Miracle-dz/UniFAR-FTUs huggingface dataset:
An Epistatic Interaction between the PAX8 and STK17B Genes in Papillary Thyroid Cancer Susceptibility

Papillary Thyroid Cancer (PTC) is a heterogeneous and complex disease; susceptibility to PTC is influenced by the joint effects of multiple common, low-penetrance genes, although relatively few have been identified to date. Here we applied a rigorous combined approach to assess both the individual and epistatic contributions of genetic factors to PTC susceptibility, based on one of the largest series of thyroid cancer cases described to date. In addition to identifying the involvement of TSHR variation in classic PTC, our pioneer study of epistasis revealed a significant interaction between variants in STK17B and PAX8. The interaction was detected by MD-MBR (p = 0.00010) and confirmed by other methods, and then replicated in a second independent series of patients (MD-MBR p = 0.017). Furthermore, we demonstrated an inverse correlation between expression of PAX8 and STK17B in a set of cell lines derived from human thyroid carcinomas. Overall, our work sheds additional light on the genetic basis of thyroid cancer susceptibility, and suggests a new direction for the exploration of the inherited genetic contribution to disease using association studies.
Tortoise and the Hare Robot: Slow and steady almost wins the race, but finishes more safely

We investigated the effects of changing the tele-operation feel of operating a robot by modifying its speed and acceleration profiles, and found that reducing a robot's maximum speed by half can reduce collisions by 32%, while only increasing navigation task time by 10%. Teleoperated robots are increasingly popular for enabling people to remotely attend meetings, explore dangerous areas, or view tourist destinations. As these robots are being designed to work in crowded areas with people, obstacles, or even unpredictable debris, interfaces that support piloting them in a safe and controlled manner are important for successful teleoperation. We investigate modifying a teleoperated robot's speed and acceleration profiles on an operator remotely navigating through an obstacle course. Our results indicate that lower maximum speeds result in lower operator workload, fewer collisions, and are only slightly slower than other profiles with a higher maximum speed. Our results raise questions about how robot designers should think about physical robot capability design and default driving software settings, the robot control interface, and the relation of robot speed to control.
Probing Galaxy Formation with He II Cooling Lines

Using high-resolution cosmological simulations, we study hydrogen and helium gravitational cooling radiation from gas accretion by young galaxies. We focus on the He II cooling lines, which arise from gas with a different temperature history (Tmax ~ 105 K) than H I line-emitting gas. We examine whether three major atomic cooling lines, H I λ1216, He II λ1640, and He II λ304, are observable, finding that Lyα and He II λ1640 cooling emission at z = 2-3 are potentially detectable with deep narrowband (R > 100) imaging and/or spectroscopy from the ground. While the expected strength of H I λ1216 cooling emission depends strongly on the treatment of the self-shielded phase of the IGM in the simulations, our predictions for the He II λ1640 line are more robust, because the He II emissivity is negligible below T ~ 104.5 K and less sensitive to the UV background. Although He II λ1640 cooling emission is fainter than Lyα by at least a factor of 10 and, unlike Lyα, might not be resolved spatially with current observational facilities, it is more suitable to study gas accretion in the galaxy formation process because it is optically thin and less contaminated by the recombination lines from star-forming galaxies. The He II λ1640 line can be used to distinguish among mechanisms for powering the so-called Lyα blobs—including gravitational cooling radiation, photoionization by stellar populations, and starburst-driven superwinds—because (1) He II λ1640 emission is limited to very low metallicity [log(Z/Z☉) ≲ -5.3] and Population III stars and (2) the blob's kinematics are probed unambiguously through the He II line width, which for cooling radiation is narrower (σ < 400 km s-1) than typical wind speeds.
Code-pointer integrity

In this chapter, we describe code-pointer integrity (CPI), a new design point that guarantees the integrity of all code pointers in a program (e.g., function pointers, saved return addresses) and thereby prevents all control-flow hijack attacks that exploit memory corruption errors, including attacks that bypass control-flow integrity mechanisms, such as control-flow bending [Carlini et al. 2015e]. We also describe code-pointer separation (CPS), a relaxation of CPI with better performance properties. CPI and CPS offer substantially better security-to-overhead ratios than the state of the art, and they are practical (CPI and CPS were used to protect a complete FreeBSD system and over 100 packages like apache and postgresql), effective (prevented all attacks in the RIPE benchmark), and efficient: on SPEC CPU2006, CPS averages 1.2% overhead for C and 1.9% for C/C++, while CPI's overhead is 2.9% for C and 8.4% for C/C++. This chapter is organized as follows: we introduce the motivation and key ideas behind CPI and CPS (Section 4.1), describe related work (Section 4.2), introduce our threat model (Section 4.3), describe CPI and CPS design (Section 4.4), present the formal model of CPI (Section 4.5), describe an implementation of CPI (Section 4.6) and the experimental results (Section 4.7), and then conclude (Section 4.8).
Preventing Unnecessary Invasive Cancer-Diagnostic Tests: Changing the Cut-off Points

Background: To determine a cut-off point of tPSA and PSAD to prevent unnecessary invasive cancer-diagnosing tests in the community. Methods: This study was performed on 688 consecutive patients referred to our center due to prostatism, suspicious lesions on digital rectal examination and/or elevated serum PSA levels. All patients underwent transrectal ultrasound guided biopsies and obtained PSAD. Serum levels of tPSA and fPSA were measured by chemiluminescence. Comparisons were done using tests of accuracy (AUC-ROC). Results: Prostate cancer was detected in 334 patients, whereas the other 354 patients were suffering from benign prostate diseases. The mean tPSA in case and control groups were 28.32±63.62 ng/ml and 7.14±10.04 ng/ml; the mean f/tPSA ratios were 0.13± 0.21 and 0.26±0.24 in PCa and benign prostate disease groups; the mean PSAD rates were 0.69±2.24, 0.12±0.11, respectively. Statistically significant differences were found (P <0.05). Using ROC curve analysis, it was revealed that AUC was 0.78 for tPSA and 0.80 for f/tPSA. Sensitivity was 71% for the cut-off value of 7.85ng/ml. For f/tPSA ratio, the optimal cut-off value was 0.13 which produced the sensitivity of 81.4% and for PSAD, it was15%. Conclusions: As this trial is different from the European and American values, we should be more cautious in dealing with the prostate cancer upon the obtained sensitivity and specificity for PCa diagnosis (7.85ng/mL for tPSA, 15% for PSAD and 0.13 for f/tPSA ratio).
Welding residual stresses: a daily history

Welding is the main joint technology used in steel manufactured products, in particular, in the shipbuilding industry. Recent works report the effect of residual stress redistribution on butt welded plates in a relatively short period after the welding procedures. The phenomenon was investigated by the daily monitoring of the welding residual stresses and the vertical displacements of the welded plate surface. The residual stress state was monitored by the magnetic method, and the absolute stress values were measured using X-ray diffraction techniques. A laser tracking device was used to measure surface displacements. The results from the monitoring performed during the first 6 days after removing the welding restrictions and 1 month later are presented.
Management of motor neurone disease

Motor neurone disease is a progressive neurodegenerative disorder leading to severe disability and death. It is clinically characterised by mixed upper and lower motor neurone involvement affecting bulbar, limb, and respiratory musculature. Recent guidelines have established diagnostic criteria and defined management of the condition. In a proportion of familial amyotrophic lateral sclerosis there is a mutation in the gene encoding the enzyme copper/zinc superoxide dismutase 1; this has allowed mutation screening and generated considerable laboratory based research. The diagnosis must be given with care and consideration and close follow up is essential. Management involves a multidisciplinary team based in the hospital and the community. Riluzole is the only drug shown to have a disease modifying effect and has been approved by the National Institute for Clinical Excellence. The essence of care is good symptomatic management, including nutritional support with percutaneous endoscopic gastrostomy and ventilatory care with non-invasive ventilation. Palliative care should be introduced before the terminal stages after careful discussion with the patient and carers. Knowledge of this condition has grown dramatically recently with a parallel improvement in treatment and ability to deal with the most troublesome problems.
Thermoelectric Properties of Silicon Germanium: An In-depth Study to the Reduction of Lattice Thermal Conductivity

Thermoelectric materials provide a solid state route for the direct conversion between thermal and electrical energy. Hence, thermal gradients can be used to generate power of up to several kWe, or driven DC power can be used to pump heat in or out of a system. Recent pushes in thermoelectric research are for power generation materials with higher efficiency. These materials can be used to recover energy from the waste heat of vehicles’ exhaust systems, and as power generators for extraterrestrial exploration when coupled with a radioactive heat source. The goal of this dissertation will be to demonstrate a new synthesis technique for the current state of the art thermoelectric material for high temperature power generation, silicon germanium (SiGe). This technique is referred to as the single element (SE) spark plasma sintering (SPS) technique because the single elements of silicon, germanium, and their n and p type dopants are alloyed together during the SPS consolidation process. This novel synthesis technique is two orders of magnitude faster than the original technique for alloying this material and one order of magnitude faster than the current technique used for alloying this material. The innovation and newness of this technique presented to the scientific community is closely tied to material science, while the understanding of the resulting thermoelectric material and its properties are perceived through a
Peptidoglycan- and Lipoteichoic Acid-induced Cell Activation Is Mediated by Toll-like Receptor 2*

The life-threatening complications of sepsis in humans are elicited by infection with Gram-negative as well as Gram-positive bacteria. Recently, lipopolysaccharide (LPS), a major biologically active agent of Gram-negative bacteria, was shown to mediate cellular activation by a member of the human Toll-like receptor family, Toll-like receptor (TLR) 2. Here we investigate the mechanism of cellular activation by soluble peptidoglycan (sPGN) and lipoteichoic acid (LTA), main stimulatory components of Gram-positive bacteria. Like LPS, sPGN and LTA bind to the glycosylphosphatidylinositol-anchored membrane protein CD14 and induce activation of the transcription factor NF-κB in host cells like macrophages. We show that whole Gram-positive bacteria, sPGN and LTA induce the activation of NF-κB in HEK293 cells expressing TLR2 but not in cells expressing TLR1 or TLR4. The sPGN- and LTA-induced NF-κB activation was not inhibited by polymyxin B, an antibiotic that binds and neutralizes LPS. Coexpression together with membrane CD14 enhances sPGN signal transmission through TLR2. In contrast to LPS signaling, activation of TLR2 by sPGN and LTA does not require serum. These findings identify TLR2 as a signal transducer for sPGN and LTA in addition to LPS.
Cohesion and Learning in a Tutorial Spoken Dialog System

Two measures of lexical cohesion were developed and applied to a corpus of human-computer tutoring dialogs. For both measures, the amount of cohesion in the tutoring dialog was found to be significantly correlated to learning for students with below-mean pretest scores, but not for those with above-mean pre-test scores, even though both groups had similar amounts of cohesion. We also find that only cohesion between tutor and student is significant: the cohesiveness of tutor, or of student, utterances is not. These results are discussed in light of previous work in textual cohesion and recall.
Preparation and performance characteristics of short-glass-fiber/maleated styrene-ethylene-butylene-styrene/polypropylene hybrid composites

Eighty/twenty polypropylene (PP)/styrene–ethylene–butylene–styrene (SEBS) and 80/20 PP/maleated styrene–ethylene–butylene–styrene (SEBS-g-MA) blends reinforced with 30 wt % short glass fibers (SGFs) were prepared by extrusion and subsequent injection molding. The influence of the maleic anhydride (MA) functional group grafted to SEBS on the properties of SGF/SEBS/PP hybrid composites was studied. Tensile and impact tests showed that the SEBS-g-MA copolymer improved the yield strength and impact toughness of the hybrid composites. Extensive plastic deformation occurred at the matrix interface layer next to the fibers of the SGF/SEBS-g-MA/PP composites during impact testing. This was attributed to the MA functional group, which enhanced the adhesion between SEBS and SGF. Differential scanning calorimetry measurements indicated that SEBS promoted the crystallization of PP spherulites by acting as active nucleation sites. However, the MA functional group grafted to SEBS retarded the crystallization of PP. Finally, polarized optical microscopy observations confirmed the absence of transcrystallinity at the glass-fiber surfaces of both SGF/SEBS/PP and SGF/SEBS-g-MA/PP hybrid composites. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 1303–1311, 2002
Aposematism and crypsis combined as a result of distance dependence: functional versatility of the colour pattern in the swallowtail butterfly larva

The idea that an aposematic prey combines crypsis at a distance with conspicuousness close up was tested in an experiment using human subjects. We estimated detectability of the aposematic larva of the swallowtail butterfly, Papilio machaon, in two habitats, by presenting, on a touch screen, photographs taken at four different distances and measuring the time elapsed to discovery. The detectability of larvae in these images was compared with images that were manipulated, using existing colours either to increase or decrease conspicuousness. Detection time increased with distance for all colourations. However, at the closest distance, detection time was longer for the larvae manipulated to be more cryptic than for the natural and more conspicuous forms. This indicates that the natural colouration is not maximally cryptic at a short distance. Further, smaller increments in distance were needed to increase detection time for the natural than for the conspicuous larva. This indicates that the natural colouration is not maximally conspicuous at longer distances. Taken together, we present the first empirical support for the idea that some colour patterns may combine warning colouration at a close range with crypsis at a longer range. The implications of this result for the evolution of aposematism are discussed.
Laparoscopic anatrophic nephrolithotomy: developments of the technique in the era of minimally invasive surgery.

BACKGROUND AND PURPOSE The complete removal of the stone is the ultimate goal in management, a result that might not be attained even after several sessions of percutaneous nephrolithotomy (PCNL) and/or extracorporeal shockwave lithotripsy (SWL) and/or retrograde intrarenal surgery (ureteroscopy). The objective of this study is to assess our technique of anatrophic nephrolithotomy, with decreased renal ischemia and reduced patient morbidity. PATIENTS AND METHODS From 2007 to 2010, we performed eight anatrophic laparoscopic nephrolithotomies in adult patients with staghorn renal calculus. The mean patient age was 49 years (range 35-62 y). The mean stone size was 53 mm (range 35-70 mm). All patients had complex renal calculi, with stones occupying more than 80% of the caliceal system. In all cases, a Double-J stent was placed before surgery. After clamping the hilum, the incision was made laterally and longitudinally through full thickness of cortex using a laparoscopic scalpel. A running cortical suture was performed with Hem-o-lok reinforcement. Renal function was assessed in three patients, using renography with technetium-99m-diethylenetriaminepentacetic acid (99mTc-DTPA), before and 3 months after the surgery. RESULTS Procedures for all patients were completed laparoscopically. The mean operative time was 142.5 minutes, and the mean warm ischemia time was 20.8 minutes. The estimated blood loss was 315 mL. The hospital stay average was 3.5 days. Only one patient had a complication--a vascular fistula with permanent postoperative hematuria. This patient subsequently underwent successful endovascular embolization. Residual stones were identified in 37% of cases (three patients) during follow-up imaging at 15 days. There were minimal changes on serum creatinine values. CONCLUSIONS Laparoscopic surgery is feasible when anatrophic nephrolithotomy is indicated. This technique minimizes the barriers of an open flank incision, while achieving excellent stone-free rates. This minimally invasive technique should be considered for complex stones that would necessitate multiple renal access tracks and secondary procedures.
Exosome-Bound WD Repeat Protein Monad Inhibits Breast Cancer Cell Invasion by Degrading Amphiregulin mRNA

Increased stabilization of mRNA coding for key cancer genes can contribute to invasiveness. This is achieved by down-regulation of exosome cofactors, which bind to 3'-UTR in cancer-related genes. Here, we identified amphiregulin, an EGFR ligand, as a target of WD repeat protein Monad, a component of R2TP/prefoldin-like complex, in MDA-MB-231 breast cancer cells. Monad specifically interacted with both the 3'-UTR of amphiregulin mRNA and the RNA degrading exosome, and enhanced decay of amphiregulin transcripts. Knockdown of Monad increased invasion and this effect was abolished with anti-amphiregulin neutralizing antibody. These results suggest that Monad could prevent amphiregulin-mediated invasion by degrading amphiregulin mRNA.
Temperature Diagnostics in Turbulent Arcs

Time averaged radial distributions of temperature and its fluctuations have been obtained for turbulent (and laminar) dc-argon arcs operated at 65 A in a 1-cm diam channel. With laminar arcs fluctuations proceeded inward from the outer edge; in the present case temperature fluctuations were about 1 percent and 4 percent at the centerline and outer edge, respectively. Relatively large fluctuations in temperature, about 5 percent, were found across the entire column where the arc was turbulent. Centerline temperatures were nearly identical for both laminar and turbulent arcs-about 10 610 K. The analytical development is an extension of the model of Schreiber and Hunter.
Disseminated candidiasis secondary to fungal and bacterial peritonitis in a young dog.

OBJECTIVE To describe a severe case of bacterial sepsis and disseminated candidiasis in a previously healthy dog. CASE SUMMARY Fungal sepsis was identified in a 2-year-old dog following intestinal dehiscence 4 days after abdominal surgery. Septic peritonitis was identified at admission and evidence of dehiscence at the previous enterotomy site was found during an exploratory laparotomy. Both gram-positive cocci and Candida albicans were cultured from the abdominal cavity. Candida sp. was also subsequently cultured from a central venous catheter. Euthanasia was performed due to failure to respond to therapy. Fungal organisms, morphologically consistent with Candida spp. , were found in the lungs and kidney on postmortem histopathologic examination indicating disseminated candidiasis. NEW OR UNIQUE INFORMATION PROVIDED Candida peritonitis is a well-recognized entity in humans and contributes to morbidity and mortality in critically ill patients. Abdominal surgery, intestinal perforation, presence of central venous catheters, and administration of broad-spectrum antibiotics are all considered to be suspected risk factors. This report describes the first known case of systemic candidiasis occurring secondary to Candida peritonitis and bacterial sepsis in a critically ill dog.
Addressing collective trauma: conceptualisations and interventions

Complex situations following war and natural disasters have a psychosocial impact not only on the individual, but also their family, community and the larger society. Fundamental changes in the functioning of the family and community can be observed as a result of these impacts. At the family level, the dynamics of single parent families, lack of trust among members, changes in significant relationships and child rearing practices are seen. Communities tend to be more dependent, passive, silent, without leadership, mistrustful and suspicious. Additional adverse effects include the breakdown of traditional structures, institutions and familiar ways of life, and deterioration in social norms, ethics and loss of social capital. Collective trauma can be studied using sophisticated multilevel statistical analysis, with social capital as a marker. A variety of community level interventions have been tried, though a scientifically robust evidence base for their effectiveness has yet to be established. This article advocates that post disaster relief, rehabilitation and development programmes need to address the problem of collective trauma, particularly using integrated holistic approaches.
The Effect of PPARα, PPARδ, PPARγ, and PPARpan Agonists on Body Weight, Body Mass, and Serum Lipid Profiles in Diet-Induced Obese AKR/J Mice

Activation of peroxisome proliferator-activated receptor (PPAR) α, δ, and γ subtypes increases expression of genes involved in fatty acid transport and oxidation and alters adiposity in animal models of obesity and type-2 diabetes. PPARpan agonists which activate all three receptor subtypes have antidiabetic activity in animal models without the weight gain associated with selective PPARγ agonists. Herein we report the effects of selective PPAR agonists (GW9578, a PPARα agonist, GW0742, a PPARδ agonist, GW7845, a PPARγ agonist), combination of PPARα and δ agonists, and PPARpan (PPARα/γ/δ) activators (GW4148 or GW9135) on body weight (BW), body composition, food consumption, fatty acid oxidation, and serum chemistry of diet-induced obese AKR/J mice. PPARα or PPARδ agonist treatment induced a slight decrease in fat mass (FM) while a PPARγ agonist increased BW and FM commensurate with increased food consumption. The reduction in BW and food intake after cotreatment with PPARα and δ agonists appeared to be synergistic. GW4148, a PPARpan agonist, induced a significant and sustained reduction in BW and FM similar to an efficacious dose of rimonabant, an antiobesity compound. GW9135, a PPARpan agonist with weak activity at PPARδ, induced weight loss initially followed by rebound weight gain reaching vehicle control levels by the end of the experiment. We conclude that PPARα and PPARδ activations are critical to effective weight loss induction. These results suggest that the PPARpan compounds may be expected to maintain the beneficial insulin sensitization effects of a PPARγ agonist while either maintaining weight or producing weight loss.