Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of outcomes of open and minimally invasive esophagectomy in 183 patients with cancer.

BACKGROUND AND OBJECTIVES Only few randomized trials or comparative studies with large number of patients have been reported on the outcomes of thoracoscopic and laparoscopic esophagectomy (TLE) with cervical anastomosis and open 3-field esophagectomy (OE) for patients with esophageal cancer. The objective of this study is to compare the safety, feasibility, and short-term outcomes between TLE and OE (via right throax, abdomen, and left neck) for esophageal cancer. METHODS Clinical and surgical data of patients with esophageal cancer who underwent either TLE or OE between February 2011 and December 2013 were retrospectively analyzed. Demographic characteristics, pathological data, operative procedures, and intraoperative and postoperative outcomes and survival in patients were compared between both groups. RESULTS Of the 183 patients included in this retrospective analysis, 94 underwent TLE and 89 underwent OE. Demographics, pathologic data, inpatient mortality, and overall surgical morbidity in both cohorts were almost identical. A significant difference was observed in blood loss (182.6±78.3 vs. 261.4±87.2 mL, P<0.001), hospital stay (13.9±7.5 vs. 17.1±10.2 days, P=0.017), overall surgical morbidity (25.5% vs. 46.1%, P=0.004), and rate of pulmonary and cardiac complication (9.6% vs. 27.0%, P=0.002; 4.1% vs. 12.4%, P=0.046) between TLE and OE groups; however, no difference in survival period was observed between the groups. CONCLUSIONS The procedure of TLE for esophageal cancer possesses advantages in intraoperative and postoperative outcomes compared with OE. The TLE procedure results in similar or potentially better outcomes.
Stress-Induced Birefringence Characteristics of Polymer Optical Rib Waveguides

We report the detailed numerical investigation of stress-induced material birefringence in polymer rib waveguide for the design of nonbirefringent waveguide devices. To accurately simulate the stress-induced effects we propose a more realistic model in the finite element analysis which considers the stresses induced over the entire sequential fabrication process. It is observed that the birefringence is nonuniform, and it is different for different etch depth and core width. The maximum birefringence in the core layer is observed near the lower cladding which decreases to zero toward the top surface. The influence of this material anisotropy on the modal birefringence is analyzed also for different rib structures. We found the stress effects on the modal birefringence to be largely affected by etch depth, while core width has small effect. It is also found that the deeply etched core has better birefringence stability. Finally, an accurate design of the zero-birefringence waveguide is illustrated by taking the stress effects into account, and the results are compared with experimental data. Excellent agreement between calculated and experimental results confirms the potential application of this work to aid in the design of polarization-insensitive waveguide devices.
Mutator-Like Element in the Yeast Yarrowia lipolytica Displays Multiple Alternative Splicings

ABSTRACT A new type of DNA transposon, Mutyl, has been identified in the sequenced genome of the yeast Yarrowia lipolytica. This transposon is 7,413 bp long and carries two open reading frames (ORFs) which potentially encode proteins of 459 and 1,178 amino acids, respectively. Whereas the first ORF shows no significant homology to previously described proteins, the second ORF shows sequence similarities with various Mutator-like element (MULE)-encoded transposases, including the bacterial transposase signature sequence. Other MULE features shared by Mutyl include a zinc finger motif in the putative transposase, a 22-bp-long imperfect inverted repeat at each end, and a 9- to 10-bp duplication of its target site in the chromosome. Of the five copies of Mutyl present in the genome, one has a deletion of the first 8 bases, and the others are full length with a single base change in one element. The first potential gene of Mutyl, mutB, was shown to be expressed in exponentially growing cells. Its sequence contains a predicted intron with two 5′ splice sites, a single branch point, and two 3′ splice sites. Its mRNA is alternatively spliced, as judged by reverse transcription-PCR, and generates four mRNAs corresponding to protein-coding sequences of 128, 156, 161, and 190 amino acids. Of the three distinct lineages characterized in Y. lipolytica, strains from the German lineage and the French lineage do not carry Mutyl. A study of the distribution of Mutyl in strains of the French lineage evidenced a recent transposition event. Taken together, these results indicate that Mutyl is still active.
TAp73 opposes tumor angiogenesis by promoting hypoxia-inducible factor 1α degradation

Significance Adaptation to hypoxia promotes cancer progression, resulting in enhanced patient mortality. Activation of hypoxia-inducible factor 1 (HIF-1) leads to a transcriptional switch, which, regulating angiogenesis, metabolism, and survival, results in hypoxia adaptation. In cancer, increased HIF-1 levels can be a result of either intratumoral hypoxia or the altered function of tumor suppressors. Our study demonstrates that the tumor suppressor TAp73, a member of the p53 family of genes, opposes HIF-1 activation in cancer cells, resulting in reduced angiogenesis and tumor progression. TAp73-depleted mice show increased tumorigenicity, associated with increased HIF-1 signaling and angiogenesis. Expression of TAp73 in human cancers predicts good survival outcome and retrocorrelates with HIF-1 expression and activation. The TAp73/HIF-1 axis plays a critical role in cancer pathogenesis. Tumor hypoxia and hypoxia-inducible factor 1 (HIF-1) activation are associated with cancer progression. Here, we demonstrate that the transcription factor TAp73 opposes HIF-1 activity through a nontranscriptional mechanism, thus affecting tumor angiogenesis. TAp73-deficient mice have an increased incidence of spontaneous and chemically induced tumors that also display enhanced vascularization. Mechanistically, TAp73 interacts with the regulatory subunit (α) of HIF-1 and recruits mouse double minute 2 homolog into the protein complex, thus promoting HIF-1α polyubiquitination and consequent proteasomal degradation in an oxygen-independent manner. In human lung cancer datasets, TAp73 strongly predicts good patient prognosis, and its expression is associated with low HIF-1 activation and angiogenesis. Our findings, supported by in vivo and clinical evidence, demonstrate a mechanism for oxygen-independent HIF-1 regulation, which has important implications for individualizing therapies in patients with cancer.
Ethanol Administration Impairs Pancreatic Repair After Injury

Objectives Alcohol abuse is one of the most common factors associated with acute and chronic pancreatitis. Although it is evident that alcohol abuse can have an important role in the development of pancreatitis, it does not seem that alcohol abuse alone is responsible for this disease. We investigated the involvement of ethanol in the impairment of pancreatic repair after induction of pancreatitis. Methods A biologically relevant mouse model of alcoholic pancreatitis, combining long-term ethanol consumption and coxsackievirus infection, was used to investigate the effects of ethanol on pancreatic regeneration. Tissues were harvested and analyzed by reverse transcription–polymerase chain reaction and immunoblot. Results These studies demonstrate that long-term ethanol consumption impairs the structural repair of the exocrine pancreas. This is accompanied by a delay in the restitution of lipase expression. In addition, impaired expression of the critical pancreatic transcription factors, PDX1 and PTF1, and the mediator of Notch signaling, HES1, was observed. Conclusions Long-term ethanol consumption impairs the structural repair and functional restitution of the pancreas after severe injury. These impairments may, in part, be explained by the impaired expression of factors important in the development and maintenance of the exocrine pancreas. Impaired pancreatic regeneration may have a role in the pathogenesis of alcoholic pancreatitis.
Chromosome Damage in Human Cells by γ Rays, α Particles and Heavy Ions: Track Interactions in Basic Dose-Response Relationships

We irradiated normal human lymphocytes and fibroblasts with 137Cs γ rays, 3.5 MeV α particles and 1 GeV/amu 56Fe ions and measured the subsequent formation of chromosome-type aberrations by mFISH at the first mitosis following irradiation. This was done for the purposes of characterizing the shape of dose-response relationships and determining the frequency distribution of various aberration types with respect to the parameters of dose, radiation quality and cell type. Salient results and conclusions include the following. For low-LET γ rays, lymphocytes showed a more robust dose response for overall damage and a higher degree of upward curvature compared to fibroblasts. For both sources of high-LET radiation, and for both cell types, the response for simple and complex exchanges was linear with dose. Independent of all three parameters considered, the most likely damage outcome was the formation of a simple exchange event involving two breaks. However, in terms of the breakpoints making up exchange events, the majority of damage registered following HZE particle irradiation was due to complex aberrations involving multiple chromosomes. This adds a decidedly nonlinear component to the overall breakpoint response, giving it a significant degree of positive curvature, which we interpret as being due to interaction between ionizations of the primary HZE particle track and long-range δ rays produced by other nearby tracks. While such track interaction had been previously theorized, to the best of our knowledge, it has never been demonstrated experimentally.
MAP-Based Online Data Association for Multiple People Tracking in Crowded Scenes

This paper presents an online data association approach to handle new detection and missing detection problems of multiple people tracking in crowded scenes. The key contribution of our paper includes two aspects: one is automatic initiation of tracking models for newly appeared detections and the other is selective update of tracking models for missing detections by occlusions. For the automatic initiation, instead of the conventional matching algorithm, our data association is solved by a maximum a posteriori probability (MAP) formulation considering object's size, center distance, motion and appearance. The selective update scheme for tracking models is developed by considering the spatial information which prevents the tracking model from being corrupted with unreliable information. Even if the head detector is less discriminative due to low number of features than full body and only the recent tracking models are used for online association purpose, the proposed method shows improved performance compared to the state-of-art offline association approach with significantly low computational load.
An online closed-to-open position loop switch for stepper motors in high reliability systems

Stepper motors are widely used in open-loop positioning applications. They are the choice of actuation for the collimators in the Large Hadron Collider, the largest particle accelerator at CERN. In this case the combination of precise positioning requirements and the highly radioactive operating environment is unique. The latter forces both the use of long cables to connect the motors to the drives and also prevents the use of standard position sensors. However, reliable and precise operation of the collimators is critical for the machine. A problem arises however from the use of stepper motors in open-loop. The mechanics of the collimators can wear due to the abrupt motion and torque profiles that are applied by the motors. Closed-loop position control allows smoother movements to be applied but it requires position feedback. The use of sensors in radioactive environments is very limited for reliability reasons. In order to allow the use of position sensors without reducing the long term reliability of the whole system, the possibility to switch online from closed to open loop is proposed and validated in this paper. It allows the use of closed-loop control when the position sensors function correctly and to switch online to open-loop when there is a sensor failure, without the need to stop the machine.
Regulation of gene expression in the mammalian eye and its relevance to eye disease

We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F2 rats generated from an SR/JrHsd × SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (α = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5′ flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor β2 associated with a decreased expression level of the gene encoding short-wavelength sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet–Biedl syndrome. These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.
Bacterial endotoxin increases type II phospholipase A2 immunoreactive content and phospholipase A2 enzymatic activity in human choriodecidua.

The aim of this study was to establish the effect of bacterial endotoxin lipopolysaccharide (LPS) on type II phospholipase A2 (PLA2) content and in vitro net PLA2 enzymatic activity in human choriodecidua. More particularly, the objective was to ascertain whether an increase in type II PLA2 tissue content and PLA2 enzymatic activity is associated with the previously documented stimulatory effect of LPS on prostaglandin E2 (PGE2) release from choriodecidua. Choriodecidua explants were incubated in RPMI 1640 (control) or RPMI 1640 containing LPS (0.1 ng/ml to 10 micrograms/ml) for up to 24 h. Under the incubation conditions utilized, LPS (1 microgram/ml) stimulated the release of PGE2 3-fold (p < 0.001, n = 4 tissues), in a time-dependent manner (p < 0.005). Tissue immunoreactive (ir)-type II PLA2 content and PLA2 enzymatic activity were determined by monoclonal antibody sandwich ELISA and radiolabeled enzyme assay procedures, respectively. The tissue content of type II PLA2 immunoreactivity in choriodecidua obtained from women (n = 7) at term but not in labor averaged 155 +/- 24 ng/ml DNA. PLA2 enzymatic activity average 29.8 +/- 5.1 pmol phosphatidylethanolamine (PE)/mg DNA/h. LPS at a concentration of 1 microgram/ml increased immunoreactive type II PLA2 tissue content by 180% of the control value (p < 0.05, n = 7) within 1 h of exposure and remained significantly elevated for 18 h when compared to controls (174% of control, p < 0.01, n = 7). (ABSTRACT TRUNCATED AT 250 WORDS)
Text compression for sentiment analysis via evolutionary algorithms

Can textual data be compressed intelligently without losing accuracy in evaluating sentiment? In this study, we propose a novel evolutionary compression algorithm, PARSEC (PARts-of-Speech for sEntiment Compression), which makes use of Parts-of-Speech tags to compress text in a way that sacrifices minimal classification accuracy when used in conjunction with sentiment analysis algorithms. An analysis of PARSEC with eight commercial and non-commercial sentiment analysis algorithms on twelve English sentiment data sets reveals that accurate compression is possible with (0%, 1.3%, 3.3%) loss in sentiment classification accuracy for (20%, 50%, 75%) data compression with PARSEC using LingPipe, the most accurate of the sentiment algorithms. Other sentiment analysis algorithms are more severely affected by compression. We conclude that significant compression of text data is possible for sentiment analysis depending on the accuracy demands of the specific application and the specific sentiment analysis algorithm used.
Brain Responses to Visceral and Somatic Stimuli in Patients With Irritable Bowel Syndrome With and Without Fibromyalgia

OBJECTIVE:Symptoms of irritable bowel syndrome (IBS) and fibromyalgia (FM) commonly coexist. We hypothesized that one of the mechanisms underlying this comorbidity is increased activation of brain regions concerned with the processing and modulation of visceral and somatic afferent information, in particular subregions of the anterior cingulate cortex (ACC). METHODS:Regional cerebral blood flow (rCBF) was assessed in age-matched female IBS (n = 10) and IBS + FM (n = 10) subjects using H215O positron emission tomography during noxious visceral (rectal) and somatic pressure stimuli.RESULTS:GI symptom severity was significantly higher in the IBS patients compared with the IBS + FM patients (p < 0.05). In addition, IBS + FM patients rated somatic pain as more intense than their abdominal pain (p < 0.05). Whereas the somatic stimulus was less unpleasant than the visceral stimulus for IBS patients without FM, the somatic and visceral stimuli were equally unpleasant in the IBS + FM group. Group differences in regional brain activation were entirely within the middle subregion of the ACC. There was a greater rCBF increase in response to noxious visceral stimuli in IBS patients and to somatic stimuli in IBS + FM patients.CONCLUSION:Chronic stimulus-specific enhancement of ACC responses to sensory stimuli in both syndromes may be associated with cognitive enhancement of either visceral (IBS) or somatic (IBS + FM) sensory input and may play a key pathophysiologic role in these chronic pain syndromes.
Increase in Endogenous Brain Superoxide Dismutase as a Potential Mechanism of Lipopolysaccharide-Induced Brain Ischemic Tolerance

A low dose (0.5 mg/kg) of lipopolysaccharide (LPS), administered 72 hours before 60-minute middle cerebral artery occlusion, induced a delayed neuroprotection proven by the significant decrease (–35%) of brain infarct volume in comparison with control, whereas infarct volumes remained unchanged in rats treated 12, 24, or 168 hours before ischemia. This delayed neuroprotective effect of LPS was induced only with low doses (0.25 to 1 mg/kg), whereas this effect disappeared with a higher dose (2 mg/kg). The delayed neuroprotection of LPS was induced in the cortical part of the infarcted zone, not in the subcortical part. The beneficial effect of LPS on consequences of middle cerebral artery occlusion was suppressed by dexamethasone (3 mg/kg) and indomethacin (3 mg/kg) administered 1 hour before LPS, whereas both drugs had no direct effect on infarct volume by themselves, suggesting that activation of inflammatory pathway is involved in the development of LPS-induced brain ischemic tolerance. Preadministration of cycloheximide, an inhibitor of protein synthesis, also blocked LPS-induced brain ischemic tolerance suggesting that a protein synthesis is also necessary as a mediating mechanism. Superoxide dismutase (SOD) could be one of the synthesized proteins because lipopolysaccharide increased SOD brain activity 72 hours, but not 12 hours, after its administration, which paralleled the development of brain ischemic tolerance. In contrast, catalase brain activity remained unchanged after LPS administration. The LPS-induced delayed increase in SOD brain content was suppressed by a previous administration of indomethacin. These data suggest that the delayed neuroprotective effect of low doses of LPS is mediated by an increased synthesis of brain SOD that could be triggered by activation of inflammatory pathway.
Molecular structure and developmental expression of three muscle‐type troponin T genes in zebrafish

Troponin T (Tnnt), a troponin component, interacts with tropomyosin and is crucial to the regulation of striated muscle contraction. To gain insight into the molecular evolution and developmental regulation of Tnnt gene (Tnnt) in lower vertebrates, zebrafish Tnnt1 (slow Tnnt), Tnnt2 (cardiac Tnnt), and Tnnt3b (fast Tnnt isoform b) were characterized. The polypeptides of zebrafish Tnnt1, Tnnt2, and Tnnt3b were conserved in the central tropomyosin‐ and C‐terminal troponin I‐binding domains. However, the N‐terminal hypervariable regions were highly extended and rich in glutamic acid in polypeptides of Tnnt1 and Tnnt2, but not Tnnt3b. The Tnnt2 and Tnnt3b contain introns, whereas Tnnt1 is intron‐free. During development, large to small, alternatively spliced variants were detected in Tnnt2, but not in Tnnt1 or Tnnt3. Whole‐mount in situ hybridization showed zebrafish Tnnt1 and Tnnt2 are activated during early somitogenesis (10 hr postfertilization, hpf) and cardiogenesis (14 hpf), respectively, but Tnnt3b is not activated until middle somitogenesis (18 hpf). Tnnt2 and Tnnt3b expression was cardiac‐ and fast‐muscle specific, but Tnnt1 was expressed in both slow and fast muscles. We propose that three, distinct, muscle‐type Tnnt evolved after the divergence of fish and deuterostome invertebrates. In zebrafish, the developmental regulation of Tnnt during somitogenesis and cardiogenesis is more restricted and simpler than in tetrapods. These new findings may provide insight into the developmental regulation and molecular evolution of vertebrate Tnnt. Developmental Dynamics 227:266–279, 2003. © 2003 Wiley‐Liss, Inc.