group was 89% [confidence limit (CL), 6197%] and in the symptomatic group, 19% (CL, 6‐39%). Patients with ulcerative colitis and asymptomatic colorectal cancer detected as part of a prevention strategy had malignancies that were less invasive and showed greatly increased survival compared with patients with symptomatic colorectal cancer.
Effects of alagebrium, an advanced glycation end‐product breaker, in patients with chronic heart failure: study design and baseline characteristics of the BENEFICIAL trial

Previous small open label studies have shown that the advanced glycation end‐product (AGE) breaker alagebrium may improve cardiac function in patients with chronic heart failure (HF). We report the design, methods and baseline characteristics of a double‐blind, placebo‐controlled, randomized trial evaluating the efficacy and safety of alagebrium (BENEFICIAL) in patients with HF and a left ventricular ejection fraction (LVEF) ≤ 0.45.
Colcemid‐treatment of heifer oocytes enhances nuclear transfer embryonic development, establishment of pregnancy and development to term

Four experiments were designed to examine the effects of colcemid, a microtubule assembly inhibitor, on the development of bovine nuclear transfer (NT) embryos in vitro and in vivo. Recipient oocytes matured at different times were exposed to colcemid. Approximately 80–93% of the exposed oocytes, with or without the first polar body (PB1), developed obvious membrane projections. In Experiment 1, oocytes matured for either 14–15 or 16–17 hr, treated with colcemid and used as recipient cytoplasm for NT resulted in over 40% blastocyst development. In Experiment 2, oocytes matured for 16–17 hr were treated with either 0.2 or 0.4 µg/ml colcemid for 2–3 or 5–6 hr, respectively. The percentages of blastocyst development (39–42%) were not statistically different among the different colcemid treatment groups, but were both higher (P < 0.05) than the control group (30%). Colcemid concentrations and length of colcemid treatment of oocytes did not affect their ability to support NT embryo development to the blastocyst and hatched blastocyst stages. Results from Experiment 3 indicate that semi‐defined medium increases morula and blastocyst development of NT embryos derived fromcolcemid‐treated oocytes under 5% CO2 in air atmosphere. In addition, cell numbers of blastocysts in colcemid‐treated groups were numerically higher than the control groups. After embryo transfer, higher (P < 0.05) pregnant rates were obtained from the colcemid‐treated group than the nontreated group. Five of 40 recipients (12.5%) which received embryos from colcemid‐treated oocytes delivered healthy calves, significantly higher than those recipients (3.3%) that received embryos derived from nontreated oocytes. Mol. Reprod. Dev. 76: 620–628, 2009. © 2009 Wiley‐Liss, Inc.
High Efficiency Video Decoding on Multicore Processor

In this paper we present a High Efficiency Video Coding(HEVC) decoder implemented using multicore processor. HEVC can support Ultra High Definition (UHD) digital TV and resolution up to 8192x4320. It aims to achieve compression rate in the range of 50% bit-rate relative to existing standards. And decoding speed should be over the 30 fps(frames per second). Although multicore processors have sufficient performance and enough memory, HEVC software cannot make use it very well. So not only the proper architecture for HEVC is needed but also modified HEVC software should be considered. Gem5 simulator was used to simulate the performance of our decoder. Base on the simulation results we suggest appropriate multicore architecture platform which can satisfy the goal of HEVC decoding speed.
Spontaneous neurodegeneration in transgenic mice with mutant prion protein

Transgenic mice were created to assess genetic linkage between Gerstmann-Straussler-Scheinker syndrome and a leucine substitution at codon 102 of the human prion protein gene. Spontaneous neurologic disease with spongiform degeneration and gliosis similar to that in mouse scrapie developed at a mean age of 166 days in 35 mice expressing mouse prion protein with the leucine substitution. Thus, many of the clinical and pathological features of Gerstmann-Straussler-Scheinker syndrome are reproduced in transgenic mice containing a prion protein with a single amino acid substitution, illustrating that a neurodegenerative process similar to a human disease can be genetically modeled in animals.
Outcomes of robotic surgery for pancreatic ductal adenocarcinoma.

BACKGROUND To explore the effectiveness, safety, and efficacy of the robot-assisted surgery in the radical resection of pancreatic ductal adenocarcinoma (PDAC). METHODS The clinical data of 72 patients with PDAC who underwent radical resection using the da Vinci Surgical System from April 2010 to December 2014 were retrospectively analyzed. RESULTS Among these 72 patients, three were converted to conventional laparotomy due to the vascular invasion or due to the difficulties in tissue isolation from the surrounding organs. Among 39 patients who underwent the pancreatoduodenectomy, the average operative time was 395.3±118.8 min, and the mean intra-operative blood loss was 447.3±269.9 mL. Among 31 patients who underwent the distal pancreatectomy (DP), the average operative time was 185.5±74.1 min, and the mean intra-operative blood loss was 267.1±305.3 mL. In two patients who received the middle pancreatectomy (MP), the average operative time was 225 min and mean intra-operative blood loss was 100 mL. Among all the 72 patients, an average of 4.2±2.6 lymph nodes were dissected, with an average hospital stay of 22.6±10.7 days. Complications were observed in 18 patients, which included pancreatic fistula (n=11), bile leak (n=5), anastomotic bleeding (n=2), pancreatic fistula complicated with portal vein thrombosis (n=1), and anastomotic bleeding complicated with acute renal failure (n=1). Except that one patient died due to post-operative bleeding and acute renal failure, all the other patients were cured after conservative treatment. These 72 patients were followed for 1-45 (15.6±5.8) months, during which 10 patients died. Eleven patients suffered from recurrence or metastasis, among which 6 had local recurrence, 4 had liver metastasis, and 1 had ascites accompnaied with incision site tumor metastasis. CONCLUSIONS Radical resection of PDAC by robotic surgical system is safe and feasible. It has less surgical trauma and enables faster post-operative recovery, and therefore can achieve the lymph node dissection scope and tumor resection margin required by the standards of radical resection for pancreatic cancer. Nevertheless, its long-term efficacy requires further validation.
Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I

The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S–23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro‐organisms. In terms of community structure, our results show that although depth‐related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface‐associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well‐defined taxonomic units.
Treatment of Premenstrual Dysphoric Disorder

Premenstrual dysphoric disorder (PMDD) is comprised of a cluster of affective, behavioral and somatic symptoms recurring monthly during the luteal phase of the menstrual cycle. The disorder affects 3–8% of menstruating women and represents the more severe and disabling end of the spectrum of premenstrual disorders, which includes premenstrual syndrome and premenstrual aggravation of underlying affective disorder. Rigorous and specific diagnostic criteria for PMDD were specified in the Diagnostic and Statistical Manual of Mental Disorders IV (1994) and reaffirmed in the Diagnostic and Statistical Manual of Mental Disorders V (2013) and, consequently, there has been a marked increase in well-designed, placebo-controlled studies evaluating treatment modalities. Although the exact pathogenesis of PMDD is still elusive, treatment of PMDD and severe premenstrual syndrome has centered on neuromodulation via serotonin reuptake inhibitor antidepressants, and ovulation suppression utilizing various contraceptive and hormonal preparations. Unlike the approach to the treatment of depression, serotonergic antidepressants need not be given daily, but can be effective when used cyclically, only in the luteal phase or even limited to the duration of the monthly symptoms. Less, well-substantiated alternative treatments, such as calcium supplementation, agnus castus (chasteberry), Hypericum perforatum (St John's wort) and cognitive/behavioral/relaxation therapies, may be useful adjuncts in the treatment of PMDD. This review provides an overview of current information on the treatment of PMDD.
Emergence of New Delhi Metallo-Beta-Lactamase (NDM-1) and Klebsiella pneumoniae Carbapenemase (KPC-2) in South Africa

ABSTRACT This report documents emergence of New Delhi metallo-beta-lactamase (NDM-1) and Klebsiella pneumoniae carbapenemase (KPC-2) in K. pneumoniae and Enterobacter cloacae in South Africa. NDM-1 producers have not been described in South Africa, and this is the first instance that KPC producers have been identified in Africa. The two patients infected with these carbapenemase-producing bacteria demised.
LAURENCIA MARILZAE SP. NOV. (CERAMIALES, RHODOPHYTA) FROM THE CANARY ISLANDS, SPAIN, BASED ON MORPHOLOGICAL AND MOLECULAR EVIDENCE 1

Laurencia marilzae Gil‐Rodríguez, Sentíes et M.T. Fujii sp. nov. is described based on specimens that have been collected from the Canary Islands. This new species is characterized by distinctive yellow–orange as its natural habitat color, a terete thallus, four pericentral cells per vegetative axial segment, presence of secondary pit‐connections between adjacent cortical cells, markedly projecting cortical cells, and also by the presence of corps en cerise (one per cell) present in all cells of the thallus (cortical, medullary, including pericentral and axial cells, and trichoblasts). It also has a procarp‐bearing segment with five pericentral cells and tetrasporangia that are produced from the third and fourth pericentral cells, which are arranged in a parallel manner in relation to fertile branchlets. The phylogenetic position of this taxon was inferred based on chloroplast‐encoded rbcL gene sequence analyses. Within the Laurencia assemblage, L. marilzae formed a distinctive lineage sister to all other Laurencia species analyzed. Previously, a large number of unique diterpenes dactylomelane derivatives were isolated and identified from this taxon. L. marilzae is morphologically, genetically, and chemically distinct from all other related species of the Laurencia complex described.
Hepatitis C Virus Stimulates the Expression of Cyclooxygenase-2 via Oxidative Stress : Role of Prostaglandin E 2 in RNA Replication

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease, which can lead to the development of liver cirrhosis and hepatocellular carcinoma. Recently, the activation of cyclooxygenase-2 (Cox-2) has been implicated in the HCV-associated hepatocellular carcinoma. In this study, we focus on the signaling pathway leading to Cox-2 activation induced by HCV gene expression. Here, we demonstrate that the HCVinduced reactive oxygen species and subsequent activation of NFB mediate the activation of Cox-2. The HCV-induced Cox-2 was sensitive to antioxidant (pyrrolidine dithiocarbamate), Ca chelator (BAPTA-AM), and calpain inhibitor (N-acetyl-Leu-Leu-Met-H). The levels of prostaglandin E2 (PGE2), the product of Cox-2 activity, are increased in HCV-expressing cells. Furthermore, HCV-expressing cells treated with the inhibitors of Cox-2 (celecoxib and NS-398) showed significant reduction in PGE2 levels. We also observed the enhanced phosphorylation of Akt and its downstream substrates glycogen synthase kinase-3 and proapoptotic Bad in the HCV replicon-expressing cells. These phosphorylation events were sensitive to inhibitors of Cox-2 (celecoxib and NS-398) and phosphatidylinositol 3-kinase (LY294002). Our results also suggest a potential role of Cox-2 and PGE2 in HCV RNA replication. These studies provide insight into the mechanisms by which HCV induces intracellular events relevant to liver pathogenesis associated with viral infection.
Phospholipids chiral at phosphorus. Steric course of the reactions catalyzed by phosphatidylserine synthase from Escherichia coli and yeast.

The steric courses of the reactions catalyzed by phosphatidylserine (PS) synthase from Escherichia coli and yeast were elucidated by the following procedure. RP and SP isomers of 1,2-dipalmitoyl-sn-glycero-3-[17O,18O]phosphoethanolamine ([17O,18O]DPPE) were synthesized with slight modification of the previous procedure [Bruzik, K. , & Tsai, M. -D. (1984) J. Am. Chem. Soc. 106, 747-754] and converted to (RP)- and (SP)-1,2-dipalmitoyl-sn-glycero-3-[16O,17O,18O]phosphoric acid ([16O,17O18O]DPPA), respectively, by incubating with phospholipase D. Condensation of [16O,17O,18O]DPPA with cytidine 5'-monophosphomorpholidate in pyridine gave the desired substrate for PS synthase, [17O,18O]cytidine 5'-diphospho-1,2-dipalmitoyl-sn-glycerol ([17O,18O]CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of [17O,18O]CDP-DPG with a mixture of L-serine, PS synthase (which converted [17O,18O]CDP-DPG to phosphatidylserine), and PS decarboxylase (which catalyzes decarboxylation of phosphatidylserine) gave [17O,18O]DPPE. The configuration and isotopic enrichments of the starting [17O,18O]DPPE and the product were analyzed by 31P NMR following trimethylsilylation of the DPPE. The results indicate that the reaction of E. coli PS synthase proceeds with retention of configuration at phosphorus, which suggests a two-step mechanism involving a phosphatidyl-enzyme intermediate, while the yeast PS synthase catalyzes the reaction with inversion of configuration, which suggests a single-displacement mechanism. Such results lend strong support to the ping-pong mechanism proposed for the E. coli enzyme and the sequential Bi-Bi mechanism proposed for the yeast enzyme, both based on previous isotopic exchange experiments.
Interactions between Neisseria meningitidis and human cells that promote colonisation and disease

Neisseria meningitidis is the leading cause of bacterial meningitis, a potentially fatal condition that particularly affects children. Multiple steps are involved during the pathogenesis of infection, including the colonisation of healthy individuals and invasion of the bacterium into the cerebrospinal fluid. The bacterium is capable of adhering to, and entering into, a range of human cell types, which facilitates its ability to cause disease. This article summarises the molecular basis of host–pathogen interactions at the cellular level during meningococcal carriage and disease.
Monitoring Conformational Rearrangements in the Substrate-binding Site of a Membrane Transport Protein by Mass Spectrometry*

Combined biochemical, biophysical, and crystallographic studies on the lactose permease of Escherichia coli suggest that Arg-144 (helix V) forms a salt bridge with Glu-126 (helix IV), which is broken during substrate binding, thereby permitting the guanidino group to form a bidentate H-bond with the C-4 and C-3 O atoms of the galactopyranosyl moiety and an H-bond with Glu-269 (helix VIII). To examine the relative interaction of Arg-144 with these two potential salt bridge partners (Glu-126 and Glu-269) in the absence of substrate, the covalent modification of the guanidino group was monitored with the Arg-specific reagent butane-2,3-dione using electrospray ionization mass spectrometry. In a functional background, the reactivity of Arg-144 with butane-2,3-dione is low (∼25%) and is reduced by a factor of approximately 2 by preincubation with ligand. Interestingly, although replacement of Glu-126 with Ala results in a 3-fold increase in the reactivity of Arg-144, replacement of Glu-269 with Ala elicits virtually no effect. Taken together, these results suggest that in the absence of substrate the interaction between Arg-144 and Glu-126 is much stronger than the interaction with Glu-269, supporting the contention that sugar recognition leads to rearrangement of charge-paired residues essential for sugar binding.
A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors

We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (–ΔG) and TF dosage. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the TF’s coding region, or at the TF’s own promoter, which determines allele-specific dosage. We find that when the TF’s coding region is heterozygous, TF alleles compete for occupancy at the cis-sites and the tighter-binding TF is dominant in proportion to the difference in binding strength. When the TF’s own promoter is heterozygous, the TF produced at the higher dosage is also dominant. Cis-site heterozygotes have additive expression and therefore codominant phenotypes. Binding dominance propagates to affect the expression of downstream loci and it is sensitive in both magnitude and direction to genetic background, but its detectability often attenuates. While binding dominance is inevitable at the molecular level, it is difficult to detect in the phenotype under some biophysical conditions, more so when TF dosage is high and allele-specific binding affinities are similar. A body of empirical research on the biophysics of TF binding demonstrates the plausibility of this mechanism of dominance, but studies of gene expression under competitive binding in heterozygotes in a diversity of genetic backgrounds are needed.
Nimodipine Improves Outcome when Given after Complete Cerebral Ischemia in Primates

Twenty-seven pigtailed monkeys (Macaca nemestrina) were subjected to 17 min of complete cerebral ischemia followed by 96 h of intensive care treatment. Fourteen of the monkeys were assigned randomly to the treatment group and received nimodipine 10 μg·kg−1 5 min postischemia followed by 1 μg·kg−1·min−1 for 10 h. Six monkeys (three treated) failed to meet preestablished protocol criteria and were excluded. The remaining treated and untreated monkeys were well matched for age, sex, and other physiologic variables. Neurologic outcome at 96 h postischemia was significantly better in the nimodipine-treated monkeys than in the controls. Eight of the 11 treated animals had an apparent normal level of consciousness; four of these had no detectable neurologic deficits and a fifth had only a slight motor apraxia. Only two of the 10 untreated animals had an apparent normal level of consciousness, and all had major neurologic deficits. Histopathologic examination showed variable ischemic neuronal change and infarction to involve gray matter in distal arterial perfusion zones. Significant white matter changes were not observed. A histopathologic scoring system yielded a significantly better mean score for the treated group than for the untreated group, and there was significant correlation between neurologic function and histopathologic findings. The authors conclude that nimodipine improves the neurologic outcome when given after an episode of complete cerebral ischemia in primates, and they recommend controlled clinical trials in patients resuscitated after cardiac arrest.
Planck pre-launch status: The HFI instrument, from specification to actual performance

Context. The High Frequency Instrument (HFI) is one of the two focal instruments of the Planck mission. It will observe the whole sky in six bands in the 100 GHz-1 THz range. Aims: The HFI instrument is designed to measure the cosmic microwave background (CMB) with a sensitivity limited only by fundamental sources: the photon noise of the CMB itself and the residuals left after the removal of foregrounds. The two high frequency bands will provide full maps of the submillimetre sky, featuring mainly extended and point source foregrounds. Systematic effects must be kept at negligible levels or accurately monitored so that the signal can be corrected. This paper describes the HFI design and its characteristics deduced from ground tests and calibration. Methods: The HFI instrumental concept and architecture are feasible only by pushing new techniques to their extreme capabilities, mainly: (i) bolometers working at 100 mK and absorbing the radiation in grids; (ii) a dilution cooler providing 100 mK in microgravity conditions; (iii) a new type of AC biased readout electronics and (iv) optical channels using devices inspired from radio and infrared techniques. Results: The Planck-HFI instrument performance exceeds requirements for sensitivity and control of systematic effects. During ground-based calibration and tests, it was measured at instrument and system levels to be close to or better than the goal specification.