nils-herrmann/clean_scirepeval huggingface dataset:
Bayesian Scalar on Image Regression With Nonignorable Nonresponse

Medical imaging has become an increasingly important tool in screening, diagnosis, prognosis, and treatment of various diseases given its information visualization and quantitative assessment. The aim of this article is to develop a Bayesian scalar-on-image regression model to integrate high-dimensional imaging data and clinical data to predict cognitive, behavioral, or emotional outcomes, while allowing for nonignorable missing outcomes. Such a nonignorable nonresponse consideration is motivated by examining the association between baseline characteristics and cognitive abilities for 802 Alzheimer patients enrolled in the Alzheimer’s Disease Neuroimaging Initiative 1 (ADNI1), for which data are partially missing. Ignoring such missing data may distort the accuracy of statistical inference and provoke misleading results. To address this issue, we propose an imaging exponential tilting model to delineate the data missing mechanism and incorporate an instrumental variable to facilitate model identifiability followed by a Bayesian framework with Markov chain Monte Carlo algorithms to conduct statistical inference. This approach is validated in simulation studies where both the finite sample performance and asymptotic properties are evaluated and compared with the model with fully observed data and that with a misspecified ignorable missing mechanism. Our proposed methods are finally carried out on the ADNI1 dataset, which turns out to capture both of those clinical risk factors and imaging regions consistent with the existing literature that exhibits clinical significance.

Field of study: Mathematics
Pine needle and semi-permeable membrane device derived organochlorine compounds (OCPs) concentrations in air in Mersin Province to Taurus, Turkey

Organochlorine pesticides (OCPs) were analyzed in three different ages (half-, 1.5-, 2.5-year-old) for needles and semi permeable membrane devices (SPMDs) at three deployment periods from sea level to 1881 meter above sea level. Individual HCHs concentrations ranged between 1.4 and 129 pg/g fw depending on the age and sampling season while 2.5-year-old needles showed higher HCHs levels compared to half and 1.5- year-old. Correlation between elevation and HCH concentration in SPMDs was found but not in needle samples. Concentrations of HCHs in SPMDs indicated clearly cold condensation effect on accumulation in winter period and increased with altitude. Concentrations of DDTs in half and 1.5-year-old needles were lower than 2.5-year-old needles. The highest total concentration of DDTs was detected in 1-year-period SPMD. Higher concentrations were found in 2.5-year-old needles for other OCPs. Seasonal and altitude-dependent changes were not observed for other OCPs in SMPDs. Total accumulation of OCPs in SPMDs were found higher than in needles. On the contrary, an increased accumulation rate was observed for HCHs in SPMD. In general, Total concentrations of DDTs and HCHs were similar to total of other OCPs in all altitudes when dominating endosulfan wasnot taken into account in the computation of total concentration of other OCPs.

Field of study: Agricultural and Food sciences
Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii.

Mannosyl-3-phosphoglycerate phosphatase (MPGP) catalyzes the dephosphorylation of alpha-mannosyl-3-phosphoglycerate (MPG) to produce alpha-mannosylglycerate (MG). In the hyperthermophile Pyrococcus horikoshii, MPGP plays a role in a series of enzyme reactions that are involved in the MG-biosynthesis pathway, which is important for maintaining life under conditions of high salt concentration. Crystal structures of P. horikoshii MPGP (PhoMPGP) in the holo form and in the apo form lacking the magnesium ion were determined by the multiple-wavelength anomalous diffraction method using SeMet-substituted PhoMPGP. PhoMPGP consists of two domains: a core domain that is conserved in the haloacid dehalogenase superfamily and a cap domain that is specific to the C2B cap subclass of the superfamily. Apo-form crystals contain two PhoMPGP molecules: one in the open conformation and the other in the closed conformation. In holo-form crystals both of the two molecules are in the closed conformation with phosphate and magnesium ions. PhoMPGP has a specific hairpin loop that is bent towards the active site in the closed conformation of both the apo and holo forms. PhoMPGP has a cavity between the two domains which is considered to be the substrate-binding site as a phosphate ion is located in the cavity, mimicking the binding manner of the phosphate group of MPG. The cavity is sequestered in the closed conformation such that a conformational change is indispensable for the release of products. A salt bridge from the general acid/base Asp10 to Arg170 is observed in the holo-form PhoMPGP which is not present in the open form. The importance of the conformational change in the activity of PhoMPGP is discussed.

Field of study: Chemistry
Accounting for differences in estrogenic responses in rainbow trout (Oncorhynchus mykiss: Salmonidae) and roach (Rutilus rutilus: Cyprinidae) exposed to effluents from wastewater treatment works.

Effluents from wastewater treatment works (WwTWs) contain estrogenic substances that induce feminizing effects in fish, including vitellogenin (VTG) synthesis and gonadal intersex. Fish vary in their responsiveness to estrogenic effluents, but the physiological basis for these differences are not known. In this study, uptake of estrogen from two WwTW effluents (measured in hydrolyzed bile) and estrogenic response (VTG induction) were compared in a salmonid (rainbow trout, Onchorhynchus mykiss) and a cyprinid fish (roach, Rutilus rutilus). Immature rainbow trout were more responsive than maturing roach to the estrogenic effluents. The more potent of the two estrogenic effluents (containing between 24.3 and 104.1 ng estradiol-17beta equivalents/L [E2eq/L]) resulted in a 700-fold and 240-fold induction of plasma VTG in male and female trout, respectively, but only a 4-fold induction in roach (and in males only). The less potent effluent (varying between 4.1 and 6.8 ng E2eq/L) induced VTG in the trout only, with a 4-fold and 18-fold induction in males and females, respectively. In fish exposed to tap water, the estrogenicity of the hydrolyzed bile was 0.03+/-0.01 ng E2eq/microL (for both sexes in trout), 0.18+/-0.04 ng E2eq/microL in male roach, and 0.88+/-0.15 ng E2eq/microL in female roach. The higher bile content of estrogen in control roach reflected their more advanced sexual status (and thus higher endogenous estrogen) compared with the immature female trout. In trout maintained in effluents, the bile content of estrogen was 100-fold and 30-fold higher than controls at WwTW A and B, respectively. Bioconcentration factors (BCFs) for estrogenic activity in bile were between 16 344 and 46 134 in trout and between 3543 and 60 192 in roach (no gender differences were apparent). There were strong correlations between VTG induction and the estrogenic activity of bile extracts for both trout and roach. The results confirm that estrogenic contaminants bioconcentrate to a high degree in fish bile and that the level (and nature) of this accumulation may accountfor responsiveness to the endocrine disruptive effects of estrogenic effluents. Immature fish were the more appropriate life stage for quantifying estrogen exposure and uptake in bile, as they contain little circulating endogenous oestrogen compared with sexual maturing fish. The nature of the estrogenic contaminants is detailed in an accompanying paper.

Field of study: Environmental science
Finite temperature QCD with $$N_f=2+1+1$$ Wilson twisted mass fermions at physical pion, strange and charm masses

We discuss recent progress in studying Quantum Chromodynamics at finite temperature using $N_f=2+1+1$ Wilson twisted mass fermions. Particular interest is in QCD symmetries and their breaking and restoration. First, we discuss the behaviour of the $\eta'$ meson at finite temperature, which is tightly connected to the axial and chiral symmetries. The results suggest a small decrease of the $\eta'$ mass in the pseudo-critical region coming close to the non-anomalous contribution and subsequent growth at large temperatures. Second, we present the first results of lattice simulations of Quantum Chromodynamics with $N_f=2+1+1$ twisted mass Wilson fermions at physical pion, strange and charm masses. We estimate the chiral pseudo-critical temperatures for different observables. Our preliminary results are consistent with a second order transition in the chiral limit, however other scenarios are not excluded.

Field of study: Physics
Identification of MicroRNA-Target Gene-Transcription Factor Regulatory Networks in Colorectal Adenoma Using Microarray Expression Data

The aim of the study was to find the key genes, microRNAs (miRNAs) and transcription factors (TFs) and construct miRNA-target gene-TF regulatory networks to investigate the underlying molecular mechanism in colorectal adenoma (CRA).  Four mRNA expression datasets and one miRNA expression dataset were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) were identified between CRA and normal samples. Moreover, functional enrichment analysis for DEGs was carried out utilizing the Cytoscape-plugin, known as ClueGO. These DEGs were mapped to STRING database to construct a protein-protein interaction (PPI) network. Then, a miRNA-target gene regulatory network was established to screen key DEMs. In addition, similar workflow of the analyses were also performed comparing the CRC samples with CRA ones to screen key DEMs. Finally, miRNA-target gene-TF regulatory networks were constructed for these key DEMs using iRegulon plug-in in Cytoscape.  We identified 514 DEGs and 167 DEMs in CRA samples compared to healthy samples. Functional enrichment analysis revealed that these DEGs were significantly enriched in several terms and pathways, such as regulation of cell migration and bile secretion pathway. A PPI network was constructed including 325 nodes as well as 890 edges. A total of 59 DEGs and 65 DEMs were identified in CRC samples compared to CRA ones. In addition, Two key DEMs in CRA samples compared to healthy samples were identified, such as hsa-miR-34a and hsa-miR-96. One key DEM, hsa-miR-29c, which was identified when we compared the differentially expressed molecules found in the comparison CRA versus normal samples to the ones obtained in the comparison CRC versus CRA, was also identified in CRC samples compared to CRA ones. The miRNA-target gene-TF regulatory networks for these key miRNAs included two TFs, one TF and five TFs, respectively.  These identified key genes, miRNA, TFs and miRNA-target gene-TF regulatory networks associated with CRA, to a certain degree, may provide some hints to enable us to better understand the underlying pathogenesis of CRA.

Field of study: Biology
HIV‐1 induces tumour necrosis factor and IL‐1 gene expression in primary human macrophages independent of productive infection

Cylokines such as tumour necrosis factor‐alpha (TNF‐a) and IL‐Iβ may play a role in immunopalhogcncsis of AIDS, We studied early effects (05‐48 h) of monocytotropic (ADA) or tymp ho tropic (1MB) strains of HIV‐1 on TNF‐α and IL‐1β mRNA expression in primary human macrophages by a semi‐quantitative reverse transcriptase‐polymcrase chain reaction (RT‐PCR) assay. Three‐day‐old monocyte‐derived macrophages were exposed either to tissue culture supernatants containing virus (at multiplicity of infection (m.o.i.) of 005) or to control supernatants frceofvirionsandgpI20. ADA strain, but not IIIB. replicated in primary tissue culture‐differentiated macrophages (TCDM). Soluble CD4 (sC D4) was used to inhibit binding of both strains to macrophages. We found that TNF‐arand IL‐lβ gene expression was induced by both strains 0‐5‐3 hafter addition of virus, and that enhanced expression of both cytokines was inhibited by sCD4. We conclude that C D4‐dependcnl binding lo ihc cell surface is sufficient to enhance TNI′‐α and ll.‐lβ mRNA. whereas productive viral replication in primary human macrophages is not required. Therefore, similar pathways regulate gene expression of TNF‐a and IL‐Iβ by macrophages during initial infection by HIV‐1 in vitro.

Field of study: Biology, Medicine
Buying Happiness in an Unequal World: Rank of Income More Strongly Predicts Well-Being in More Unequal Countries

Does income rank matter more for well-being in more unequal countries? Using more than 160,000 observations from 24 countries worldwide, we replicate previous studies and show that the ranked position of an individual’s income strongly predicts life evaluation and positive daily emotional experiences, whereas absolute and reference income generally have weak or no effects. Furthermore, we find the association between income rank and an individual’s well-being to be significantly larger in countries where income inequality, represented by the share of taxable income held by the top 1% of income earners, is high. These results are robust to using an alternative measure of income inequality and different reference group specifications. Our findings suggest that people in more unequal societies place greater weight on the pursuit of higher income ranks, which may contribute to enduring income inequality in places where greater well-being can be bought from moving up the income ladder.

Field of study: Psychology
The activation and inhibition of 5-nucleotidase.

The activation and inhibition of 5-nucleotidase have not been much studied. According to previous papers by Reis (1937, 1950) magnesium activates this enzyme to a much smaller extent than it does the non-specific phosphomonoesterase 'alkaline phosphatase'. Kaye (1955) mentions that zinc inhibits 5-nucleotidase, but his evidence in scanty. We have limited our study to human tissues, and have used aorta wall as a source of 5-nucleotidase, where it is free from non-specific phosphatase activity, and placenta, which has both enzymes.

Field of study: Biology, Computer science
Eocene Vertebrates, Coprolites, and Plants in the Golden Valley Formation of Western North Dakota

An early Eocene date for the origin of the Golden Valley Formation in North Dakota is confirmed by the discovery of fossil fish, amphibians, reptiles, birds, and mammals. Riparian and aquatic animals and plants that were associated in this early Tertiary biofacies indicate warm, humid, swampy lowlands with subtropical forests bordering sluggish streams. Montmorillonite in the formation may represent ash from volcanoes to the west.

Field of study: Geology
A three-state biological point process model and its parameter estimation

The Poisson random process is widely used to describe experiments involving discrete arrival data. However, for creating models of egg-laying behavior in neural biology studies on the nematode C. elegans, we have found that homogeneous Poisson processes are inadequate to capture the measured temporal patterns. We present here a novel three-state model that effectively represents the measured temporal patterns and that correlates well with the cellular and molecular mechanisms that are known to be responsible for the measured behavior. Although the model involves a combination of two Poisson processes, it is surprisingly tractable. We derive closed-form expressions for the probabilistic and statistical properties of the model and present a maximum likelihood method to estimate its parameters. Both simulated and experimental results are illustrated. The experiments with measured data show that the egg-laying patterns fit the three-state model very well. The model also may be applicable in quantifying the link between other neural processes and behaviors or in other situations where discrete events occur in clusters.

Field of study: Engineering
AOA Pseudolinear Target Motion Analysis in the Presence of Sensor Location Errors

This paper presents new pseudolinear estimation algorithms for angle-of-arrival (AOA) target motion analysis when the sensor locations are not precisely known. Sensor location errors can cause significant performance degradation for the existing pseudolinear estimator (PLE) and its variants. In particular, we analytically show that, in the presence of sensor location errors, the well-known weighted instrumental variable estimator (WIVE) is no longer asymptotically unbiased due to the non-vanishing correlation between the instrumental variable matrix and the pseudolinear noise vector. To ameliorate this bias problem, a novel bias compensation method is developed for the WIVE, which is proven to be approximately efficient for a large number of measurements under the small noise assumption. In addition, a selective-angle-measurement (SAM) strategy is integrated into the bias-compensated WIVE (BCWIVE) to strengthen the correlation between the instrumental variable matrix and the measurement matrix, alleviating the performance degradation in large AOA and sensor location noises, and unfavourable geometries. The performance advantages of the proposed BCWIVE and SAM-BCWIVE over the PLE, its WIVE variants and the maximum likelihood estimator are demonstrated by way of extensive simulation examples.

Field of study: Engineering
Assessment of Urea Appearance Rates and Net Nitrogen Deficits in Patients With Acute Renal Failure Receiving Continuous Venovenous Hemofiltration

To investigate the impact of the nutritional regimen on the urea appearance rate (UAR) and net nitrogen deficit (NND) in patients with acute renal failure (ARF) receiving continuous venovenous hemofiltration (CWH). Comparison of estimated energy expenditure using a modification of the Harris-Benedict equation versus measured energy expenditure was performed.  Noninterventional study with prospective data collection.  Tertiary care hospital.  Forty consecutive patients age 52 ± 20 years (mean ± SD) with ARF who required CWH between June 1991 and June 1992.  Noninterventional study. ■  UAR and NND were calculated for each study day. Total calories, nonprotein calories, and grams of protein per day, and estimated energy needs were quantified for all patients. Energy expenditure was measured for 10 patients.  Patients were treated with CWH for a total of 357 days. Estimated energy needs (2,408 ± 515 kcal/d) correlated well with measured energy needs (2,348 ± 706 kcal/d; r = 0.78). The mean UAR was 13.2 ± 4.7 g N/d. There was no difference in mean UAR between patients receiving less than 1.0 g versus 1.0 g or more of protein/kg/d. The mean NND was −8.3 ± 6.1 g N/d. Those patients receiving 1.0 g or more of protein/kg/d (n = 16) had a significantly lower NND than those patients who received less. Five patients receiving 1.0 g or more of protein/kg/d achieved a positive nitrogen balance. These patients had a nonprotein calorie-to-nitrogen ratio (132 ± 37) that was significantly less than that administered to patients who did not achieve a positive nitrogen balance (169 ± 33; P > 0.05).  Estimated energy expenditures using a modified Harris-Benedict equation provided moderate predictability with measured energy expenditures. The provision of 1.0 g or more of protein/kg/d did not increase the UAR and was associated with a decreased NND. The provision of a lower nonprotein calorie-to-nitrogen ratio in patients receiving 1.0 g or more of protein/kg/d was associated with a positive nitrogen balance.

Field of study: Medicine
The determination of N,N-dimethyl-4-aminoazobenzene and its reduction products by anodic voltammetry at a glassy carbon electrode

The oxidation of N,N-dimethl-4-aminoazobenzene at a rotating and stationary glassy carbon disk electrode in a medium of 40% (v/v) acetic acid was studied in the framework of a systematic study of methods for determing the efficiency of the destruction of the genotoxic derivatives of this substance; conditions were found for the determination using direct current and differential pulse voltammetry. Analogous conditions were used to determine aniline, N,N-dimethylaniline and N,N-dimethyl- p -phenylendiamine as model substances representing possible products of the reductive splitting of genotoxic azocompounds. The determination limit of the method is less than 1 . 10 -5 mol l -1 and its selectivity is completely satisfactory for controlling the efficiency of the destruction.

Field of study: Chemistry
shou shu zhi liao da mian ji nao geng si he bing xiao nao mu qie ji zuo 60 li lin chuang fen xi

目的 提高幕上大面积脑梗死合并小脑幕切迹疝患者救治成功率.方法 采取去骨瓣减压术联合小脑幕切开术对60例幕上大面积脑梗死合并小脑幕切迹疝进行手术治疗.结果 60例患者,死亡9例与既往病例相比该方法提高治愈率,降低病死率.结论去骨瓣减压术联合小脑幕切开术对大面积脑梗死合并小脑幕切迹疝有效的治疗方法.

Field of study: Medicine
Interfacial Reaction of Molten Sn on a Strained Cu
Electroplated Layer

Interfacial reactions of molten Sn on a Cu electroplated layer with and without strain were investigated. A Cu layer electroplated on a rectangular Si substrate was subjected to tensile stress by bending the Si substrate on a three-point bending apparatus. Two intermetallic compounds, Cu6Sn5 and Cu3Sn, were formed at the Sn/Cu interface after reflow at 260°C for 10 min to 30 min, regardless of the strain. Top-view examination revealed that the tensile strain had significant effects on the surface morphology of the Cu6Sn5 grains. On the nonstrained Cu layer, ovoid-shaped Cu6Sn5 grains were formed first after soldering, but long, prismatic Cu6Sn5 grains precipitated on the existing ovoid-shaped grains after solidification in air. On the strained Cu layer, only ovoid-shaped Cu6Sn5 grains but no long, prismatic ones were found after solidification. A possible mechanism is proposed to explain the absence of long, prismatic Cu6Sn5 grains on the strained Cu layer.

Field of study: Materials science
Relationship Between Pharmacy Students’ Use of Self-Regulated Learning Strategies and Course Outcomes

To determine the relationship between student-reported, self-regulated learning (SRL) with use of supplementary material, and overall performance in an advanced therapeutics course in a Doctor of Pharmacy program.  A modified version of the Self-Regulated Strategy Inventory (SRSI-SI) was used to measure three distinct SRL factors: managing study behaviors, managing environment, and maladaptive regulatory behaviors. An instructor created a supplemental 36-question practice quiz and flashcard activity. The in-class assessment and the three SRL factors were analyzed using the practice quiz, and the association between overall course grade and score in each factor domain was determined by regression.  Two-hundred seven students (98%) completed the SRSI. One hundred fifty-eight (79%) students reported using the optional practice quiz and doing so was associated with significantly higher in-class quiz scores (8.2 vs 7.6 out of 10) and higher overall course grade (88.0% vs 85.3%). Students reporting use of the optional practice quiz were significantly less likely to report poor study behaviors, inability to manage study environment, and maladaptive study habits. Lower overall course grades were significantly associated with maladaptive study habits.  A positive association was determined between use of instructor-created supplemental activities and in-class quiz scores, self-regulated study behaviors, and overall course performance. Maladaptive study habits were associated with a modest negative correlation with overall course grade. The results suggest that when instructors create optional supplementary activities and assessments, many of the students who would benefit the most from the use of these activities fail to utilize the opportunity for extra practice.

Field of study: Education, Medicine