Miracle-dz/UniFAR-FTUs huggingface dataset:
Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages

The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.
TOPOLOGY OPTIMIZATION OF COMPLIANT MECHANISMS USING THE HOMOGENIZATION METHOD

A procedure to obtain a topology of an optimal structure considering flexibility is presented. The methodology is based on a mutual energy concept for formulation of flexibility and the homogenization method. A multi-objective optimization problem is formulated as an application of compliant mechanism design. Some examples of the design of compliant mechanisms for plane structures are presented. ( 1998 John Wiley & Sons, Ltd.
Pregnancy-associated Hypertriglyceridemia in Normal and Diabetic Women: Differences in Insulin-dependent, Non-insulin-dependent, and Gestational Diabetes

In this study longitudinal observations of plasma lipo-proteins were made in pregnant diabetic women classified according to the National Diabetes Data Group. Sequential measurements at second trimester (25–27 wk), third trimester (34–37 wk), and 3 mo postpartum (control period) were carried out in 18 diabetic and 6 normal women. In 15 diabetic and 4 normal women from this group, 24-h plasma glucose, serum C-peptide levels, and HbA1c concentrations were measured. Another group of 15 normal and 18 diabetic women underwent determinations of fasting plasma lipoproteine and other parameters at one or more of the test periods. Insulin-dependent diabetic patients (IDDM, type I) as a group did not differ from normal controls in mean plasma levels of total cholesterol (CHOL), triglyceride (TG), very-low-density lipoprotein triglyceride (VLDL TG), low-density lipoprotein cholesterol (LDL CHOL), high-density lipoprotein cholesterol (HDL CHOL), or ratios of TG:CHOL in LDL or HDL during mid or late pregnancy or 3 mo postpartum. In marked contrast, non-insulin-dependent diabetics (NIDDM, type II) had significantly higher total fasting TG at second trimester (P < 0.005), third trimester (P < 0.03), and postpartum (P < 0.01). VLDL TG levels at the second trimester, third trimester, and postpartum also were higher than in women with IDDM or normals. In NIDDM subjects the accentuated hypertriglyceridemia during second and third trimesters was also apparent in elevated LDL TG:CHOL and HDL TG:CHOL ratios. These differences were not correlated with prepregnancy weight, weight gain during gestation, or diabetic control. Women with gestational diabetes (GDM) also had significantly higher TG levels at second trimester and postpartum. Mean HDL CHOL levels were significantly lower in patients with NIDDM and GDM than in controls and IDDM patients throughout pregnancy and 3 mo postpartum. Two of 21 normals and one woman with IDDM diabetes had spontaneously reversible pregnancy-evoked hypertriglyceridemia. These results indicate that women with IDDM diabetes do not differ from normal women with respect to pregnancy-associated changes in lipid metabolism. On the other hand, women with NIDDM and GDM exhibit a pregnancy-associated hypertriglyceridemia.
Intracellular activities of roxithromycin used alone and in association with other drugs against Mycobacterium avium complex in human macrophages

Recent reports have shown that roxithromycin possesses significant activity against atypical mycobacteria, including the Mycobacterium avium complex (MAC), and that its extracellular anti-MAC activity is further enhanced in two- or three-drug combinations with ethambutol, rifampin, amikacin, ofloxacin, and clofazimine. In accordance with the above data, the anti-MAC potential of roxithromycin used alone and in combination with the above-mentioned antituberculous drugs was screened intracellularly against five clinical MAC isolates (from both human immunodeficiency virus-positive and human immunodeficiency virus-negative patients), phagocytized by human monocyte-derived macrophages. The results showed that roxithromycin used alone and within clinically achievable levels was active against all of the MAC isolates tested. Screening of two-drug combinations showed that both rifampin and clofazimine further increased the intracellular activity of roxithromycin against all five isolates by 35 to 80% (ethambutol, ofloxacin, and amikacin resulted in increased intracellular activity against one, two, and four isolates, respectively). For the three-drug combinations, the combination of roxithromycin plus ethambutol used with rifampin or clofazimine was the most uniformly active against all five MAC isolates, with activity increases of 42 to 90%, followed by roxithromycin plus ethambutol used with amikacin, which resulted in activity increases of 15 to 90%. The overall level of intracellular killing after 5 days of drug addition, in comparison with growth in untreated controls, varied from 1 to 3 log units depending on the individual MAC isolate and/or drug combination used.
Hypertension and Risk of Cataract: A Meta-Analysis

Background Cataract is the major cause of blindness across the world. Many epidemiologic studies indicated that hypertension might play an important role in the development of cataract, while others not. We therefore conducted this meta-analysis to determine the relationship between risk of cataract and hypertension. Methods Retrieved studies on the association of hypertension with cataract risk were collected from PubMed, Web of Science and the Cochrane Library during June 2014 and were included into the final analysis according to the definite inclusion criteria. Odds ratio (OR) or risk ratio (RR) were pooled with 95% confidence interval (CI) to evaluate the relationship between hypertension and cataract risk. Subgroup analyses were carried out on the basis of cataract type, race and whether studies were adjusted for main components of metabolic syndrome (MS). Results The final meta-analysis included 25 studies (9 cohort, 5 case-control and 11 cross-sectional) from 23 articles. The pooled results showed that cataract risk in populations with hypertension significantly increased among cohort studies (RR 1.08; 95% CI: 1.05–1.12) and case-control or cross-sectional studies (OR 1.28; 95% CI: 1.12–1.45). This association was proved to be true among both Mongolians and Caucasians, and the significance was not altered by the adjustment of main components of MS. Subgroup analysis on cataract types indicated that an increased incidence of posterior subcapsular cataract (PSC) resulted among cohort studies (RR 1.22; 95% CI: 1.03–1.46) and cross-sectional/case-control studies (OR 1.23; 95% CI: 1.09–1.39). No association of hypertension with risk of nuclear cataract was found. Conclusions The present meta-analysis suggests that hypertension increases the risk of cataract, especially PSC. Further efforts should be made to explore the potential biological mechanisms.
“The Sun Kings: The Unexpected Tragedy of Richard Carrington and the Tale of How Modern Astronomy Began”

List of Illustrations ix Acknowledgments xi Prologue: The Dog Years 1 Chapter One: The First Swallow of Summer 9 Chapter Two: Herschel's Grand Absurdity 25 Chapter Three: The Magnetic Crusade 47 Chapter Four: The Solar Lockstep 58 Chapter Five: The Day and Night Observatory 71 Chapter Six: The Perfect Solar Storm 80 Chapter Seven: In the Grip of the Sun 93 Chapter Eight: The Greatest Prize of All 98 Chapter Nine: Death at the Devil's Jumps 117 Chapter Ten: The Sun's Librarian 129 Chapter Eleven: New Flare, New Storm, New Understanding 148 Chapter Twelve: The Waiting Game 168 Chapter Thirteen: The Cloud Chamber 179 Epilogue: Magnetar Spring 188 Bibliography 191 Index 207
Horizontal-Humidity Gradient From One Single-Scanning Microwave Radiometer

We present a method for deriving horizontal-humidity variability from a single-scanning passive microwave radiometer (MWR). The MWR used has full scanning capabilities in azimuth and elevation and is sensitive to the path of integrated water vapor as well as cloud liquid water. Applying a simple linear-gradient model together with an assumed vertical profile derived from the closest radiosonde ascent, the strength and direction of the horizontal-humidity gradient can be determined with a temporal resolution on the order of 15-20 min. For the case of an approaching frontal system, the derived humidity field can explain up to 88% of the measured humidity variance-the missing variance can most probably be attributed to convective activity.
A Messy State of the Union: Taming the Composite State Machines of TLS

Implementations of the Transport Layer Security (TLS) protocol must handle a variety of protocol versions and extensions, authentication modes, and key exchange methods. Confusingly, each combination may prescribe a different message sequence between the client and the server. We address the problem of designing a robust composite state machine that correctly multiplexes between these different protocol modes. We systematically test popular open-source TLS implementations for state machine bugs and discover several critical security vulnerabilities that have lain hidden in these libraries for years, and have now finally been patched due to our disclosures. Several of these vulnerabilities, including the recently publicized FREAK flaw, enable a network attacker to break into TLS connections between authenticated clients and servers. We argue that state machine bugs stem from incorrect compositions of individually correct state machines. We present the first verified implementation of a composite TLS state machine in C that can be embedded into OpenSSL and accounts for all its supported cipher suites. Our attacks expose the need for the formal verification of core components in cryptographic protocol libraries, our implementation demonstrates that such mechanized proofs are within reach, even for mainstream TLS implementations.
Association Study Between Polymorphisms of PRMT6, PEX10, SOX5, and Nonobstructive Azoospermia in the Han Chinese Population1

ABSTRACT A previous genomewide association study of nonobstructive azoospermia (NOA) in the Han Chinese population identified three risk loci (rs12097821, rs2477686, and rs10842262) and provided strong evidence for a genetic influence in male infertility. However, recently, a follow-up study of these single nucleotide polymorphism (SNP) loci in the Japanese population showed that none of them were significantly associated with NOA. Therefore, we conducted an association study, consisting of 550 NOA cases and 555 normal controls, to further validate whether the risk of those three SNPs still existed in an independent Han Chinese male population. The association studies did not support the association of rs12097821 and rs2477686 with NOA for both genotype and allele distributions, but rs10842262 in the SOX5 gene was significantly associated with NOA (chi square = 9.31; P = 0.0095 and chi square = 9.27; P = 0.0023, respectively). Our study provides genetic evidence for SOX5 polymorphism in NOA, contributing to predicting males at high risk of NOA in Han Chinese population. Considering genetic differences among populations, future validating studies in independent samples are suggested.
Proximal-Type Epithelioid Sarcoma: Report of Two Cases in the Perineum: Differential Diagnosis and Review of Soft Tissue Tumors With Epithelioid and/or Rhabdoid Features

The authors report two cases of perineal proximal-type epithelioid sarcoma in middle-aged men, age 51 and 43 years old. Both tumors were located in the right side. In the first patient a 7.5-cm, well-encapsulated tumor was completely excised. The second patient was a referral case with incomplete excision, but the computed tomography scan and magnetic resonance imaging showed a 14-cm nonencapsulated tumor involving the soft tissues of the inner thigh and perineum, as well as metastasis in right inguinal and retroperitoneal lymph nodes. Both neoplasms had a predominant solid pattern alternating with occasional discohesive areas. Both were composed of large oval to polygonal cells with vesicular nuclei, conspicuous nucleoli, and amphophilic to eosinophilic cytoplasm. Rhabdoid phenotype was identified in the second case only. The first neoplasm displayed 15% necrosis, 7 mitoses per 10 high-power field, focal vascular invasion, and no extracapsular invasion. The other exhibited 60% necrosis, 12 mitoses per 10 high-power fields, extensive vascular invasion, no distinct capsule, and invasion of the surrounding fatty tissue. Both were positive for vimentin, cytokeratin, epithelial membrane antigen, and CD34. Muscle-specific actin was negative in the first case and focally positive in the second. CD56 was positive in the second case and negative in the first case. Desmin, CD45, CD30, factor VIII, CD31, S100, HMB45, calretinin, and synaptophysin were negative in both. Since proximal-type epithelioid sarcoma can be confused with a number of other soft tissue tumors with epithelioid and/or rhabdoid features, the authors emphasize the immunohistochemical differential diagnosis.
Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
Molecular Dynamics Simulation and Measurement of Contact Angle of Water Droplet on a Platinum Surface

A water liquid droplet in contact with a platinum surface was simulated by the molecular dynamics method. Water molecules were modeled by SPC/E and one layer of harmonic molecules represented the platinum surface with the constant temperature heat bath model using the phantom molecules. Here, the water-platinum pair potential developed by Spohr (1989) based on extended Hückel calculations was employed. In the spreading process of the liquid droplet on the platinum surface, the area of contact region between water and platinum expanded just in proportional to the one-third power of time. This spreading rate was clearly in contrast to the case of Lennard-Jones droplet. The contact angles of water on a platinum surface under saturated conditions are measured. The measurements are made in a vacuum container using de-ionized and degassed water on a clean platinum surface. The equilibrium static, advancing and receding contact angles are measured by changing the orientation of the platinum surface. The droplets of different masses are placed on the horizontal platinum surface. The surface is the inclined to 20, 30 and 40 degrees. The advancing and receding contact angles under these conditions are measured.
Coverage rewarded: Test input generation via adaptation-based programming

This paper introduces a new approach to test input generation, based on reinforcement learning via easy to use adaptation-based programming. In this approach, a test harness can be written with little more effort than is involved in naïve random testing. The harness will simply map choices made by the adaptation-based programming (ABP) library, rather than pseudo-random numbers, into operations and parameters. Realistic experimental evaluation over three important fine-grained coverage measures (path, shape, and predicate coverage) shows that ABP-based testing is typically competitive with, and sometimes superior to, other effective methods for testing container classes, including random testing and shape-based abstraction.
Left and right brain-oriented hemisity subjects show opposite behavioral preferences

Introduction: Recently, three independent, intercorrelated biophysical measures have provided the first quantitative measures of a binary form of behavioral laterality called “Hemisity,” a term referring to inherent opposite right or left brain-oriented differences in thinking and behavioral styles. Crucially, the right or left brain-orientation of individuals assessed by these methods was later found to be essentially congruent with the thicker side of their ventral gyrus of the anterior cingulate cortex (vgACC) as revealed by a 3 min MRI procedure. Laterality of this putative executive structural element has thus become the primary standard defining individual hemisity. Methods: Here, the behavior of 150 subjects, whose hemisity had been calibrated by MRI, was assessed using five MRI-calibrated preference questionnaires, two of which were new. Results: Right and left brain-oriented subjects selected opposite answers (p > 0.05) for 47 of the 107 “either-or,” forced choice type preference questionnaire items. The resulting 30 hemisity subtype preference differences were present in several areas. These were: (1) in logical orientation, (2) in type of consciousness, (3) in fear level and sensitivity, (4) in social-professional orientation, and (5) in pair bonding-spousal dominance style. Conclusions: The right and left brain-oriented hemisity subtype subjects, sorted on the anatomical basis of upon which brain side their vgACC was thickest, showed 30 significant differences in their “either-or” type of behavioral preferences.
Multiplicity of Aromatic Ring Hydroxylation Dioxygenase Genes in a Strong PCB Degrader, Rhodococcus sp. Strain RHA1 Demonstrated by Denaturing Gradient Gel Electrophoresis

To address the multiplicity of aromatic ring hydroxylation dioxygenases, we used PCR amplification and denaturing gradient gel electrophoresis (DGGE). The amplified DNA fragments separated into five bands, A to E. Southern hybridization analysis of RHA1 total DNA using the probes for each band showed that band C originated from a couple of homologous genes. The nucleotide sequences of the bands showed that bands A, C, and E would be parts of new dioxygenase genes in RHA1. That of band B agreed with the bphA1 gene, which was characterized previously. That of band D did not correspond to any known gene sequences. The regions including the entire open reading frames (ORFs) were cloned and sequenced. The nucleotide sequences of ORFs suggested that the genes of bands A,C, and E may respectively encode benzoate, biphenyl, and polyhydrocarbon dioxygenases. Northern hybridization indicated the induction of the gene of band A by benzoate and biphenyl, and that of the gene of band C by biphenyl and ethylbenzene, supporting the above notions. The gene of band E was not induced by any of these substrates. Thus the combination of DGGE and Southern hybridization enable us to address the multiplicity of the ring hydroxylation dioxygenase genes and to isolate some of them.
Differential Compliance Measured by the Function Recording and Analysis System in the Assessment of Vertebral Subluxation

This study presents the theory of differential compliance and the clinical application of instrumentation designed for its detection in the clinical setting. The engineering principle of using a mechanical impulse to excite a structure coupled to sensors to measure the response, has been employed in the design of the Function Recording and Analysis System (FRAS). This system, linked to software which analyzes input data, is further designed to graphically display relative differences in vertebral compliance. The present study employed assessment of a region of the spine encompassing the occiput to the third thoracic vertebra as a model to demonstrate how compliance measurements can be obtained, graphically displayed, and interpreted. The reliability of the instrumentation to accurately and consistent- ly measure different levels of compliance was tested on three artificial substrates of varying "stiffness" and three human tissue locations exhibiting different "stiffness" including the heel, palm, and finger tip. Moreover, intra- and inter-exam- iner reliability in the use of the system has also been reported. Statistical evaluation of repeated measures for each of these categories included analysis by chi-square, Pearson product moment correlation, and intraclass correlation coeffi- cients (ICC). Results indicated a high level of consistency of the instrument in measuring substrates of varying com- pliance. Moreover, strong intra-examiner reliability (ICC ≥ 0.90), and inter-examiner reliability (ICC = 0.65) suggest a consistent use of the instrument among and between practitioners. These findings indicate a useful role for the FRAS in the characterization of vertebral subluxation, as well as serving as one means of assessing changes in flexibility of the spine following the chiropractic adjustment.