Miracle-dz/UniFAR-FTUs huggingface dataset:
American Journal of Epidemiology Original Contribution Circulating 25-hydroxyvitamin D and Risk of Kidney Cancer Cohort Consortium Vitamin D Pooling Project of Rarer Cancers

which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Although the kidney is a major organ for vitamin D metabolism, activity, and calcium-related homeostasis, little is known about whether this nutrient plays a role in the development or the inhibition of kidney cancer. To address this gap in knowledge, the authors examined the association between circulating 25-hydroxyvitamin D (25(OH)D) and kidney cancer within a large, nested case-control study developed as part of the Cohort Consortium Vitamin D Pooling Project of Rarer Cancers. Concentrations of 25(OH)D were measured from 775 kidney cancer cases and 775 age-, sex-, race-, and season-matched controls from 8 prospective cohort studies. Overall, neither low nor high concentrations of circulating 25(OH)D were significantly associated with kidney cancer risk. Although the data showed a statistically significant decreased risk for females (odds ratio ¼ 0.31, 95% confidence interval: 0.12, 0.85) with 25(OH)D concentrations of 75 nmol/L, the linear trend was not statistically significant and the number of cases in this category was small (n ¼ 14). The findings from this consortium-based study do not support the hypothesis that vitamin D is inversely associated with the risk of kidney cancer overall or with renal cell carcinoma specifically. In the United States, kidney cancer incidence has been increasing at a rate of approximately 2% per year and accounts for 2.6% of all newly diagnosed cancer cases (1). Renal cell carcinoma is the most common type of kidney cancer, and incidence rates of this histologic type are twice as high among males compared with females (2). The established risk factors for renal cell carcinoma are cigarette smoking, hypertension, and obesity (3). Recent widespread interest has focused on the health-promoting effects of vitamin D, the ''sunshine'' vitamin. Vitamin D is well known for its role in promoting bone health through the regulation of bone growth and remodel-ing as well as calcium homeostasis (4). In addition, there is increasing laboratory evidence that vitamin D is an anticarcinogenic agent (4, 5). Vitamin D is obtained from exposure to ultraviolet light (sunlight) and certain foods such as oily fish and vitamin-D-fortified milk, orange juice, and cereal. It is metabolized to 25-hydroxyvitamin D (25(OH)D), the accepted biomarker of vitamin D status (6), which is activated to 1,25 dihydroxyvitamin D in the kidney. This
Significance of Pretreatment Hemoglobin-Albumin-Lymphocyte-Platelet Index for the Prediction of Suboptimal Surgery in Epithelial Ovarian Cancer

Background Epithelial ovarian cancer (EOC) is the leading cause of death in gynecological cancers in developed countries. In recent years, there has been a growing need for economical and accurate pretreatment laboratory investigations to assess the prognosis of patients with advanced EOC (AEOC). We aimed to investigate the role of the hemoglobin-albumin-lymphocyte-platelet (HALP) index in suboptimal cytoreduction and oncological outcomes. Methods A prognostic prediction model for diagnosing suboptimal cytoreduction for patients with AEOC receiving neoadjuvant chemotherapy (NACT) was developed. Multivariate logistic regression analysis was performed to identify the independent predictors of suboptimal cytoreduction, with a P-value < 0.05, and then transformed into risk-scoring systems. Internal validation was performed using the bootstrapping procedure, and predictive cytoreduction (PSC) scores were compared using non-parametric receiver operating characteristic (ROC) regression. Survival analysis was performed using Kaplan-Meier estimation and Cox proportional regression. Results In total, 473 patients were analyzed, and the rate of suboptimal surgery was 43%. A scoring system in predicting suboptimal cytoreduction included age, cancer antigen (CA)-125 level before surgery, performance status, cycles of chemotherapy, peritoneal cancer index, and HALP index ≤ 22.6. The model had good discriminative ability (area under the ROC (AUROC), 0.80; 95% confidence interval (CI), 0.76 - 0.84), outperforming the PSC score (AUROC, 0.75; 95% CI, 0.71 - 0.80). The score was divided into the low-risk (positive predictive value (PPV), 22.4; 95% CI, 17.8 - 27.7), moderate-risk (PPV, 65.9; 95% CI, 56.9 - 74.0), and high-risk (PPV, 90.6; 95% CI, 79.3 - 96.9) groups. The HALP index score of ≤ 22.6 was independently associated with progression-free survival (hazard ratio (HR), 2.92; 95% CI, 1.58 - 5.40) and overall survival (HR, 2.66; 95% CI, 1.57 - 4.49). Conclusion The HALP index is a newly predicted factor for suboptimal cytoreduction and oncological outcomes in patients with AEOC after NACT.
The Corticostriatal System in Dissociated Cell Culture

The sparse connectivity within the striatum in vivo makes the investigation of individual corticostriatal synapses very difficult. Most studies of the corticostriatal input have been done using electrical stimulation under conditions where it is hard to identify the precise origin of the cortical input. We have employed an in vitro dissociated cell culture system that allows the identification of individual corticostriatal pairs and have been developing methods to study individual neuron inputs to striatal neurons. In mixed corticostriatal cultures, neurons had resting activity similar to the system in vivo. Up/down states were obvious and seemed to encompass the entire culture. Mixed cultures of cortical neurons from transgenic mice expressing green fluorescent protein with striatal neurons from wild-type mice of the same developmental stage allowed visual identification of individual candidate corticostriatal pairs. Recordings were performed between 12 and 37 days in vitro (DIV). To investigate synaptic connections we recorded from 69 corticostriatal pairs of which 44 were connected in one direction and 25 reciprocally. Of these connections 41 were corticostriatal (nine inhibitory) and 53 striatocortical (all inhibitory). The observed excitatory responses were of variable amplitude (−10 to −370 pA, n = 32). We found the connections very secure – with negligible failures on repeated stimulation (approximately 1 Hz) of the cortical neuron. Inhibitory corticostriatal responses were also observed (−13 to −314 pA, n = 9). Possibly due to the mixed type of culture we found an inhibitory striatocortical response (−14 to −598 pA, n = 53). We are now recording from neurons in separate compartments to more closely emulate neuroanatomical conditions but still with the possibility of the easier identification of the connectivity.
Pregnancy Experiences of First-Time Fathers in Iran: A Qualitative Interview Study

Background: Fatherhood, similarly to motherhood, is an important role and responsibility. For accepting this role, one needs to be well-prepared. Awareness of father’s experiences of pregnancy can help us to develop plans for the promotion of the role of fatherhood. Objectives: The purpose of this study was to explore how first time fathers describe their experiences of pregnancy. Patients and Methods: The data in this qualitative study were collected by individual open-ended interviews in five public health prenatal care clinics in Tehran, Iran, during 2010 ‒ 2011. Participants were 26 Iranian and Moslem first-time fathers living in Tehran, whose partner was in the 32th to 40th week of her normal pregnancy. Qualitative content text analysis was used for analyzing interviews. Results: Through analysis of fathers’ experiences of their wives’ pregnancy, four categories, as well as associated subcategories, emerged. The categories include: “Emotional responses to pregnancy, Feeling of change, Accepting the reality and satisfaction, Developing identity as a father. ” These categories describe the phenomenon of “Transition to fatherhood”. Conclusions: Transition to fatherhood extends beyond only moderate mental and social changes, and may be influenced by cultural background and beliefs. Therefore, caregivers should be aware of fathers' changes and needs during pregnancy, and support them while taking into consideration their culture and beliefs.
Modeling Virus Self-Assembly Pathways: Avoiding Dynamics Using Geometric Constraint Decomposition

We develop a model for elucidating the assembly pathways by which an icosahedral viral shell forms from 60 identical constituent protein monomers. This poorly understood process a remarkable example of macromolecular self-assembly occuring in nature and possesses many features that are desirable while engineering self-assembly at the nanoscale. The model uses static geometric and tensegrity constraints to represent the driving (weak) forces that cause a viral shell to assemble and hold it together. The goal is to answer focused questions about the structural properties of a successful assembly pathway. Pathways and their properties are carefully defined and computed using computational algebra and geometry, specifically state-of-art concepts in geometric constraint decomposition. The model is analyzable and refinable and avoids expensive dynamics. We show that it has a provably tractable and accurate computational simulation and that its predictions are roughly consistent with known information about viral shell assembly. Justifications for mathematical and biochemical assumptions are provided, and comparisons are drawn with other virus assembly models. A method for more conclusive experimental validation involving specific viruses is sketched. Overall, the paper indicates a strong and direct, mutually beneficial interplay between (a) the concepts underlying macromolecular assembly; and (b) a wide variety of established as well as novel concepts from combinatorial and computational algebra, geometry and algebraic complexity.
Effect of D-mannitol on nitrogen retention, fiber digestibility and digesta transit time in adult rabbits.

The aim of the current study was to elucidate the effect of gastrointestinal retention time of digesta on fiber digestibility in adult rabbits fed indigestible, but fermentable, sugar D-mannitol. Six adult rabbits were fed alternately a commercial diet containing 5% glucose and a diet containing D-mannitol. Total feces and urine were collected during the experimental period. Nitrogen (N) balance, digestibility of nutrients, and gastrointestinal mean retention time (MRT) were measured. The results indicated that urinary excretion was significantly lowered, whereas N retention and N accumulation rates were significantly increased in the D-mannitol group compared with the glucose group (P < 0.05). However, fecal N excretion was unaffected. Absorption of crude ash (CA) and acid detergent fiber (ADF) digestibility were significantly higher in the D-mannitol group compared with the glucose group (P < 0.05). The addition of D-mannitol to the diet did not affect the MRT of liquid digesta, but increased the MRT of solid digesta compared with the glucose group (P < 0.05). These results suggest that the addition of D-mannitol to the diet stimulates cecal bacterial growth, thereby increasing N utilization and digesta retention time.
Metabolic Syndrome and Other Cardiovascular Risk Factors Among Police Officers

Background: Police force constitutes a special occupational group. They have been shown to be at high risk for the development of cardiovascular diseases. A multitude of factors may be responsible for this. There is very limited documentation of their health status and health surveillance activities are inadequate. Aim: The present study was designed to measure the prevalence of metabolic syndrome and other cardiovascular risk factors among police officers. Materials and Methods: The design was cross-sectional and spanned 900 policemen (n = 900). A pre-tested questionnaire was used for collecting historical data. Anthropometric and biochemical measurements were carried out using standard techniques. MS was diagnosed using the National Cholesterol Education Program—Adult Treatment Panel III criteria. Statistical analysis was performed using the SPSS 16.0 software. Results: MS was observed in 16.8% of the study population. High blood pressure and hyper-triglyceridemia were the commonest abnormalities. The prevalence of other cardiovascular risk factors were high body mass index (65.6%), hypertension (37.7%), diabetes (7%), smoking (10%), and alcohol use (48%). Conclusion: Our study identified police officers as a high-risk group for developing CVDs. The findings underscore the need for regular surveillance and lifestyle interventions in this important occupational group.
Nervous system adverse responses to topiramate in the treatment of neuropsychiatric disorders

Importance of the field: Nervous system adverse drug reactions (NS-ADRs), such as cognitive complaints and paresthesia, are among the most frequent and clinically important ADRs of topiramate. Studying ADR profiles across disorders is clinically relevant because treatment decision-making in neuropsychiatry is highly guided by ADR profiles. Areas covered in this review: We used medline searches (until July 2009) to review the NS-ADRs of topiramate across the most investigated topiramate indications: alcohol dependence, essential tremor, binge-eating disorder, bulimia nervosa, migraine and epilepsy. We compared NS-ADRs between these disorders but did not carry out meta-analysis. What the reader will gain: ADR profiles greatly differed between disorders. Drop-outs due to ADRs highly varied between disorders: from 2% in the bulimia nervosa group to 29% in the migraine group. Paresthesia was the most common NS-ADR for all disorders but frequencies also differed between disorders. Cognitive complaints were frequent and were reported in comparable proportions. Take home message: When prescribing topiramate in neuropsychiatry, physicians should be aware that NS-ADR profiles have been found to differ between disorders. Differences in drop-out rates due to ADRs and in frequencies of specific NS-ADRs across disorders must be taken into account when evaluating the potential harm of topiramate in clinical practice.
Nitric oxide synthases in heart failure.

SIGNIFICANCE The regulation of myocardial function by constitutive nitric oxide synthases (NOS) is important for the maintenance of myocardial Ca(2+) homeostasis, relaxation and distensibility, and protection from arrhythmia and abnormal stress stimuli. However, sustained insults such as diabetes, hypertension, hemodynamic overload, and atrial fibrillation lead to dysfunctional NOS activity with superoxide produced instead of NO and worse pathophysiology. RECENT ADVANCES Major strides in understanding the role of normal and abnormal constitutive NOS in the heart have revealed molecular targets by which NO modulates myocyte function and morphology, the role and nature of post-translational modifications of NOS, and factors controlling nitroso-redox balance. Localized and differential signaling from NOS1 (neuronal) versus NOS3 (endothelial) isoforms are being identified, as are methods to restore NOS function in heart disease. CRITICAL ISSUES Abnormal NOS signaling plays a key role in many cardiac disorders, while targeted modulation may potentially reverse this pathogenic source of oxidative stress. FUTURE DIRECTIONS Improvements in the clinical translation of potent modulators of NOS function/dysfunction may ultimately provide a powerful new treatment for many hearts diseases that are fueled by nitroso-redox imbalance.
On Mentoring

As academic clinicians and investigators, it is important to facilitate the training of young investigators and clinicians so they can become knowledgeable, competent, and independent in their careers. This process of mentoring is a form of facilitative learning that has its origins extending thousands of years. It began with the “oral law” or the passing down of knowledge from generation to generation in many cultures such as the tribes in Africa, Native Americans, and Orthodox Judaism. This process allows for the continuation of traditional values and, with regard to the field of medicine, can preserve medical and scientific knowledge and wisdom through apprenticeship, where the protégés later become mentors to future generations. Within academic medicine, this process has become formalized through training grants from the National Institutes of Health (e.g., T32 awards), preceptorships, residencies, and fellowships. Yet, there has been limited attention to the process of mentoring. How should the mentor and mentee interact? What are the goals, benefits, and challenges of mentoring? Finally, how do we judge success? This column sets forth some suggested guidelines for trainee supervision through a mentoring relationship with a senior faculty member in a research or clinical environment.
Spatial Variation of Slip Behavior Beneath the Alaska Peninsula Along Alaska‐Aleutian Subduction Zone

We resurveyed preexisting campaign Global Positioning System (GPS) sites and estimated a highly precise GPS velocity field for the Alaska Peninsula. We use the TDEFNODE software to model the slip deficit distribution using the new GPS velocities. We find systematic misfits to the vertical velocities from the optimal model that fits the horizontal velocities well, which cannot be explained by altering the slip distribution, so we use only the horizontal velocities in the study. Locations of three boundaries that mark significant along‐strike change in the locking distribution are identified. The Kodiak segment is strongly locked, the Semidi segment is intermediate, the Shumagin segment is weakly locked, and the Sanak segment is dominantly creeping. We suggest that a change in preexisting plate fabric orientation on the downgoing plate has an important control on the along‐strike variation in the megathrust locking distribution and subduction seismicity.
Assessment of the Northern Rockfish stock in the Bering Sea/Aleutian Islands

1) Catch data was updated through 2018, and total catch for 2019 was projected. 2) The 2018 AI survey biomass estimate and age composition was included in the assessment. 3) The 2016 AI survey age composition replaced the 2016 survey length composition, and the 2018 AI survey age compositions were included in the assessment. 4) The 2015 fishery age composition replaced the 2015 fishery length composition, and the 2017 fishery age composition was included in the assessment. 5) The 2016 and 2018 fishery length composition data were included in the assessment. 6) The fishery and survey age compositions were recomputed by applying subarea (i.e., not global) age-length keys to subarea length compositions, due to spatial differences in size at age. 7) Separate weight at age curves were computed for the fishery and the population, and each were computed as an average of subarea weights at age (weighted by subarea survey abundance and fishery catch, respectively).
Crystal structure of human selenocysteine tRNA

Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNASec. tRNASec has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNASec has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNASec. Instead, tRNASec has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNASec to be the target of the Sec synthesis/incorporation machineries.
The Influence of Arabinoxylan on the Properties of Sourdough Wheat Bread

Sourdough bread is a traditional product made using lactic acid bacteria (LAB) and yeast. The influence of rye arabinoxylans (AXs) of different molar masses on sourdough wheat bread has not been studied to date. The aim of this study was to research the influence of arabinoxylans of different molar masses on the properties of sourdough wheat bread. The breads were baked using the sourdough method with wheat flour without and with 1% or 2% rye AX with different molar masses, which were unmodified, partially enzymatically hydrolyzed and cross-linked. The addition of all the AX preparations significantly increased the water absorption of the wheat flour. In particular, the addition of the preparation of cross-linked arabinoxylans at an amount of 2% caused the highest increase (by 9.8%) in the addition of water to the wheat flour dough. It was shown that a 2% addition of partially hydrolyzed AXs, with a low molar mass (190,440 g/mol), had the highest influence on increasing (by 23.7%) the volume of the bread and decreasing (by 41%) the crumb hardness of the sourdough bread, determined on the day of baking. The addition of the cross-linked AXs at an amount of 2% had the strongest influence on increasing the moisture content of the crumbs on the day of baking, both in the central (by 2.6%) and peripheral (by 5.1%) parts of the bread compared to the bread without the addition of AXs. The breads with all the AX preparations after the first and third days of storage had a higher crumb moisture content compared to the bread without the AXs.
Complexity of lower extremity peripheral artery disease reflects the complexity of coronary artery disease

We investigated the relationship between peripheral artery disease complexity and coronary artery disease complexity in patients with peripheral artery disease. A total of 449 patients were enrolled. SYNTAX score, a marker of coronary artery disease complexity, was assessed by dedicated computer software and complexity of peripheral artery disease was determined by Trans Atlantic Inter-Society Consensus II classification. The SYNTAX score of patients with minimal peripheral artery disease, Trans Atlantic Inter-Society Consensus A, Trans Atlantic Inter-Society Consensus B, Trans Atlantic Inter-Society Consensus C and Trans Atlantic Inter-Society Consensus D were 5 (11), 12.5 (13.25), 20 (14), 20.5 (19) and 27.5 (19), respectively (values in brackets represent the interquartile range). SYNTAX score and Trans Atlantic Inter-Society Consensus class was moderately correlated (r = 0.495, p < 0.001). In multivariate regression analysis male sex (B = 0.169, p < 0.001, CI95% = 0.270–0.735), Log10 SYNTAX score (B = 0.282, p < 0.001, CI95% = 0.431–0.782), Log10 creatinine (B = 0.081, p = 0.036, CI95% = 0.043–1.239), low-density lipoprotein (B = 0.114, p = 0.003, CI95% = 0.001–0.006) and high-density lipoprotein (B = −0.360, p < 0.001, CI95% = −0.063 to −0.041) were the independent predictors of Trans Atlantic Inter-Society Consensus II class. We have shown that patients with complex peripheral artery disease had complex coronary artery disease.