nils-herrmann/clean_scirepeval huggingface dataset:
Coexistence of Perineural Invasion and Lymph Node Metastases Is a Poor Prognostic Factor in Patients with Locally Advanced Rectal Cancer after Preoperative Chemoradiotherapy Followed by Radical Resection and Adjuvant Chemotherapy

To determine the role of lymph node metastases (ypN) and perineural invasion (PNI) in patients with locally advanced rectal cancer (LARC).  Eighty-eight LARC patients receiving preoperative chemoradiotherapy from April 2006 to November 2011 were enrolled in this study. Univariate and multivariate analyses were conducted to determine the association between clinicopathologic features and clinical outcome.  The presence of ypN (p = 0.011) and PNI (p = 0.032) was a significant adverse prognostic factor for disease-free survival (DFS). High histologic grade (p = 0.015), PNI+ (p = 0.043) and ypN+ (p = 0.041) were adverse prognostic factors for overall survival (OS). Positive PNI was significantly associated with a higher risk of distant failure (odds ratio = 6.09; 95% CI: 1.57-27.05; p = 0.008). Moreover, patients with a coexistence of ypN+ and PNI+ had the significantly worst DFS (p < 0.001) and OS rates (p < 0.001) compared with other phenotypes.  The presence of either PNI or ypN was a significant prognostic factor for predicting poor survival rates in LARC patients, especially those with a coexistence of both factors. Accordingly, we recommend an intensive follow-up and therapeutic programs for LARC patients with simultaneous PNI+ and ypN+.

Field of study: Medicine
The Superconductor-Superinsulator Transition: S-duality and the QCD on the Desktop

We show that the nature of quantum phases around the superconductor-insulator transition (SIT) is controlled by charge-vortex topological interactions, and does not depend on the details of material parameters and disorder. We find three distinct phases, superconductor, superinsulator, and bosonic topological insulator. The superinsulator is a state of matter with infinite resistance in a finite temperature range, which is the S-dual of the superconductor and in which charge transport is prevented by electric strings binding charges of opposite sign. The electric strings ensuring linear confinement of charges are generated by instantons and are dual to superconducting Abrikosov vortices. Material parameters and disorder enter the London penetration depth of the superconductor, the string tension of the superinsulator and the quantum fluctuation parameter driving the transition between them. They are entirely encoded in four phenomenological parameters of a topological gauge theory of the SIT. Finally, we point out that, in the context of strong coupling gauge theories, the many-body localization phenomenon that is often referred to as an underlying mechanism for superinsulation is a mere transcription of the well-known phenomenon of confinement into solid-state physics language and is entirely driven by endogenous disorder embodied by instantons with no need of exogenous disorder.

Field of study: Physics
Unpacking Body Image Concerns and Disordered Eating for Transgender Women: The Roles of Sexual Objectification and Minority Stress

Synthesizing both objectification theory (Fredrickson & Roberts, 1997) and minority stress theory (Meyer, 2003), the present study used a pantheoretical model of dehumanization (Moradi, 2013) to examine body image concerns and disordered eating symptomatology with 205 transgender women from the United States. Objectification theory constructs (i.e., sexual objectification, internalization of sociocultural standards of attractiveness, body surveillance, body dissatisfaction) and minority stress-related variables (i.e., antitransgender discrimination) were examined as direct and indirect predictors of disordered eating. Results of a latent variable SEM (with a higher-order dehumanization factor comprised of sexual objectification and discrimination) generally provided support for our hypothesized direct and indirect relations. As expected, dehumanization was related directly to internalization and disordered eating and had significant indirect links to body surveillance, body dissatisfaction, and disordered eating via internalization. Potential implications of a pantheoretical model for future research with transgender women are discussed.

Field of study: Psychology
Odor and Odorous Chemical Emissions from Animal Buildings: Part 4. Correlations Between Sensory and Chemical Measurements

This study supplemented the National Air Emissions Monitoring Study (NAEMS) with one year of comprehensive measurements of odor emission at five swine and four dairy buildings. The measurements included both standard human sensory measurements using dynamic forced-choice olfactometry and chemical analysis of the odorous compounds using gas chromatography-mass spectrometry. In this article, multilinear regressions between odor and gas concentrations (a total of 20 compounds including H2S, NH3, and VOCs) were investigated. Regressions between odor and gas emission rates were also tested. It was found that gas concentrations, rather than emission rates, should be used to develop multilinear regression models. For the dairy sites, H2S, NH3, acetic acid, propanoic acid, 2-methyl propanoic, and pentanoic acids were observed to be the compounds with the most significant effect on sensory odor. For the swine sites, in addition to these gases, higher molecular weight compounds such as phenol, 4-methyl phenol, 4-ethyl phenol, and 1H-indole were also observed to be significant predictors of sensory odor. When all VOCs were excluded from the model, significant correlations between odor and H2S and NH3 concentrations were still observed. Although these coefficients of determination were lower when only H2S and NH3 were used, they can be used to predict odor variability by up to 83% when VOC data are unavailable.

Field of study: Agricultural and Food sciences
Risk factors for progression to end-stage renal disease in children with posterior urethral valves.

To identify the variables which affect long-term renal outcome in children with posterior urethral valves (PUV).



Retrospective analysis of 260 children with PUV who underwent ablation of valves in 1992-2008 at our tertiary care center. The following risk factors for progression to end-stage renal disease (ESRD) were analyzed: nadir serum creatinine greater than 1.0mg/dl, bilateral grade 3 or higher VUR at diagnosis, recurrent febrile UTIs, and severe bladder dysfunction. Patients were divided into two groups: those who developed ESRD (group 1) and those who did not (group 2).



Forty (17.62%) patients had nadir serum creatinine >1mg/dl. At time of initial presentation, high-grade VUR was seen in 63.1% and 33.5% of groups 1 and 2, respectively (P=0.002). Overall, 77 (34%) of the boys developed breakthrough urinary tract infections: 37.03% and 33.5% in groups 1 and 2, respectively (P=1). Fifty-nine (26%) patients were found to have severe bladder dysfunction: 77.8% and 19% in groups 1 and 2, respectively (P<0.0001). Twenty-seven (11.89%) patients progressed to ESRD, at mean age of 11.21 years (5-16). On univariate analysis, the risk-predicting variables were: nadir serum creatinine value greater than 1mg/dl (P<0.0001), bilateral high-grade VUR (P=0.002) and severe bladder dysfunction (P<0.0001). On multivariate logistic regression analysis, nadir serum creatinine greater than 1mg/dl (OR 23.79; CI 8.20-69.05) and severe bladder dysfunction (OR 5.67; CI 1.90-16.93) were found to be independent risk factors predictive of ultimate progression to ESRD.



Nadir serum creatinine and bladder dysfunction are the main factors affecting long-term renal outcome in cases of PUV. Early identification and treatment of bladder dysfunction may thus be beneficial.

Field of study: Medicine
Zeeman Splitting and Spin-Orbit Torques in Single Ni Nanoparticles

We discuss measurements of discrete electron-in-a-box levels in Ni nanoparticles, using tunneling spectroscopy at 0.06K temperature. We use the amplitudes of the Zeeman-split levels to obtain the spin-transfer rate associated with sequential electron tunneling. In a strong magnetic field, the spin and the charge transfer rates are comparable, which demonstrates strong enhancement compared to the Slonczewski form of spin-transfer torque. In a low magnetic field, the discrete levels broaden into energy bands. The bandwidth is comparable to the spin-orbit energy $\epsilon_{so}\approx$ 0.6meV. The bands are interpreted in terms of the spectra of magnetic excitations close in energy and the van Hove singularity in their density of states, driven by mesoscopic spin-orbit torques. In those circumstances, the effective spin-transfer rate is far higher than the charge-transfer rate.

Field of study: Physics
Comparative analysis of photosensitivity in photosystem I donor and acceptor side mutants of Chlamydomonas reinhardtii

Electron input from plastocyanin into photosystem I (PSI) is slowed down in the Chlamydomonas reinhardtii mutants affected at the donor side (PsaF or PsaB, lumenal loop j) of PSI. In contrast, electron exit from PSI to ferredoxin is diminished in the PSI acceptor side PsaC mutants K35E and FB 1 . Although, the electron transfer reactions are diminished to a similar extent in both type of mutants, the PsaC mutants K35E and FB 1 are more light-sensitive than the PsaF-deficient strain 3bF or the PsaB mutants E613N and W627F. To assess the differential photosensitivity of donor and acceptor side mutants fluorescence transients, gross oxygen evolution and uptake, PSII photo-inhibition and rate of recovery were measured as well as NADP + photoreduction. The NADP + photoreduction measurements indicated that the donor side is limiting the reduction rate. In contrast, measurements of gross oxygen evolution and uptake showed that the reducing side limits linear electron transfer. However, under high light, donor and acceptor side mutations lead to PSII photo-inhibition and to a diminished rate of PSII recovery, cause lipid peroxidation and result in a decrease in the levels of PSI and PSII. The wild type is not affected under the same conditions. These responses are most pronounced in the PsaC-K35E and PsaB-W627F mutants, and they correlate with the light sensitivity of these strains. The correlation between limitation of electron transfer through PSI and the formation of reactive oxygen species as a cause for the light-sensitivity is discussed.

Field of study: Environmental science
Epidemiology of cervical-root caries on teeth: High prevalence in the coca leaf chewing in the Andean people.

Cervical-root caries on teeth often called rampant caries or circular caries often suffered by children who consumed bottled sweet milk. In adult, cervical-root caries occurs in unique cases such as cancer patients who undertake chemotherapy, and narcotic addicts.  The research was aimed to study the dental and oral health of Andean people who have traditionally been chewing coca-leaves as a part of their cultural and integral lives.  The subject of study was 210 Aymara people from highland Chile and Bolivia, Andes. They were given questionnaire whether they chew coca leaves or not. Without knowing whether one chewed coca leaves or not, each individual was examined for: the carious teeth, the caries location, the periodontal stage, the oral pH, the molar radices, the molar loss, and the total number of teeth preserved.  The result showed that people who chewed coca-leaves every day suffered cervical-root caries on their molar teeth, only radices of molars preserved, or even lost their molar teeth. They also suffered tongue desquamation and periodontal damage at the buccal area of molar teeth. In contrast, those who did not chew coca-leaves were relatively free from these dental disadvantages. Statistical analysis showed significantly high correlation between duration and intensity of chewing coca leaves with dental disadvantages (R=0,62 for molar loss; R=0,63 for bad periodontal status; and R =0,54 for cervical-root caries).  It is concluded that habitual chewing of coca leaves damaged the periodontal region of the molar area, caused the root of the molar teeth to expose and led to cervical-root caries, then, only roots of molar preserved, and last, the lost of molar teeth. The high prevalence of cervical-root caries in coca-leaves chewers is in accord with other conditions such as cancer patients who undertake chemotherapy, and narcotic addicts. The alkaloid in the coca leaves are associated with the drying out the mouth leading to less self-cleansing and damaging the cervical-root area. Understanding the cultural tradition in a society is important if we were to understand the disease processes.  coca leaves - Andes - epidemiology - cervical-root caries - molar

Field of study: Medicine
Estimating the budget impact of new technologies added to the National List of Health Services in Israel: stakeholders' incentives for adopting a financial risk-sharing mechanism.

The Israeli National List of Health Services (NLHS) is updated annually according to a government allocated budget. The estimated annual cost of each new technology added to this list is based on budget-impact estimations provided by the HMOs and the manufacturers. The HMOs argue that once a new technology is reimbursed, extensive marketing efforts by industry expands demand and renders the allocated budget insufficient. Industry claims that HMOs, in order to secure a sufficient budget, tend to over-estimate the number of target patients. We provide a framework for a financial risk-sharing mechanism between HMOs and the industry, which may be able to balance these incentives and result in more accurate early budget-impact estimates.



To explore the current stakeholders' incentives and behaviors under the existing process of updating the NLHS, and to examine the possible incentives for adopting a financial risk-sharing mechanism on early budget-impact estimations.



According to the financial risk-sharing mechanism, HMOs will be partially compensated by the industry if actual use of a technology is substantially higher than what was projected. HMOs will partially refund the government for a budget that was not fully used. To maintain profits, we assume that the industry will present a more realistic budget-impact analysis. HMOs will be less apprehensive of technology promotion, as they would be compensated in case of budget under-estimation. In case of over-estimation of technology use, the budget re-allocated will be used to enlarge the NLHS which is in the best interest of the health technology industry. Our proposed risk-sharing mechanism is expected to counter balance incentives and disincentives that currently exist in adopting new health technologies in the Israeli healthcare system.

Field of study: Medicine, Political science
Mucosal lymphocyte subsets and HLA‐DR antigen expression in paediatric Helicobacter pylori‐associated gastritis

Paediatric studies may provide important insights into the immunopathology of Helicobacter pylori‐associated gastritis, as mucosal changes reflect different stages of the immunoinflammatory response. We characterized, by quantitative immunohistochemistry, gastric mucosal lymphocyte phenotype and HLA‐DR antigen expression and evaluated correlation with histopathology, in H. pylori‐infected (Hp+ve) and uninfected children (Hp–ve). In the infected group, lamina propria CD3+ and IgA plasmocyte cell numbers were significantly higher and a trend for predominance of CD8+ over CD4+ was observed both in epithelium and lamina propria. A correlation of inflammation score with lamina propria CD3+ and CD4+ cell numbers and of CD45RO+ T lymphocytes with density of colonization was observed. The proportion of epithelial cells expressing HLA‐DR antigen was significantly higher in the Hp+ve group and furthermore, glandular HLA‐DR expression correlated with lamina propria CD3+ cell numbers, emphasizing the potential role of epithelial cells as antigen‐presenting cells at this stage of infection.

Field of study: Biology, Medicine
Distributed dynamic modelling of a refrigerated room

The prediction of velocity and temperature distributions in a refrigerated room generally requires the simultaneous solution of the equations governing the flow pattern (Navier-Stokes equations) and the energy equation. Basically these are interacting non-linear differential equations requiring simultaneous integration by an iteration process. The specific application of advanced computer packages for this purpose in refrigeration is still in the early stages; even for one steady-state simulation the computation times are high because of the very complicated shape of the air space in a refrigerated room loaded with produce. The method of simultaneous integration becomes unattractive, especially for non-steady-state thermal conditions, if many runs are to be made with different values of the input parameters. In instances where the air cooler fans dominate the flow pattern, the equations can be decoupled. Moreover, the energy equation can be linearized with reasonable model assumptions, and will then not require an iteration process for integration. The simulation described here includes a compression refrigerating machine with capacity control, and was validated by measurements taken from a laboratory-scale cold store.

Field of study: Engineering
THE NAME 2004 FIELD CAMPAIGN AND MODELING STRATEGY

The North American Monsoon Experiment (NAME) is an internationally coordinated process study aimed at determining the sources and limits of predictability of warm-season precipitation over North America. The scientific objectives of NAME are to promote a better understanding and more realistic simulation of warm-season convective processes in complex terrain, intraseasonal variability of the monsoon, and the response of the warm-season atmospheric circulation and precipitation patterns to slowly varying, potentially predictable surface boundary conditions. During the summer of 2004, the NAME community implemented an international (United States, Mexico, Central America), multiagency (NOAA, NASA, NSF, USDA) field experiment called NAME 2004. This article presents early results from the NAME 2004 campaign and describes how the NAME modeling community will leverage the NAME 2004 data to accelerate improvements in warm-season precipitation forecasts for North America.

Field of study: Environmental science
Time-reversal symmetry breaking state in dirty three-band superconductor

I study the effects of disorder on the superconductivity of a three-band model with repulsive interband pairing. Such a model can support several possible superconducting order parameters, including a complex time-reversal symmetry breaking (TRSB) state. Impurity scattering suppresses the critical temperature of all these states, but the complex state survives, and remains a part of the phase diagram of the model even in the presence of moderate amount of disorder. This means that the TRSB states could be experimentally accessible in multiband materials like iron pnictides and chalcogenides.

Field of study: Physics
Phenotype databases for genetic screens in human cells.

Genetic screens are powerful tools to identify components that make up biological systems. Perturbations introduced by methods such as RNA interference (RNAi) or CRISPR/Cas9-mediated genome editing lead to biological phenotypes that can be examined to understand the molecular function of genes in the cell. Over the years, many of such experiments have been conducted providing a wealth of knowledge about genotype-to-phenotype relationships. These data are a rich source of information and it is in a common interest to make them available in a simplified and integrated format. Thus, an important challenge is that genetic screening data can be stored in databases in standardized ways, allowing users to gain new biological insights through data mining and integrated analyses. Here, we provide an overview of available phenotype databases for human cells. We review in detail two databases for high-throughput screens, GenomeRNAi and GenomeCRISPR, and describe how these resources are integrated into the German Network for Bioinformatics Infrastructure de.NBI as part of the European infrastructure for life-science information ELIXIR.

Field of study: Biology, Engineering
TH‐D‐M100J‐02: Quantitative Interstitial Multispectral Diffuse Optical Tomography of Human Prostate Using a Priori Structure Information

To develop an interstitial multispectral diffuse optical tomography (iDOT) system to quantify optical properties, drug concentration and tissue oxygenation of prostate before and after photodynamic  iDOT system uses continuous‐wave measurements from 12 motorized isotropic detectors inserted in the prostate. Optical properties of prostate were reconstructed using single‐wavelength measurements at 732nm. Six point‐sources were introduced interstitially. Multispectral iDOT acquired the absorption spectra in 650–850nm region emitted from 6 optic fibers connected to a halogen lamp. The multispectral method directly reconstructs tissue chromophore concentrations and Mie scattering factors through incorporation of a priori anatomic information and spectral properties. The accuracy and convergence of the reconstruction algorithms were tested in mathematical phantoms with known geometry and optical property distribution. Clinical iDOT were performed on 12 patients for single‐wavelength optical property measurement and 2 patients for spectral measurements.  Phantom study results demonstrated that iDOT can reliably recover the optical properties, chromophore concentrations and scattering factors in clinical‐relevant geometries with fast convergence. In clinical studies, the averaged reconstructed pretreatment μa and μs′ at 730nm varied between .003mm−1 and .162cm−1(mean .03±.02mm−1) and .11 and 4.4mm−1 (mean 1.4±1.1mm−1) among 12 patients. The absorption coefficients for some patients were significantly reduced post‐treatment due to photobleaching of the photosensitizer. For multispectral measurements, the pretreatment total hemoglobin concentration was found between 51μM and 370μM, with oxygen saturation of 67%–90%. There was no significant change post‐treatment. The pretreatment photosensitizer concentration varied from 1.4 to 9.2ng/mg for 2 patients. Up to 66% decrease of photosensitizer concentration was observed in one patient in the post‐treatment measurements.  Preliminary clinical results showed significant inter‐ and intra‐prostatic variation in tissueoptical properties, oxygenation and photosensitizer concentration, suggesting that parameters other than anatomical information should be considered for PDT treatment planning.

Field of study: Medicine, Physics
Regeneration of dye-saturated quaternized cellulose by bisulfite-mediated borohydride reduction of dye azo groups: An improved process for decolorization of textile wastewaters

Cellulosics modified to contain quaternary ammonium groups have a strong affinity for anionic dyes. Therefore, ion exchangers based on quaternized cellulose or lignocellulose can be used to remove textile dyes from wastewater. However, restoration of exchanger binding capacity is poor using conventional, low-cost regenerants. Experiments were conducted with two monoazo dyes, Orange II (Acid Orange 7) and Remazol Red F3B (Reactive Red 180), to determine whether reductive cleavage of dye azo bonds improves exchanger regenerability. Treatment with the redox couple KBH4/NaHSO3 fully restored the binding capacity of Orange II-saturated quaternized cellulose. KBH4/NaHSO3 treatment of quaternized cellulose saturated with Remazol Red F3B (hydrolyzed, unreactive form) restored 74% of the exchanger binding capacity, which increased to 95% with a subsequent wash with NaOH or NaClO4. High-performance liquid chromatography was used to confirm that KBH4/NaHSO3 reductively cleaved dye azo bonds. Bisulfite was found to f...

Field of study: Environmental science