Miracle-dz/UniFAR-FTUs huggingface dataset:
XRCC1 Arg399Gln Gene Polymorphism and Hepatocellular Carcinoma Risk in the Italian Population

Background The human X-ray repair cross-complementing protein 1 (XRCC1) gene encodes for one of the major repair factors involved in base excision repair (BER), which is reported to be associated with the risk of several cancers. A few studies have explored the association between risk of hepatocellular carcinoma (HCC) and single-nucleotide polymorphisms (SNPs) in different DNA repair genes, with contradictory results. The purpose of this study was to evaluate the association between XRCC1 Arg399Gln polymorphism and susceptibility to HCC. Methods A total of 89 HCC patients and 99 randomly selected healthy controls were enrolled. Genotyping of XRCC1 rs25487 was performed by high-resolution melting analysis and Sanger sequencing. Results On univariate analysis, a statistically significant association was found between risk of HCC and XRCC1 399Arg/Gln genotype (odd ratio [OR] = 1.88; 95% CI, 1.04-3.43), which was confirmed after adjusting by sex (OR = 1.94; 95% CI, 1.04-3.63). Although not significant, Kaplan-Meier analysis showed a decreased median survival in Arg/Gln genotype carriers in comparison with Arg/Arg carriers. Conclusions To our knowledge, this is the first study reporting an association between BER SNP and HCC risk in a population of central-southern Italy.
Precise Control of Target Temperature Using N6-Cyclohexyladenosine and Real-Time Control of Surface Temperature.

Targeted temperature management is standard of care for cardiac arrest and is in clinical trials for stroke. N6-cyclohexyladenosine (CHA), an A1 adenosine receptor (A1AR) agonist, inhibits thermogenesis and induces onset of hibernation in hibernating species. Despite promising thermolytic efficacy of CHA, prior work has failed to achieve and maintain a prescribed target core body temperature (Tb) between 32°C and 34°C for 24 hours. We instrumented Sprague-Dawley rats (n = 19) with indwelling arterial and venous cannulae and a transmitter for monitoring Tb and ECG, then administered CHA via continuous IV infusion or intraperitoneal (IP) injection. In the first experiment (n = 11), we modulated ambient temperature and increased the dose of CHA in an attempt to manage Tb. In the second experiment (n = 8), we administered CHA (0.25 mg/[kg·h]) via continuous IV infusion and modulated cage surface temperature to control Tb. We rewarmed animals by increasing surface temperature at 1°C h-1 and discontinued CHA after Tb reached 36.5°C. Tb, brain temperature (Tbrain), heart rate, blood gas, and electrolytes were also monitored. Results show that titrating dose to adjust for individual variation in response to CHA led to tolerance and failed to manage a prescribed Tb. Starting with a dose (0.25 mg/[kg·h]) and modulating surface temperature to prevent overcooling proved to be an effective means to achieve and maintain Tb between 32°C and 34°C for 24 hours. Increasing surface temperature to 37°C during CHA administration brought Tb back to normothermic levels. All animals treated in this way rewarmed without incident. During the initiation of cooling, we observed bradycardia within 30 minutes of the start of IV infusion, transient hyperglycemia, and a mild hypercapnia; the latter normalized via metabolic compensation. In conclusion, we describe an intravenous delivery protocol for CHA at 0.25 mg/(kg·h) that, when coupled with conductive cooling, achieves and maintains a prescribed and consistent target Tb between 32°C and 34°C for 24 hours.
Interactions between changing pCO2, N2 fixation, and Fe limitation in the marine unicellular cyanobacterium Crocosphaera

We examined the physiological responses of steady‐state iron (Fe)‐replete and Fe‐limited cultures of the biogeochemically critical marine unicellular diazotrophic cyanobacterium Crocosphaera at glacial (19 Pa; 190 ppm), current (39 Pa; 380 ppm), and projected year 2100 (76 Pa; 750 ppm) CO2 levels. Rates of N2 and CO2 fixation and growth increased in step with increasing partial pressure of CO2 (pCO2), but only under Fe‐replete conditions. N2 and carbon fixation rates at 75 Pa CO2 were 1.4‐1.8‐fold and 1.2‐2.0‐fold higher, respectively, relative to those at present day and glacial pCO2 levels. In Fe‐replete cultures, cellular Fe and molybdenum quotas varied threefold and were linearly related to N2 fixation rates and to external pCO2. However, N2 fixation and trace metal quotas were decoupled from pCO2 in Fe‐limited Crocosphaera. Higher CO2 and Fe concentrations both resulted in increased cellular pigment contents and affected photosynthesis vs. irradiance parameters. If these results also apply to natural Crocosphaera populations, anthropogenic CO2 enrichment could substantially increase global oceanic N2 and CO2 fixation, but this effect may be tempered by Fe availability. Possible biogeochemical consequences may include elevated inputs of new nitrogen to the ocean and increased potential for Fe and/or phosphorus limitation in the future high‐CO2 ocean, and feedbacks to atmospheric pCO2 in both the near future and over glacial to interglacial timescales.
High Serum Bilirubin Levels, NT-pro-BNP, and Lactate Predict Mortality in Long-Term, Severely Ill Respiratory ECMO Patients

Mortality in patients treated with extracorporeal membrane oxygenation (ECMO) is high. Therefore, it is crucial to better understand conditions that are associated with mortality in ECMO patients. In this retrospective analysis, we observed 51 patients treated with high-flow ECMO in 2013 and 2014 at our center. We recorded laboratory values and intensive care procedures. The hypothesis of bilirubin being a predictor of mortality during ECMO treatment was initially addressed. Therefore, laboratory values were obtained before initiation and at the time of highest bilirubin throughout the procedure. Receiver operating characteristic (ROC) curves and survival analysis were conducted. Our cohort consisted of patients with advanced age (median: 55 years; range: 22–76) and high mortality (26/51; 51%). Lactate, bilirubin, and NT-pro-BNP were significantly (p < 0.05) associated with mortality in univariable analyses. The cut-off values with highest Youden’s index were bilirubin ≥10 mg/dl, lactate ≥2.25 mmol/L, and NT-pro-BNP ≥11,500 pg/ml. A multivariable analysis, revealed an area under the curve (AUC) of 0.85 (95% confidence interval [CI]: 0.74–0.97), sensitivity of 0.79, and specificity of 0.91. Bilirubin, lactate, and NT-pro-BNP were associated with mortality during ECMO treatment. However, laboratory values were only evaluated at the time of peak bilirubin.
PICT-1 triggers a pro-death autophagy through inhibiting rRNA transcription and AKT/mTOR/p70S6K signaling pathway

PICT-1 was originally identified as a tumor suppressor. Here, we found that PICT-1 overexpression triggered pro-death autophagy without nucleolar disruption or p53 accumulation in U251 and MCF7 cells. Truncated PICT-1 fragments 181-346 and 1-346, which partly or totally lack nucleolar localization, showed weaker autophagy-inducing effects than full-length PICT-1 and a well-defined nucleolar mutant (181-479). Furthermore, PICT-1 partly localizes to the nucleolar fibrillar center (FC) and directly binds to ribosomal DNA (rDNA) gene loci, where it interacts with upstream binding factor (UBF). Overexpression of PICT-1 or the 181-479 mutant, but not the 1-346 or 181-346 mutants, markedly inhibited the phosphorylation of UBF and the recruitment of rRNA polymerase I (Pol I) to the rDNA promoter in response to serum stimulation, thereby suppressing rRNA transcription, suggesting that rRNA transcription inhibition might be an important contributor to PICT-1-induced autophagy. This is supported by the finding that CX-5461, a specific Pol I inhibitor, also induced autophagy. In addition, both CX-5461 and PICT-1, but not the 1-346 or 181-346 mutants, significantly suppressed the activation of the Akt/mTOR/p70S6K signaling pathway. Our data show that PICT-1 triggers pro-death autophagy through inhibition of rRNA transcription and the inactivation of AKT/mTOR/p70S6K pathway, independent of nucleolar disruption and p53 activation.
How Many Teeth are Extracted as Part of Orthodontic Treatment? A Survey of 2038 UK Residents

In their classic article on the subject Peck and Peck [1] reported extraction frequencies taken from 12 studies over a 66 year period, that varied between 6.5 % to 83.5 %. They also recognised that the decision to extract teeth as part of orthodontic treatment was both contentious and emotive. To quote "For years the question of extracting permanent teeth as part of corrective orthodontics has provoked professional controversy and debate, often of religious intensity".
A low rank Hankel matrix reconstruction method for ultrafast magnetic resonance spectroscopy

Magnetic resonance spectroscopy has many important applications in bio-engineering while acquiring high dimensional spectroscopy is usually time consuming. Non-uniformly sampling can speed up the data acquisition but the missing data points have to be restored with proper signal models. In this work, a specific two dimensional (2D) magnetic resonance signal, in which the first dimension lies in frequency domain while the second dimension lies in time domain, is reconstructed with a proposed low rank Hankel-matrix method. This method explores two general properties: 1) the rank of a structured matrix, converted from a 2D exponential signal, is equal to the number of 2D spectral peaks; 2) this rank is small if the spectrum is sparse. Results on real magnetic resonance spectroscopy show that proposed method outperforms the state-of-compressed sensing method on recovering low-intensity spectral peaks.
Follicle-Stimulating Hormone Increases the Risk of Postmenopausal Osteoporosis by Stimulating Osteoclast Differentiation

Objective The objectives of this study were to observe the changes in follicle-stimulating hormone (FSH) and bone mineral density (BMD) in postmenopausal women, to research the relationship between FSH and postmenopausal osteoporosis, and to observe the effects of FSH on osteoclast differentiation in RAW264.7 cells. Methods We analyzed 248 postmenopausal women with normal bone metabolism. A radioimmunoassay (RIA) was used to detect serum FSH, luteinizing hormone (LH), and estradiol (E2). Dual-energy X-ray absorptiometry was used to measure forearm BMD. Then, we analyzed the age-related changes in serum FSH, LH and E2. Additionally, FSH serum concentrations were compared between a group of postmenopausal women with osteoporosis and a control group. Osteoclasts were induced from RAW264.7 cells in vitro by receptor activator of nuclear factor kappa B ligand (RANKL), and these cells were treated with 0, 5, 10, and 20 ng/ml FSH. After the osteoclasts matured, tartrate-resistant acid phosphatase (TRAP) staining was used to identify osteoclasts, and the mRNA expression levels of genes involved in osteoclastic phenotypes and function, such as receptor activator of NF-κB (Rank), Trap, matrix metalloproteinase-9 (Mmp-9) and Cathepsin K, were detected in different groups using real-time PCR (polymerase chain reaction). Results 1. FSH serum concentrations in postmenopausal women with osteoporosis increased notably compared with the control group. 2. RANKL induced RAW264.7 cell differentiation into mature osteoclasts in vitro. 3. FSH increased mRNA expression of genes involved in osteoclastic phenotypes and function, such as Rank, Trap, Mmp-9 and Cathepsin K, in a dose-dependent manner. Conclusions The circulating concentration of FSH may play an important role in the acceleration of bone loss in postmenopausal women. FSH increases osteoclastogenesis in vitro.
Kernel Learning in Support Vector Machines using Dual-Objective Optimization

Support vector machines (SVMs) are very popular methods for solving classification problems that require mapping input features to target labels. When dealing with real-world data sets, the different classes are usually not linearly separable, and therefore support vector machines employ a particular kernel function. Such a kernel function computes the similarity between two input patterns, but has as drawback that all input dimensions are considered equally important for computing this similarity. In this paper we proposea novel method that uses the dual objective of the SVM in order to update scaling weight vectors to scale different input features. We developed a gradient descent method that updates the scaling weight vectors to minimize the dual objective, after which the SVM is retrained, and this procedure is repeated a number of times. Experiments on noisy data sets show that our proposed algorithm leads to significantly higher accuracies than obtained with the standard SVM.
Cigarette Smoking, STAT4 and TNFRSF1B Polymorphisms, and Systemic Lupus Erythematosus in a Japanese Population

Objective. Recent studies have identified signal transducer and activator of transcription 4 (STAT4) as a susceptibility gene for systemic lupus erythematosus (SLE) in different populations. Similarly, tumor necrosis factor receptor superfamily, member 1B (TNFRSF1B) has been reported to be associated with SLE risk in Japanese populations. Along with environmental factors such as smoking, both polymorphisms may modulate an individual’s susceptibility to SLE. We investigated these relationships in a case-control study to evaluate risk factors for SLE among Japanese women. Methods. We investigated the relationship of the STAT4 rs7574865 and TNFRSF1B rs1061622 polymorphisms to SLE risk with special reference to their combination and interaction with cigarette smoking among 152 SLE cases and 427 controls. Results. The TT genotype of STAT4 rs7574865 was significantly associated with increased risk of SLE (OR 2.21, 95% CI 1.10–4.68). Subjects with at least one G allele of TNFRSF1B rs1061622 had an increased risk of SLE (OR 1.56, 95% CI 0.99–2.47). The attributable proportion due to the interaction between the TNFRSF1B rs1061622 genotypes and smoking was estimated to be 0.49 (95% CI 0.07–0.92), indicating that 49% of the excess risk for SLE in smokers with at least one G allele was due to an additive interaction. A lack of significant associations of STAT4 with smoking was observed. No significant gene-gene interactions were found among polymorphisms of STAT4 and TNFRSF1B. Conclusion. Our findings suggest that the association between cigarette smoking and SLE could be differentiated by the TNFRSF1B rs1061622 T allele among female Japanese subjects. This preliminary exploratory result should be confirmed in a larger study.
Waveform optimization for radio-frequency wireless power transfer : (Invited paper)

In this paper, we study the waveform design problem for a single-input single-output (SISO) radio-frequency (RF) wireless power transfer (WPT) system in frequency-selective channels. First, based on the actual non-linear current-voltage model of the diode at the energy receiver, we derive a semi-closed-form expression for the deliverable DC voltage in terms of the incident RF signal and hence obtain the average harvested power. Next, by adopting a multisine waveform structure for the transmit signal of the energy transmitter, we jointly design the multisine signal amplitudes and phases over all frequency tones according to the channel state information (CSI) to maximize the deliverable DC voltage or harvested power. Although our formulated problem is non-convex and difficult to solve, we propose two suboptimal solutions to it, based on the frequency-domain maximal ratio transmission (MRT) principle and the sequential convex optimization (SCP) technique, respectively. Using various simulations, the performance gain of our solutions over the existing waveform designs is shown.
Prevalence of blindness and cataract surgical coverage in Narayani Zone, Nepal: a rapid assessment of avoidable blindness (RAAB) study

Background The 1981 Nepal Blindness Survey first identified the Narayani Zone as one of the regions with the highest prevalence of blindness in the country. Subseuqently, a 2006 survey of the Rautahat District of the Narayani Zone found it to have the country’s highest blindness prevalence. This study examines the impact on blind avoidable and treatable eye conditions in this region after significant increase in eye care services in the past decade. Methods The rapid assessment of avoidable blindness (RAAB) methodology was used with mobile data collection using the mRAAB smartphone app. Data analysis was done using the standard RAAB software. Based on the 2011 census, 100 clusters of 50 participants aged 50 years or older were randomly sampled proportional to population size. Results Of the 5000 participants surveyed, 4771 (95.4%) were examined. The age-adjusted and sex-adjusted prevalence of bilateral blindness, severe visual impairment (SVI) and moderate visual impairment (MVI) were 1.2% (95% CI 0.9% to 1.5%), 2.5% (95% CI 2.0% to -3.0%) and 13.2% (95% CI 11.8% to 14.5%), respectively. Cataract remains the primary cause of blindness and SVI despite cataract surgery coverage (CSC) of 91.5% for VA<3/60. Women still account for two-thirds of blindness. Conclusion The prevalence of blindness in people over the age of 50 years has decreased from 6.9% in 2006 to 1.2%, a level in keeping with the national average; however, significant gender inequity persists. CSC has improved but continues to favour men.
Selected Factors in Reading Comprehension for Deaf and Hearing Adults: Phonological Skills and Metacognition

Abstract: The purpose of the study was to identify factors related to reading comprehension, and to compare similarities and differences in the reading processes of deaf and hearing adults. The sample included four groups, each consisting of 15 adults. The groups were identified as (a) deaf high-achieving readers, (b) deaf low-achieving readers, (c) hearing high-achieving readers, and (d) hearing low-achieving readers. Measurement instruments included a demographic form along with assessments of reading comprehension, phonological skills, and metacognition, the latter of which contained both a making-inferences measure and a think-aloud discussion with a reading strategies checklist. Results indicated that deaf high-achieving readers performed similarly to hearing high-achieving readers, except for phonological skills, and that for all participants, phonological skills and metacognition were related to reading comprehension skills.
The combining DAG: a technique for parallel data flow analysis

The availability of multiprocessor systems has recently generated an increased interest in the design and implementation of parallel compilers. The authors present a parallel algorithm for performing data flow analysis which is an important component of any compiler. Data flow information is used in various phases of compilation including code generation, code scheduling, traditional optimizing transformations and parallelizing transformations. A single program compilation may involve the computation of the solution to several data flow problems and possibly solutions to the same problem multiple times at different points in the language translation process. Thus, for large programs the data flow analysis performed during compilation can be time-consuming. Data flow analysis is also used in other program tools such as editors, testers, and debuggers. <<ETX>>
AustLll's aide — natural language legislative rulebases

Aide (`AustLII Inferencing Development Environment') provides a quasi-natural language form of knowledge representation which is reasonably close to statutory language, but at the same time represents knowledge so that it can be used by an inferencing engine using predicate calculus. Aide also provides a supportive development environment for the user by parse tree differentiation to assist the user choosing the correct parsing of rules. The development environment and the user environment are both web-based, facilitating collaborative development of knowledgebases, and the integration of inferencing dialogues with legal source texts on the web.
Brittle fracture in disordered materials: A spring network model

A model for investigating the influence of distributed disorder on the failure of brittle materials is introduced. The model assumes that microstructural features of a material can be represented by simple linear springs with a failure threshold, and that the entire material can be represented by a connected network of such springs. Distributed disorder is introduced by allowing spring-to-spring variations in spring characteristics such as the modulus and the failure strain. The conditions under which such a spring network model is valid for studying failure are discussed. The consequences of distributed residual stress disorder on macroscopic mechanical behavior are then studied using the network model, and a brittle to ductile-like transition in the stress-strain behavior is observed with increasing disorder. All the qualitative features of the network results can be described theoretically by a statistical analysis of this problem. Finally, notch tests are performed to evaluate the strength and toughness of the ductile-like materials as compared to the uniform (no disorder) material, and the ductile-like material is found to have (i) a larger work of fracture, (ii) comparable strength in the presence of processing flaws, and (iii) the possibility of larger toughness. Based on these results, the possibility of observing such ductile-like behavior in real composite materials is discussed.
Photosynthesis Activates Plasma Membrane H+-ATPase via Sugar Accumulation1[OPEN]

Photosynthesis activates the plasma membrane H+-ATPase in Arabidopsis mesophyll cells through C-terminal phosphorylation, and this activation is mediated by photosynthetic sugars, including sucrose. Plant plasma membrane H+-ATPase acts as a primary transporter via proton pumping and regulates diverse physiological responses by controlling secondary solute transport, pH homeostasis, and membrane potential. Phosphorylation of the penultimate threonine and the subsequent binding of 14-3-3 proteins in the carboxyl terminus of the enzyme are required for H+-ATPase activation. We showed previously that photosynthesis induces phosphorylation of the penultimate threonine in the nonvascular bryophyte Marchantia polymorpha. However, (1) whether this response is conserved in vascular plants and (2) the process by which photosynthesis regulates H+-ATPase phosphorylation at the plasma membrane remain unresolved issues. Here, we report that photosynthesis induced the phosphorylation and activation of H+-ATPase in Arabidopsis (Arabidopsis thaliana) leaves via sugar accumulation. Light reversibly phosphorylated leaf H+-ATPase, and this process was inhibited by pharmacological and genetic suppression of photosynthesis. Immunohistochemical and biochemical analyses indicated that light-induced phosphorylation of H+-ATPase occurred autonomously in mesophyll cells. We also show that the phosphorylation status of H+-ATPase and photosynthetic sugar accumulation in leaves were positively correlated and that sugar treatment promoted phosphorylation. Furthermore, light-induced phosphorylation of H+-ATPase was strongly suppressed in a double mutant defective in ADP-glucose pyrophosphorylase and triose phosphate/phosphate translocator (adg1-1 tpt-2); these mutations strongly inhibited endogenous sugar accumulation. Overall, we show that photosynthesis activated H+-ATPase via sugar production in the mesophyll cells of vascular plants. Our work provides new insight into signaling from chloroplasts to the plasma membrane ion transport mechanism.
Fatal Deer Tick Virus Infection in Maine

Deer tick virus (DTV), a genetic variant (lineage II) of Powassan virus, is a rare cause of encephalitis in North America. We report a fatal case of DTV encephalitis following a documented bite from an Ixodes scapularis tick and the erythema migrans rash associated with Lyme disease.