Miracle-dz/UniFAR-FTUs huggingface dataset:
llus Reduction during Bird Evolution

Background: One of the most puzzling events in evolution is the reduction and loss of the phallus in birds. All birds reproduce by internal fertilization, but only w3% of birds have retained a phallus capable of intromission. A number of hypotheses have been proposed for the evolutionary mechanisms that drove phallus reduction; however, the underlying developmental mechanisms are unknown. Results: We investigated genital development in two sister clades of birds, Galliformes (land fowl), most of which lack an intromittent phallus, and Anseriformes (waterfowl), which have well developed phalluses; and in two outgroups, Paleognathae (emus) and Crocodilia (alligators). Galliform embryos undergo cryptic development of a genital tubercle, the precursor of the phallus, but this later undergoes apoptosis, leading to regression of the tubercle. At the molecular level, a derived pattern ofBmp4 expression was identified in chick (a galliform) genital tubercles. Inhibition of Bmp signaling in chick genitalia rescues cells from apoptosis and prevents phallus regression, whereas activation of Bmp signaling in duck (an anseriform) genitalia induces a galliform-like pattern of apoptosis. Thus, distal Bmp activity is necessary and sufficient to induce apoptosis in Galloanserae genital tubercles. Conclusions: Our results indicate that evolutionary reduction of the intromittent phallus in galliform birds occurred not by disruption of outgrowth signals but by de novo activation of cell death by Bmp4 in the genital tubercle. These findings, together with discoveries implicating Bmps in evolution of beak shape, feathers, and toothlessness, suggest that modulation of Bmp gene regulation played a major role in the evolution of avian morphology.
Age-related decrease in resting energy expenditure in sedentary white women: effects of regional differences in lean and fat mass.

BACKGROUND Lean mass and resting energy expenditure (REE) decrease with age. However, it is unknown whether age-related changes in regional lean and fat mass are responsible for the age-related decrease in REE. OBJECTIVE Our objective was to determine how regional lean and fat mass vary with age and whether age is independently related to REE after adjustment for regional fat and lean mass. DESIGN The study was a cross-sectional evaluation of 58 white women aged 23-77 y. Regional and whole-body lean and fat mass were measured by dual-energy X-ray absorptiometry, subcutaneous abdominal tissue (SAT) and intraabdominal adipose tissue (IAF) by computed tomography, and REE by ventilated-canopy indirect calorimetry. RESULTS Independent of other significant correlates, age was significantly and independently associated with greater IAF (beta = 0.49) and less leg lean mass (beta = -0.35). IAF (r = -0.28) and IAF:SAT (r = -0.31) correlated negatively with REE. REE was negatively associated with greater age (beta = -0.42), independent of changes in lean and fat mass in different parts of the body. By contrast, trunk lean (beta = 0.27) and leg fat (beta = 0.27) mass were associated with greater REE independent of age and other body-composition variables. CONCLUSIONS These results suggest that trunk lean mass (presumably primarily organ tissue) is relatively resistant to age-related changes in body composition, whereas muscle mass, especially leg muscle, tends to be lost. These data also suggest that the age-related decreases in REE are not fully explained by changes in body composition.
Socio-Ecological Mechanisms Supporting High Densities of Aedes albopictus (Diptera: Culicidae) in Baltimore, MD

Abstract Social, ecological, and climatic factors interact creating a heterogeneous matrix that determines the spatiotemporal distribution of mosquitoes and human risks of exposure to the diseases they transmit. We explore linkages between the social and institutional processes behind residential abandonment, urban ecology, and the interactions of socio-ecological processes with abiotic drivers of mosquito production. Specifically, we test the relative roles of infrastructure degradation and vegetation for explaining the presence of Aedes albopictus Skuse 1894 to better predict spatial heterogeneity in mosquito exposure risk within urban environments. We further examine how precipitation interacts with these socially underpinned biophysical variables. We use a hierarchical statistical modeling approach to assess how environmental and climatic conditions over 3 years influence mosquito ecology across a socioeconomic gradient in Baltimore, MD. We show that decaying infrastructure and vegetation are important determinants of Ae. albopictus infestation. We demonstrate that both precipitation and vegetation influence mosquito production in ways that are mediated by the level of infrastructural decay on a given block. Mosquitoes were more common on blocks with greater abandonment, but when precipitation was low, mosquitoes were more likely to be found in higher-income neighborhoods with managed container habitat. Likewise, although increased vegetation was a negative predictor of mosquito infestation, more vegetation on blocks with high abandonment was associated with the largest mosquito populations. These findings indicate that fine spatial scale modeling of mosquito habitat within urban areas is needed to more accurately target vector control.
mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay

As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation.
Phylogeny and Classification of Carex Section Ovales (Cyperaceae)

Section Ovales is the most species‐rich section of the sedge genus Carex in the New World. Phylogenetic analyses of molecular data recover a predominantly New World clade as sister to a solitary east Asian species, C. maackii. Nuclear ribosomal DNA are congruent in the placement of all taxa within the section, with a solitary exception: incongruence between ITS and ETS data in the placement of C. bonplandii and C. roraimensis suggests a hybrid origin for this lineage. Biogeography correlates strongly with phylogeny in the section, but there have been at least two instances of long‐range dispersal, one from an eastern North American clade to western North America and one from the New World to Eurasia. Morphological characters studied are all homoplastic. Developing a comprehensive infrasectional classification with a phylogenetic basis would be complicated by the fact that most of the novel morphological characters in the section have evolved within relatively small, independent clades.
Impact of glucocorticoid receptor gene Bcl-1 variant on temporomandibular disorders

Objectives: Temporomandibular Disorders (TMD) constitute a heterogeneous group of disorders characterized by alterations in mandibular movement. The aim of this study was to investigate the association between the Bcl1 variant of NR3C1 gene and TMD susceptibility in Turkish population. Method: NR3C1 gene BcI1 variant of 100 TMD patients and 105 healthy controls was genotyped by polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFLP). Results: There was also no significant difference in regard to genotype and allele frequencies between the patients and the controls (OR 0.216 (95% Cl: 0.85-2.04); p=0.216). However, present study found that numeric pain rating scale was higher in patients with CC and CG genotypes. Discussion: Although the NR3C1 Bcl1 variant did not show any difference between the TMD and the control groups, we thought that this variant could be correlated with pain intensity in patients. Further studies with different ethnic subjects are needed to confirm the results.
Strain mapping in free-standing heterostructured wurtzite InAs/InP nanowires

The strain distribution in heterostructured wurtzite InAs/InP nanowires is measured by a peak finding technique using high resolution transmission electron microscopy images. We find that nanowires with a diameter of about 20 nm show a 10 nm strained area over the InAs/InP interface and the rest of the wire has a relaxed lattice structure. The lattice parameters and elastic properties for the wurtzite structure of InAs and InP are calculated and a nanowire interface is simulated using finite element calculations. Both the method and the experimental results are validated using a combination of finite element calculations and image simulations.
1 Genome comparison implies the role of Wsm 2 in membrane trafficking 2 and protein degradation 3 4 5 6

Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa) and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of Wsm2 may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative Wsm2 ancestor loci
On Event-Chain Monte Carlo Methods

In this dissertation we consider a pair of continuous-time, non-reversible, rejectionfree, and piecewise deterministic MCMC methods, referred to as Event-Chain Monte Carlo methods; respectively reflect-ECMC and flip-ECMC. We compare the two methods in a handful of settings, and find that in all cases the performance of the reflect-ECMC algorithm is superior. We consider extensions of the algorithms proposed in the context of large-scale Bayesian analysis, and combine various improvements proposed in the literature yielding a method which we demonstrate to outperform all previously considered methods for Bayesian logistic regression. Still in a Bayesian context, we show how the reflection algorithm scales in the limit as the number of observations n→∞, and find that as was previously demonstrated for the flip algorithm that it is possible, using a combination of sub-sampling and control variate ideas, to obtain a reflect-ECMC method for which the cost of obtaining an independent point is O(1) in n. Furthermore, we present the first detailed discussion concerning the tuning of the parameters of these two methods, and we demonstrate empirically the considerable efficiency gains which are made possible by the use of a non-diagonal ‘mass matrix’ for the reflect algorithm; this we do using a real-data logistic regression example, and an example in which the target distribution is that of a latent field in a Poisson-Gaussian Markov random field model. I dedicate this work to Grandpa and Grand-papa, who did not live to see me fully grown how I wish I could see you now. to Grandma, who would have been proud to send a grandson off to Oxford, as she did her son many years ago; whose unwavering cheer was constantly uplifting, until the very end, how dearly I miss you. and, to Mormor, whom I will call as soon as I submit, if my writing is not up to Desbarats standard, I will try harder next time. And finally, to my father, who might (I hope) at last bury his fears that I should end up working at Canadian Tire.
A 114-pW PMOS-only, trim-free voltage reference with 0.26% within-wafer inaccuracy for nW systems

A sub-nW voltage reference is presented that uses only PMOS transistors, thereby providing inherently low process variation and enabling trim-free operation for LDOs and other applications in nW microsystems. Sixty chips from 3 different wafers in 180nm CMOS are measured, showing an untrimmed within-wafer σ/μ of 0.26% and wafer-to-wafer σ/μ of 1.9%. Measurement results also show a temperature coefficient of 48-124ppm/°C from -40°C to 85°C. Outputting a 0.986V reference voltage, the reference operates down to 1.2V and consumes 114pW at 25°C.
Effects of a novel selective peroxisome proliferator‐activated receptor‐α modulator, pemafibrate, on hepatic and peripheral glucose uptake in patients with hypertriglyceridemia and insulin resistance

Pemafibrate is a novel selective peroxisome proliferator‐activated receptor‐α modulator with potent triglyceride‐lowering and high‐density lipoprotein cholesterol‐raising effects. We showed that pemafibrate decreased the homeostatic model assessment for insulin resistance in patients with dyslipidemia. To investigate how pemafibrate improves insulin sensitivity, we used a hyperinsulinemic‐euglycemic clamp technique to determine the splanchnic and peripheral glucose uptake in patients with hypertriglyceridemia and insulin resistance.
Low serum concentrations of 25-hydroxyvitamin D in older persons and the risk of nursing home admission.

BACKGROUND The prevalence of vitamin D deficiency in nursing home patients is high. OBJECTIVE We aimed to ascertain whether lower serum 25-hydroxyvitamin D [25(OH)D] concentrations increase the risk of future nursing home admission and early death. DESIGN We included 1260 independent, community-dwelling persons aged > or =65 y who were participating in the Longitudinal Aging Study Amsterdam (1995-1996). Study outcomes were time to nursing home admission during 6 y of follow-up and time to death until 1 April 2003. RESULTS Vitamin D deficiency [25(OH)D < 25 nmol/L] and insufficiency [25(OH)D = 25-49.9 nmol/L] were present in 127 (10.1%) and 462 (36.7%) subjects, respectively. During follow-up, 138 subjects (11.0%) were admitted to nursing homes, and 380 subjects (30.2%) died. The risk of nursing home admission for participants with 25(OH)D deficiency was 53 cases per 1000 person-years higher than that for those with high 25(OH)D (> or =75 nmol/L) concentrations (58 compared with 5 cases). After adjustment for potential confounders, the hazard ratio (95% CI) of nursing home admission was 3.48 (1.39, 8.75) for vitamin D-deficient, 2.77 (1.17, 6.55) for vitamin D-insufficient, and 1.92 (0.79, 4.66) for vitamin D-borderline persons as compared with persons with high 25(OH)D (P for trend = 0.002). The results remained after additional adjustment for frailty indicators. Lower 25(OH)D was associated with higher mortality risk, but this association was not significant after adjustment for frailty indicators. CONCLUSION Lower serum 25(OH)D concentrations in older persons are associated with a greater risk of future nursing home admission and may be associated with mortality.
MicroRNA31-NDRG3 regulation axes are essential for hepatocellular carcinoma survival and drug resistance.

BACKGROUNDS Hepatocellular carcinoma (HCC) is an epithelial cancer that originates from hepatocytes and it is the most common primary malignant tumor of the liver. Till now the prognosis of HCC patients is generally poor. The molecular mechanism giving rise to HCC development and recurrence is still largely unknown. MicroRNA-31 (miR-31) is among the most commonly altered microRNAs in human cancers, and alternations of miR-31 expression were reported to play pivotal roles in tumorigenesis and tumor progression. METHODS In this work, the primary biological function of miR-31 in HCC tumorigenesis was investigated. RESULTS Our data showed that overexpression of miR-31 induced markedly inhibition of HCC cell proliferation, migration in vitro and inhibited xenograft tumor growth in vivo. One target gene of miR-31, NDRG3, was also demonstrated indispensable for HCC cell survival. Furthermore, miR-31 and NDRG3 were both essential for HCC cell drug resistance in adriamycin. CONCLUSIONS We conclude that miR-31 is a crucial regulator in hepatocellular carcinoma, miR-31 and its target gene NDRG3 may be potential therapeutic targets for HCC treatment in the future.
Pentadecanoic acid in serum as a marker for intake of milk fat: relations between intake of milk fat and metabolic risk factors.

BACKGROUND The fatty acid composition of the diet is known to be partially reflected by the fatty acid composition of serum lipids. OBJECTIVE We examined whether pentadecanoic acid (15:0) in serum lipids can be used as a marker for intake of milk fat, the major dietary source of 15:0. We also investigated the relations between intake of milk fat and cardiovascular disease risk factors. DESIGN Sixty-two 70-y-old men completed 7-d dietary records. The intake of milk products was studied in relation to the proportions of 15:0 in serum cholesterol esters and phospholipids, as well as to the clinical characteristics of these men, by using Spearman's rank correlation. RESULTS The proportions of 15:0 in serum cholesterol esters were positively related to butter intake (r = 0.36. P = 0.004) and to the total amount of fat from milk products (r = 0.46, P < 0.0001): 15:0 in phospholipids was related to the amount of fat from milk and cream (r = 0.34, P = 0.008) and to the total amount of fat from milk products (r = 0.34, P = 0.008). Inverse associations were found between intake of milk products and body mass index, waist circumference, LDL-HDL ratio, HDL triacylglycerols, and fasting plasma glucose, whereas relations to HDL cholesterol and apolipoprotein A-I tended to be positive. CONCLUSIONS The results suggest that 15:0 in serum can be used as a marker for intake of milk fat. The explanation for the inverse associations between the intake of milk products and certain cardiovascular risk factors is not known.
Alpha(1)-antitrypsin and antichymotrypsin in human milk: origin, concentrations, and stability.

BACKGROUND The protease inhibitors alpha(1)-antitrypsin and antichymotrypsin are present in human milk, but little is known about their roles in protein digestion during infancy. It has been hypothesized that alpha(1)-antitrypsin and antichymotrypsin may modulate digestion in the infant gut. OBJECTIVE We determined whether the mammary gland expresses alpha(1)-antitrypsin and antichymotrypsin, measured alpha(1)-antitrypsin and antichymotrypsin throughout lactation, assessed the resistance of alpha(1)-antitrypsin to proteolysis, and determined the potential of alpha(1)-antitrypsin to affect the survival of other milk proteins. DESIGN A pool of complementary DNA from the human mammary gland was analyzed with polymerase chain reaction to detect genes for alpha(1)-antitrypsin and antichymotrypsin. alpha(1)-Antitrypsin and antichymotrypsin concentrations were measured in milk samples obtained longitudinally (days 4-47) from 8 women. An in vitro model of infant digestion was used to assess the digestive stability of alpha(1)-antitrypsin against pepsin and pancreatin. Lactoferrin, with alpha(1)-antitrypsin present, was digested by pancreatin, and the digested proteins were separated. RESULTS Alpha(1)-antitrypsin and antichymotrypsin concentrations were high in early milk and decreased throughout lactation. Polymerase chain reaction products were detected for both genes. After in vitro digestion, much of the alpha(1)-antitrypsin was still intact, whereas many other milk proteins were digested. Much of the lactoferrin was still intact after digestion, but only when alpha(1)-antitrypsin was added. CONCLUSIONS The results suggest that alpha(1)-antitrypsin and antichymotrypsin are produced by the mammary gland and are present in milk in relatively high amounts in early lactation. alpha(1)-Antitrypsin may survive digestion and may affect the survival of other proteins.
Aberrant Promoter Methylation of PCDH17 (Protocadherin 17) in Serum and its Clinical Significance in Renal Cell Carcinoma

Background Current studies indicated that PCDH17 functions as a tumor suppressor, which is frequently inactivated by aberrant promoter methylation in urologic tumors. The main purpose of this study was to investigate the methylation status of PCDH17 in serum and its clinical significance in renal cell carcinoma (RCC). Material/Methods The methylation status of PCDH17 in serum samples of 142 RCC patients and 34 controls was evaluated by methylation-specific PCR (MSP). Then we correlated PCDH17 methylation status with the clinicopathologic features of RCC patients and patient outcomes. Results We found that PCDH17 was more frequently methylated in RCC patients than in controls. Moreover, PCDH17 methylation in serum was significantly correlated with advanced stage (p=0.044), higher grade (p=0.019), lymph node metastasis (p=0.008) and tumor progression (p<0.001). In addition, patients with methylated PCDH17 had shorter progression-free survival (p<0.001) and overall survival (p=0.017) than patients without, and PCDH17 methylation in serum was an independent prognostic factor for worse progression-free survival (HR: 4.215, 95% CI: 1.376–9.032, p<0.001) and overall survival (HR: 5.092, 95% CI: 1.149–12.357, p=0.046) of patients with RCC. Conclusions The present study indicates that PCDH17 methylation in serum is a frequent event in RCC and associated with risk factors of poor outcomes. Moreover, PCDH17 methylation in serum is a potential prognostic biomarker for patients with RCC after surgery.