Miracle-dz/UniFAR-FTUs huggingface dataset:
Viability of Large‐ and Small‐Sized Adults in Fluctuating Vole Populations

Peak populations of many species of lemmings and voles contain adults 20-30% larger than adults found in low populations (the Chitty effect). What is the adaptive advantage of being large? We try to answer this question by analyzing the survival rates of large- and small-size adults of 4 Microtus species. Two alternative hypotheses are proposed to explain the adaptive value of large size. Large adults may be r-selected genotypes at an adaptive advantage in increasing populations. Microtus pennsyl- vanicus and male M. townsendii fit this alternative because the survival advantage of large size is positively related to population growth rate and negatively related to density. Alternatively, large adults may be a-selected genotypes at an adaptive advantage in high density populations when aggres- sion is important. Microtus californicus and M. ochrogaster fit this hypothesis because in these species the survival advantage of large size is positively related to density and negatively related to population growth rate. Thus large body size may be adaptive for quite contrary reasons in different species of cyclic voles and lemmings.
Application of an In Vivo Hepatic Triacylglycerol Production Method in the Setting of a High-Fat Diet in Mice

High-fat (HF) diets typically promote diet-induced obesity (DIO) and metabolic dysfunction (i.e., insulin resistance, hypertriglyceridemia, and hepatic steatosis). Dysfunction of triacylglycerol (TAG) metabolism may contribute to the development of hepatic steatosis, via increased de novo lipogenesis or repackaging of circulating nonesterified fatty acids (NEFAs). Hepatic TAG production (HTP) rate can be assessed through injecting mice with nonionic detergents that inhibit tissue lipoprotein lipase. Potential confounding effects of detergent-based HTP tests (HTPTs) used in longitudinal studies—including the impact on food intake, energy balance, and weight gain—have not been reported. To examine this, male C57BL/6J mice were fed a 10% or 60% kcal diet. After 4 weeks, the mice underwent an HTPT via poloxamer 407 intraperitoneal injections (1000 mg/kg). Weight gain, energy intake, and postabsorptive TAG levels normalized 7–10 days post-HTPT. The post-HTPT recovery of body weight and energy intake suggest that, in metabolic phenotyping studies, any additional sample collection should occur at least 7–10 days after the HTPT to reduce confounding effects. Diet-specific effects on HTP were also observed: HF-fed mice had reduced HTP, plasma TAG, and NEFA levels compared to controls. In conclusion, the current study highlights the procedural and physiological complexities associated with studying lipid metabolism using a HTPT in the DIO mouse model.
MicroRNA analysis of breast ductal fluid in breast cancer patients

Recent studies suggest that microRNAs show promise as excellent biomarkers for breast cancer; however there is still a high degree of variability between studies making the findings difficult to interpret. In addition to blood, ductal lavage (DL) and nipple aspirate fluids represent an excellent opportunity for biomarker detection because they can be obtained in a less invasive manner than biopsies and circumvent the limitations of evaluating blood biomarkers with regards to tissue of origin specificity. In this study, we have investigated for the first time, through a real-time PCR array, the expression of 742 miRNAs in the ductal lavage fluid collected from 22 women with unilateral breast tumors. We identified 17 differentially expressed miRNAs between tumor and paired normal samples from patients with ductal breast carcinoma. Most of these miRNAs have various roles in breast cancer tumorigenesis, invasion and metastasis, therapeutic response, or are associated with several clinical and pathological characteristics of breast tumors. Moreover, some miRNAs were also detected in other biological fluids of breast cancer patients such as serum (miR-23b, -133b, -181a, 338-3p, -625), plasma (miR-200a), and breast milk (miR-181a). A systems biology analysis of these differentially expressed miRNAs points out possible pathways and cellular processes previously described as having an important role in breast cancer such as Wnt, ErbB, MAPK, TGF-β, mTOR, PI3K-Akt, p53 signaling pathways. We also observed a difference in the miRNA expression with respect to the histological type of the tumors. In conclusion, our findings suggest that miRNA analysis of breast ductal fluid is feasible and potentially very useful for the detection of breast cancer.
Bronchoscopy Using Virtual Navigation and Endobronchial Ultrasonography with a Guide Sheath (EBUS-GS) with or without Fluoroscopy for Peripheral Pulmonary Lesions.

OBJECTIVE Endobronchial ultrasonography and guide sheath (EBUS-GS) technique has high diagnostic yield in lung nodules. Virtual bronchoscopic navigation (VBN) can lead bronchoscope to the target bronchi. The aim of this prospective study was to compare the diagnostic yield of two bronchoscopic procedures: bronchoscopy under EBUS-GS and VBN with or without x-ray fluoroscopy in small peripheral pulmonary lesions (PPLs, ≤30mm) with apparent CT-bronchus sign. METHODS 31 patients with PPLs which had apparent CT-bronchus sign were randomly assigned to the X-ray or the non-X-ray groups (18 with and 13 without fluoroscopy) between September 1, 2012, and September 30, 2015. A bronchoscope was introduced into the target bronchus using the VBN system. Sites of specimen sampling were verified using EBUS-GS with or without fluoroscopy. RESULTS The overall diagnostic yield was 83.3% in the X-ray and 69.2% in the non-X-ray group. The diagnostic yield of malignancy was 88.2% and 81.8%, respectively. The duration of the examination and time elapsed until the first EBUS visualization were similar in the X-ray and the non-X-ray group (9.0 (5.8-20.) min vs 11.0 (5.3-17.3) min, and 2.5 (1.3-14.2) min vs 4.1 (1.4-8.1) min, respectively). The fluoroscopy exposure time was 3.7 (2.9-10.56) min. The only adverse event was mild pneumothorax in a patient from the non-X-ray group, who had consequent TBB under fluoroscopy. CONCLUSIONS There was a possibility that VBN-guided EBUS-transbronchial diagnosis without fluoroscopy might be equivalent to that under fluoroscopy. Further multi-center randomized study may be desired. (UMIN000008592).
Identification of biomarkers for childhood obesity based on expressional correlation and functional similarity

The aim of the current study was to identify potential biomarkers of childhood obesity, and investigate molecular mechanisms and candidate agents in order to improve therapeutic strategies for childhood obesity. The GSE9624 gene expression profile was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in omental adipose tissues were analyzed with limma package by comparing samples from obese and normal control children. Two-way hierarchical clustering was applied using the pheatmap package. The co-expression (CE) analysis was performed using online CoExpress software. Subsequent to functional classification via the GOSim package, the gene network enriched by DEGs was visualized using the Cytoscape package. The codon usage bias of the DEGs was then examined using the CAI program from the European Molecular Biology Open Software Suite. In total, 583 DEGs (273 upregulated genes and 310 downregulated genes) were observed in the omental adipose tissues between samples from obese and normal control children. Hierarchical clustering identified a significant difference between samples from obese and normal control children. Subsequent to CE analysis, 130 DEGs, which were classified into 4 clusters, were selected. The following 3 upregulated and 2 downregulated genes were identified to be significant: Upregulated genes, microtubule-associated protein tau (MAPT), destrin (actin depolymerizing factor) (DSTN) and spectrin, β, non-erythrocytic 1 (SPTBN1); downregulated genes, Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) and spindle and kinetochore associated complex subunit 1 (SKA1). The top 3 amino acids were identified to be glycine, leucine and serine with a high bias. The DEGs MAPT, DSTN, SPTBN1, ARHGEF2 and SKA1 are suggested to be candidate biomarkers for childhood obesity.
Polydiglycosylphosphate Transferase PdtA (SCO2578) of Streptomyces coelicolor A3(2) Is Crucial for Proper Sporulation and Apical Tip Extension under Stress Conditions

ABSTRACT Although anionic glycopolymers are crucial components of the Gram-positive cell envelope, the relevance of anionic glycopolymers for vegetative growth and morphological differentiation of Streptomyces coelicolor A3(2) is unknown. Here, we show that the LytR-CpsA-Psr (LCP) protein PdtA (SCO2578), a TagV-like glycopolymer transferase, has a dual function in the S. coelicolor A3(2) life cycle. Despite the presence of 10 additional LCP homologs, PdtA is crucial for proper sporulation. The integrity of the spore envelope was severely affected in a pdtA deletion mutant, resulting in 34% nonviable spores. pdtA deletion caused a significant reduction in the polydiglycosylphosphate content of the spore envelope. Beyond that, apical tip extension and normal branching of vegetative mycelium were severely impaired on high-salt medium. This growth defect coincided with the mislocalization of peptidoglycan synthesis. Thus, PdtA itself or the polydiglycosylphosphate attached to the peptidoglycan by the glycopolymer transferase PdtA also has a crucial function in apical tip extension of vegetative hyphae under stress conditions. IMPORTANCE Anionic glycopolymers are underappreciated components of the Gram-positive cell envelope. They provide rigidity to the cell wall and position extracellular enzymes involved in peptidoglycan remodeling. Although Streptomyces coelicolor A3(2), the model organism for bacterial antibiotic production, is known to produce two distinct cell wall-linked glycopolymers, teichulosonic acid and polydiglycosylphosphate, the role of these glycopolymers in the S. coelicolor A3(2) life cycle has not been addressed so far. This study reveals a crucial function of the anionic glycopolymer polydiglycosylphosphate for the growth and morphological differentiation of S. coelicolor A3(2). Polydiglycosylphosphate is attached to the spore wall by the LytR-CpsA-Psr protein PdtA (SCO2578), a component of the Streptomyces spore wall-synthesizing complex (SSSC), to ensure the integrity of the spore envelope. Surprisingly, PdtA also has a crucial role in vegetative growth under stress conditions and is required for proper peptidoglycan incorporation during apical tip extension.
Comparison of 25 Gauge Cutting with Noncutting Needles for Post Dural Puncture Headache in Obstetric Patients

Introduction: Post dural puncture headache (PDPH) is the most common complication of dural puncture, occurring in up to 36.5% of spinal taps. Clinical and laboratory research have shown that use of small gauge needles particularly of the pencil point design is associated with lower incidence of PDPH then traditional cutting needles. Objective: To compare the frequency and severity of postdural puncture headache between 25G cutting and non cutting needles used for subarachnoid block in patients undergoing cesarean section. Study design: Randomized clinical trial Place and duration of study: Department of anesthesiology, Dow university of Health Sciences, Karachi, Pakistan, during January 10, 2008 to July 9, 2008 Subject and methods: Sixty consecutive under the age of 35 years with class ASA I and II women were enrolled and randomly divided into two groups of equal size with 30 women in each group. The frequency and severity of PDPH was compared between 25G cutting and non cutting needles in patients under going elective cesarean section under spinal anaesthesia. Results: The average age of the patients was 30.23 ± 6.6 years and 31.34 ± 5.6 in group I and group II respectively. There was no difference in baseline characteristics between groups as shown in Table 2. Lumbar puncture was successful in most of the patients in first attempt, 17 (90%) and 25 (83.3%) in group I and group II respectively. Out of 60 patients, 21.7% (13/60) patients had developed post dural puncture headache. Eleven (36.7%) of 30 patients had observed post dural puncture headache in group-I (25G cutting needles) and only 2 of 30 patients (6.7%) in group-II (25G non cutting needles). Severity of post dural puncture headache was significantly high in group-I than group-II on day 2 and day 3, (Chi-square test=8.56, df=3, P=0.036). None of the patients had traumatic punctures. Conclusion: The frequency and severity of PDPH was higher in 25G cutting spinal needle group as compared to non cutting needle.
The importance of food presentation for animal welfare and conservation

The feeding of all captive animals is more complex than offering a diet with the correct balance of nutrients; the diet should be offered in a manner that is appropriate for the reasons why that animal is kept in captivity. The roles of the modern zoo are to conserve species from extinction, to educate people about conservation, to provide a place of scientific research and to provide a place of public entertainment (Tudge, 1991). Underpinning these four roles is the welfare of the animals. Thus, an appropriate feeding programme for zoo-housed animals must consider the diet in terms of nutrients and how the diet is presented to the animals in terms of the four objectives of modern zoos and animal welfare. TYPE OF FOOD OFFERED TO CARNIVORES Within many of the world’s zoological collections three types of food are commonly offered to obligate carnivores such as felids; these are, whole carcasses, prepared (muscle) meat and complete (soft textured) diets. Each of these types of foods offered can create problems with physical health, animal welfare, re-introduction or animal husbandry.
Expression of Hyaluronidase-4 in a Rat Spinal Cord Hemisection Model

Study Design Examination of hyaluronidase-4 (Hyal-4) expression in a rat spinal cord hemisection model. Purpose To determine the status of Hyal-4 expression after hemisection of the spinal cord, and the relationship between its expression and that of chondroitin sulfate proteoglycans (CSPGs). Overview of Literature CSPGs are expressed at the site of spinal cord injury and inhibit axon regeneration. Administration of exogenous chrondroitinase ABC (ChABC), derived from bacteria, digested CSPGs and promoted axonal regrowth. Using a rat hemisection model, we have demonstrated peak CSPGs levels at by 3 weeks after injury but then decreased spontaneously. Could there be an endogenous enzyme similar to ChABC in the spinal cord? It has been suggested that Hyal-4 is involved in CSPG degradation. Methods A rat hemisection model was prepared and spinal cord frozen sections were prepared at 4 days and 1, 2, 3, 4, 5, and 6 weeks post-cordotomy and stained for CSPGs and Hyal-4 and subjected to Western blotting. Results CSPGs appeared at the injury site at 4 days after hemisection, reached a peak after 3 weeks, and then decreased. Hyal-4 was observed around the injury site from 4 days after cordotomy and increased until after 5-6 weeks. Double staining showed Hyal-4 around CSPGs. Western blotting identified a band corresponding to Hyal-4 from 4 days after hemisection. Conclusions Hyal-4 was expressed in a rat hemisection model in areas surrounding CSPGs, and as its peak was delayed compared with that of CSPGs. These results suggest the involvement of Hyal-4 in the digestion of CSPGs.
Chapter 2 Spatial Encoding – Basic Imaging Sequences

This chapter presents the basic techniques for generating images with magnetic resonance. First, the usage of gradients for slice selection, frequency and phase encoding is explained. The concept of k-space is introduced and imperfections of the encoding methods are demonstrated by means of the point spread function. The most prominent imaging techniques based on gradient and spin echo signals are presented. Finally, alternative encoding procedures are described briefly.
Analysis of the Isothermal Structure Development in Waxy Crude Oils under Quiescent Conditions

Isothermal crystallization and structure development was studied for three different waxy crude oils. The transformation from sol to gel was followed by small-amplitude dynamic rheometry, which closely tracks the development of the three-dimensional network as the initially formed crystallites grow, aggregate, and interact with each other. The kinetics of the crystallization-induced gelation was analyzed with the phenomenological Avrami model. The analysis was performed for a temperature range of about 15 K and was limited to the early stages of transformation. Both the Avrami exponent n and the rate constant k are dependent on the crystallization temperature, meaning that the nucleation and crystal growth mechanisms and rates are dependent on the degree of supercooling. Higher Avrami constants and lower Avrami coefficients (higher rate of crystal growth) were observed under higher supercooling conditions. The results discussed allowed the predominant mechanisms for nucleation and crystal growth, occurring as a function of temperature (i.e., supercooling degree) and waxy crude oil composition, to be defined.
Acetylation of WRN Protein Regulates Its Stability by Inhibiting Ubiquitination

Background WRN is a multi-functional protein involving DNA replication, recombination and repair. WRN acetylation has been demonstrated playing an important role in response to DNA damage. We previously found that WRN acetylation can regulate its enzymatic activities and nuclear distribution. Methodology/Principal Finding Here, we investigated the factors involved in WRN acetylation and found that CBP and p300 are the only major acetyltransferases for WRN acetylation. We further identified 6 lysine residues in WRN that are subject to acetylation. Interestingly, WRN acetylation can increase its protein stability. SIRT1-mediated deacetylation of WRN reverses this effect. CBP dramatically increases the half-life of wild type WRN, while mutation of these 6 lysine residues (WRN-6KR) abrogates this increase. We further found that WRN stability is regulated by the ubiquitination pathway and WRN acetylation by CBP significantly reduces its ubiquitination. Importantly, we found that WRN is strongly acetylated and stabilized in response to mitomycin C (MMC) treatment. H1299 cells stably expressing WRN-6KR, which mimics unacetylated WRN, display significantly higher MMC sensitivity compared with the cells expressing wild-type WRN. Conclusion/Significance Taken together, these data demonstrate that WRN acetylation regulates its stability and has significant implications regarding the role of acetylation on WRN function in response to DNA damage.
Relativistic electron energy loss and induced radiation emission in two-dimensional metallic photonic crystals. I. Formalism and surface plasmon polariton

A fully relativistic description of the electron energy loss and the induced radiation emission in arbitrary arrays of nonoverlapping metallic cylinders is presented in terms of the multiple scattering method on the basis of vector cylindrical waves. Numerical analysis is given for dilute and dense arrays of Aluminum cylinders with a nanoscale diameter. The results of the electron energy loss spectrum are well correlated with the dispersion relation of coupled surface plasmon polaritons, and can be interpreted with an effective medium approximation when the electron runs inside the arrays. In addition, the cavity modes localized in the grooves between the cylinders can strongly affect the electron energy loss spectrum.
Examining Trust for Organizational Collaborations via the Virtual World

Virtual worlds (VW) have paved a new and important channel for organizational collaborations. However, analysts have noted that several organizations that had invested in utilizing the VW as a nouveau channel for communication and collaboration are stepping back due to limited user response. Motivated by this observation, we propose a ‘virtual world trust-theoretic model’ for communication and collaborations in virtual worlds. The model, grounded in literature on organizational communication and trust, theoretically examines the role of trust in developing behavioural intentions for using this rich virtual communication medium for collaborations. We test the proposed model via data collected from 197 VW users in Singapore. Results establish the important roles of perceived structural assurance and perceived social presence for fostering user trust in VW. Our findings also indicate that user trust is a key factor in influencing organizational members to develop behavioural intention to use the VW for collaborations. Implications for research and practice are discussed.
Systematic Reviews and Meta- and Pooled Analyses Parental Tobacco Smoking and Acute Myeloid Leukemia The Childhood Leukemia International Consortium

The association between tobacco smoke and acute myeloid leukemia (AML) is well established in adults but not in children. Individual-level data on parental cigarette smoking were obtained from 12 case-control studies from the Childhood Leukemia International Consortium (CLIC, 1974 – 2012), including 1,330 AML cases diagnosed at age <15 years and 13,169 controls. We conducted pooled analyses of CLIC studies, as well as meta-analyses of CLIC and non-CLIC studies. Overall, maternal smoking before, during, or after pregnancy was not associated with childhood AML; there was a suggestion, however, that smoking during pregnancy was associated with an increased risk in Hispanics (odds ratio = 2.08, 95% confidence interval (CI): 1.20, 3.61) but not in other ethnic groups. By contrast, the odds ratios for paternal lifetime smoking were 1.34 (95% CI: 1.11, 1.62) and 1.18 (95% CI: 0.92, 1.51) in pooled and meta-analyses, respectively. Overall, increased risks from 1.2- to 1.3-fold were observed for pre- and postnatal smoking ( P < 0.05), with higher risks reported for heavy smokers. Associations with paternal smoking varied by histological type. Our analyses suggest an association between paternal smoking and childhood AML. The association with maternal smoking appears limited to Hispanic children, raising questions about ethnic differences in tobacco-related exposures and biological mechanisms, as well as study-specific biases.
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer observed community composition versus expected (r(2) = 0.95) compared with 515F-Y/806R (r(2) ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4-10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.