Miracle-dz/UniFAR-FTUs huggingface dataset:
X‐ray crystallographic studies of the denaturation of ribonuclease S

In an attempt to view the onset of urea denaturation in ribonuclease we have collected X‐ray diffraction data on ribonuclease S crystals soaked in 0, 1.5, 2, 3, and 5 molar urea. At concentrations above 2 M urea, crystals were stabilized by glutaraldehyde crosslinking. We have also collected data on ribonuclease S crystals at low pH in an attempt to study the onset of pH denaturation. The resolution of the datasets range from 1.9 to 3.0 Å. Analysis of the structures reveals an increase in disorder with increasing urea concentration. In the 5 M urea structure, this increase in disorder is apparent all over the structure but is larger in loop and helical regions than in the β strands. The low pH structure shows a very similar pattern of increased disorder. In addition there is a major change in the position of the main chain (> 1 Å) in the 65–72 turn region. This region has previously been shown to be involved in one of the initial steps of unfolding in the reduction of ribonuclease A. Crystallographic analyses in the presence of denaturant, when combined with controlled crosslinking, can thus provide detailed structural information that is related to the initial steps of unfolding in solution. Proteins 1999;36:282–294. © 1999 Wiley‐Liss, Inc.
N‐ and O‐Glycans Are Not Directly Involved in the Oligomerization and Apical Sorting of GPI Proteins

Oligomerization of glycosyl‐phosphatidylinositol‐anchored proteins (GPI‐APs) into high molecular weight complexes is an essential step for their apical sorting in polarized epithelial cells. However, the mechanism by which apical GPI‐APs oligomerize is still unclear. To investigate the possible role of N‐ and O‐glycosylation, we have analysed the behaviour of two glycosylated GPI‐anchored apical proteins, p75GPI and placental alkaline phosphatase (PLAP), and their glycosylation mutants. We found that both the N‐ and O‐glycosylation mutants are apically sorted, associate to detergent‐resistant microdomains and are able to oligomerize, like the wild‐type proteins, suggesting that glycosylation does not have a direct role in GPI‐AP oligomerization and apical sorting. Interestingly, when cells are depleted of cholesterol and treated with tunicamycin, treatments that by themselves do not affect PLAP sorting, PLAP is not able to oligomerize and is missorted to the basolateral surface, thus supporting an indirect role of N‐glycosylation, possibly mediated by a raft‐associated glycosylated interactor.
A Computational Model of Light-Sheet Fluorescence Microscopy using Physically-based Rendering

We present a physically-based computational model of the light sheet ﬂuorescence microscope (LSFM). Based on Monte Carlo ray tracing and geometric optics, our method simulates the operational aspects and image formation process of the LSFM. An extension for previous ﬂuorescence models is developed to account for the intrinsic characteristics of ﬂuorescent dyes in order to accurately simulate light interaction with ﬂuorescent-tagged biological specimen. This extension was quantitatively validated against the ﬂuorescence brightness equation and experimental spectra of different dyes. We demonstrate ﬁrst results of our rendering pipeline to a simpliﬁed brain tissue model reconstructed from the somatosensory cortex of a young rat.
Expressional Control of a Cadmium-transporting P1B-type ATPase by a Metal Sensing Degradation Signal*

Cadmium is a highly toxic environmental contaminant implicated in various diseases. Our previous data demonstrated that Pca1, a P1B-type ATPase, plays a critical role in cadmium resistance in yeast S. cerevisiae by extruding intracellular cadmium. This illustrates the first cadmium-specific efflux pump in eukaryotes. In response to cadmium, yeast cells rapidly enhance expression of Pca1 by a post-transcriptional mechanism. To gain mechanistic insights into the cadmium-dependent control of Pca1 expression, we have characterized the pathway for Pca1 turnover and the mechanism of cadmium sensing that leads to up-regulation of Pca1. Pca1 is a short-lived protein (t½ < 5 min) and is subject to ubiquitination when cells are growing in media lacking cadmium. Distinct from many plasma membrane transporters targeted to the vacuole for degradation via endocytosis, cells defective in this pathway did not stabilize Pca1. Rather, Pca1 turnover was dependent on the proteasome. These data suggest that, in the absence of cadmium, Pca1 is targeted for degradation before reaching the plasma membrane. Mapping of the N terminus of Pca1 identified a metal-responding degradation signal encompassing amino acids 250–350. Fusion of this domain to a stable protein demonstrated that it functions autonomously in a metal-responsive manner. Cadmium sensing by cysteine residues within this domain circumvents ubiquitination and degradation of Pca1. These data reveal a new mechanism for substrate-mediated control of P1B-type ATPase expression. Cells have likely evolved this mode of regulation for a rapid and specific cellular response to cadmium.
Experimental analysis of surface roughness scattering in FinFET devices

The surface roughness scattering in n-type FinFET devices is accurately analyzed based on mobility measurements at low temperatures. Using the top/side wall current separation technique, the effective mobility for each surface has been extracted. Considering the second order mobility degradation factor, the surface roughness scattering of top and sidewall conduction has been quantitatively compared.
A dynamic model of N metabolism in the lactating dairy cow and an assessment of impact of N excretion on the environment.

Improving N utilization in dairy cows and especially reducing N output in excreta is desirable due to global concerns of agricultural contribution of N to environmental pollution, particularly as ammonia. Data from five N balance experiments were used to develop a dynamic model that was evaluated with independent data. Model predictions of feces, urine, and milk outputs were close to observed values. Statistical analysis showed that 96% of mean square prediction error for feces and urine N output predictions was due to random variation. However, the model tends to overpredict milk N output, especially at higher N intake levels. Evaluation of model predictions for independent experimental observations from Agricultural Development Advisory Service at Bridgets (U.K.) showed good agreement between predicted and observed urine N output (95% due to random variation). However, there was a slight underprediction for fecal N output (14% mean square prediction error due to bias) and overprediction of milk N output (22% of mean square prediction error due to bias). The model predictions of N outputs in excreta were sensitive to changes in energy concentration of the diet. Dietary protein degradability had only a small influence on predicted fecal N output. However, the model was sensitive in its predictions of urine N when protein degradability was varied. Application of the model to assess reduction in ammonia emissions from dairy cows showed that increasing the energy concentration could potentially reduce ammonia emissions by up to 25% per cow. Similarly, reducing CP concentration in the diet to about 16% could reduce ammonia production by 20% and lower degradability of CP to match microbial requirement by 19% per cow. The model is a first step toward a mechanistic approach of nutrient modeling, and it is a valuable method for predicting N excretions and estimating N emissions from dairy systems.
First in vivo evaluation of liposome-encapsulated 223Ra as a potential alpha-particle-emitting cancer therapeutic agent.

BACKGROUND Liposomes carrying chemotherapeutics have had some success in cancer treatment and may also be suitable carriers for therapeutic radionuclides. This study was designed to evaluate the biodistribution and to estimate the radiation doses of the alpha emitter 223Ra loaded into pegylated liposomes in selected tissues. MATERIALS AND METHODS 223Ra was encapsulated in pegylated liposomal doxorubicin (PLD) by ionophore-mediated loading. The biodistribution of liposomal 223Ra was compared to free cationic 223Ra in Balb/C mice. RESULTS Liposomal 223Ra circulated in the blood with an initial half-life in excess of 24 hours, which agreed well with that reported for PLD in rodents, while the blood half-life of cationic 223Ra was considerably less than an hour. When liposomal 223Ra was catabolized, the released 223Ra was either excreted or taken up in the skeleton. This skeletal uptake increased up to 14 days after treatment, but did not reach the level seen with free 223Ra. Pre-treatment with non-radioactive PLD 4 days in advance lessened the liver uptake of liposomal 223Ra. Dose estimates showed that the spleen, followed by bone surfaces, received the highest absorbed doses. CONCLUSION Liposomal 223Ra was relatively stable in vivo and may have potential for radionuclide therapy and combination therapy with chemotherapeutic agents.
Experimental and numerical study on hydrodynamics of swimming paddle for a shoal crab robot

The rigid swimming paddle as an auxiliary motive power underwater is modeled and designed as the first attempt for the shoal crab robot Crabot-I. In this work, the hydrodynamics of a swimming paddle is investigated numerically and experimentally. The primary focus of our study is related specifically to the effect of St on hydrodynamic performance of a single swimming paddle in lift-based and drag-based modes, and the load-generating mechanism by studying the relations among evolution of vortex, pressure distribution and load characteristics, as well as demonstration and validation in low-speed tunnel. The results of numerical calculations by CFD and tests in the Ship Maneuverability Laboratory (HEU) Water Tunnel are both used to demonstrate fundamental properties of swimming paddle, and to provide a reference for the further research on subsea swimming gait based on the synergetic motion of two paddles.
Multiple sequence motifs are involved in SV40 enhancer function.

A systematic mutagenesis of the SV40 enhancer indicates that it spans approximately 100 bp and is composed of at least two distinct DNA domains which exhibit very little enhancing activity on their own. Their association results in a 400‐fold enhancement of transcription, virtually irrespective of their relative orientation and, to some extent, of the distance between them. Enhancer activity can also be generated by duplication of either domain. We show also that the activity of each domain is due to the presence of several specific sequence motifs. These motifs are found assorted in different combinations in other viral and cellular enhancers.
Male Reproductive Hormones and Thyroid Function in Pesticide Applicators in the Red River Valley of Minnesota

In the present effort, 144 pesticide applicators and 49 urban control subjects who reported no chronic disease were studied. Applicators provided records of the season's pesticides used by product, volumes, dates, and methods of application. Blood specimens for examination of hormone levels were obtained in summer and fall. In the herbicide-only applicator group, significant increases in testosterone levels in fall compared to summer and also elevated levels of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) in the fall were noted. With respect to fungicide use, in an earlier cross-sectional epidemiologic study, data demonstrated that historic fungicide use was associated with a significant alteration of the sex ratio of children borne to applicators. As before, among current study subjects it was noted that historic fungicide use was associated with increased numbers of girls being born. Lower mean total testosterone concentrations by quartile were also correlated with increased numbers of live-born female infants. A downward summer to fall seasonal shift in thyroid-stimulating hormone (TSH) concentrations occurred among applicators but not among controls. Farmers who had aerial application of fungicides to their land in the current season showed a significant shift in TSH values (from 1.75 to 1.11 mU/L). Subclinical hypothyroidism was noted in 5/144 applicators (TSH values >4.5 mU/L), but not in urban control subjects. Based on current and past studies, it was concluded that, in addition to pesticide exposure, individual susceptibility and perhaps economic factors may play a supporting role in the reported results.
Prevalance of proteinuria in Mexico: a conjunctive consolidation approach with other cardiovascular risk factors: the Mexican Health Survey 2000.

BACKGROUND A number of cross-sectional or serial studies have demonstrated the clinical impact of microproteinuria and macroproteinuria by identifying individuals at risk of both end-stage renal disease and major cardiovascular events. This study focused on the prevalence of proteinuria in Mexico and its relationship with other cardiovascular risk factors such as hypertension, type 2 diabetes mellitus, body mass index, smoking, age, and gender. METHODS The prevalence of proteinuria in Mexico was obtained from the probabilistic cross-sectional national health survey performed in the year 2000. The proportion of urine dipstick samples that tested positive for protein (defined as > or =1+) in adults from 20 to 69 years of age was determined. The analysis was performed using both algebraic and multicategorical models. Potential interactions between proteinuria and other major cardiovascular risk factors were investigated. RESULTS A total of 46,523 adult survey participants were included in the analysis. In the general population, 9.2% had proteinuria. By univariate, multivariate, and multicategorical analysis, hypertension, diabetes, obesity, and age were strongly associated with the prevalence of proteinuria (P < 0.001). However, in Mexico, the specific distribution of age groups demonstrated that the absolute number of patients without hypertension that had proteinuria is not irrelevant. To identify 1 case of proteinuria, one would need to screen 3 persons with diabetes mellitus, 5 patients with hypertension without diabetes, or 6 persons over the age of 55 years. When proteinuria is present, the probability of having a noncommunicable chronic disease or other major cardiovascular risk factor is more than 85%. CONCLUSION Proteinuria is prevalent. When considered together, dipstick-positive proteinuria, blood pressure level, body mass index > or =30 m(2)/kg, and abnormal fasting blood glucose measured on a single occasion identifies different segments of the population. Studies such as this may be a suitable initial clinical approach to general population screening for renal and cardiovascular risk stratification.
Using sulfur hexafluoride as a gaseous tracer to study ventilation systems in mines

The Bureau of Mines found sulfur hexafluoride (SF/sub 6/), released from a lecture bottle, to be an ideal gaseous tracer for studying mine ventilation systems. Air samples were collected in glass syringes and analyzed by electron-capture gas chromatography. In these studies, the lower limit of detection was about 1 part per billion by volume (ppB) of SF/sub 6/ per part of air. Experiments conducted in a Pennsylvania limestone mine showed this technique useful in evaluating the effectiveness of auxiliary fans, measuring low flow velocities, probing the air circulating near a working face region where ventilation appeared to be poor, and estimating volumetric flow rates in airways of large cross-sectional area and having low flow velocities. This technique was also used in a western vein-type metal mine to measure the amount of return air being recirculated into the intake air due to leakage through old stoped areas.
Luciferin‐Regenerating Enzyme Crystal Structure Is Solved but its Function Is Still Unclear

Contribution of luciferin‐regenerating enzyme (LRE) for in vitro recycling of D‐luciferin has been reported. According to crystal structure of LRE, it is a beta‐propeller protein which is a type of all β‐protein architecture. In this overview, reinvestigation of the luciferase‐based LRE assays and its function is reported. Until now, sequence of LRE genes from four different species of firefly has been reported. In spite of previous reports, T‐LRE (from Lampyris turkestanicus) was cloned and expressed in Escherichia coli as well as Pichia pastoris in a nonsoluble form as inclusion body. According to recent investigations, bioluminescent signal of soluble T‐LRE–luciferase‐coupled assay increased and then reached an equilibrium state in the presence of D‐cysteine. In addition, the results revealed that both D‐ and L‐cysteine in the absence of T‐LRE caused a significant increase in bioluminescence intensity of luciferase over a long time. Based on activity measurements and spectroscopic results, D‐cysteine increased the activity of luciferase due to its redox potential and induction of conformational changes in structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE (at least T‐LRE) on luciferase activity, most of the increase in luciferase activity is caused by direct effect of D‐cysteine on structure and activity of firefly luciferase. Moreover, bioinformatics analysis cannot support the presence of LRE in peroxisome of photocytes in firefly lanterns.
DINAMIKA LEMBAGA PENDIDIKAN TINGGI ISLAM DI INDONESIA

Abstrak : Tulisan ini berupaya menganalisis dinamika perkembangan Pendidikan Tinggi Islam di Indonesia dari perspektif sejarah. Penulis mengklaim bahwa Perguruan tinggi Islam pertama di Indonesia adalah STI (Sekolah Tinggi Islam) didirikan di Jakarta pada tahun 1945, yang tiga tahun kemudian ditransformasi menjadi UII (Universitas Islam Indonesia) di Yogyakarta. Pada tahun 1951, selanjutnya, pemerintah mendirikan PTAIN di Yogyakarta dengan menegerikan fakultas agama Islam pada UII. Disamping itu, pemerintah mendirikan ADIA (Akademi Dinas Ilmu Agama) di Jakarta pada tahun 1957. Hasil perkawinan kelembagaan antara PTAIN dan ADIA melahirkan IAIN atau al-Jamiah al-Islamiyah al-Hukumiyah didirikan pada tahun 1960 di Yogyakarta. Cabang - cabang IAIN di daerah ditingkatkan statusnya oleh pemerintah pada tahun 1997 menjadi STAIN. Perkembangan paling signifikan terjadi pada tahun 2002 dimana beberapa IAIN dan STAIN dikonversi menjadi UIN. Penulis mengklaim bahwa format terakhir ini merupakan perkembangan paling sentral di era globalisasi dengan konsep integrasi ilmu. Abstract : The Dynamics of Islamic Higher Education Institutions in Indonesia . This paper seeks to analyze the dynamics of the development of Islamic Higher Education in Indonesia from a historical perspective. The author claimed that the first Islamic College in Indonesia was the STI (Islamic High School) founded in Jakarta in 1945, which three years later was transformed into UII (Islamic University of Indonesia) in Yogyakarta. In 1951, furthermore, the government established PTAIN in Yogyakarta integrated in UII. In addition, the government established ADIA (Akademi Dinas Ilmu Agama) in Jakarta in 1957. The result of institutional marriage between PTAIN and ADIA gave birth to IAIN or al-Jamiah al-Islamiyah al-Hukumiyah was founded in 1960 in Yogyakarta. The IAIN branches in the region were upgraded by government in 1997 to become STAIN. The most significant developments occurred in 2002 where some IAIN and STAIN were converted to UIN. The author claims that this last format is the most central development in the era of globalization with the concept of science integration. Kata Kunci: Indonesia, lembaga pendidikan tinggi, UIN, IAIN, STAIN
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.
Practical aspects of DNA-based forensic studies in dentistry

Forensic dentistry as a science has evolved from simple methods of age estimation and bite-mark analysis, to a new era of genetic and serological investigations. DNA analysis in forensic science requires a sample or source from either an individual (living or dead) or a crime/incident site. The orofacial region is a good source of such material, due to the fact that certain oral tissues are relatively resistant to environmental degradation and destruction by thermal, electrical, and mechanical insult. Dentists may be called upon to provide samples and expert analysis in many such situations. Sources include soft and hard tissues of teeth and jaws, saliva, biopsy material, and mucosal swabs. Tissue samples should be handled with care, and correct protocol in collection and preparation has to be followed. This ensures a high yield of the required DNA. Hard tissues like teeth require specialized procedures to extract the genetic material. Research has shown that there is a wide variation in the quality and quantity of DNA extracted from different individuals from the same site even under similar conditions. This necessitates calibration of the various methods to achieve best results. DNA analysis can provide highly accurate identification if used correctly. Here a description of the various sources in the oral region has been provided from which samples could be forwarded to the forensic laboratory. Most commonly employed techniques of collection and handling for laboratory procedures have been outlined.
Pax‐3, a novel murine DNA binding protein expressed during early neurogenesis.

We describe the isolation and characterization of Pax‐3, a novel murine paired box gene expressed exclusively during embryogenesis. Pax‐3 encodes a 479 amino acid protein with an Mr of 56 kd containing both a paired domain and a paired‐type homeodomain. The Pax‐3 protein is a DNA binding protein that specifically recognizes the e5 sequence present upstream of the Drosophila even‐skipped gene. Pax‐3 transcripts are first detected in 8.5 day mouse embryos where they are restricted to the dorsal part of the neuroepithelium and to the adjacent segmented dermomyotome. During early neurogenesis, Pax‐3 expression is limited to mitotic cells in the ventricular zone of the developing spinal cord and to distinct regions in the hindbrain, midbrain and diencephalon. In 10–12 day embryos, expression of Pax‐3 is also seen in neural crest cells of the developing spinal ganglia, the craniofacial mesectoderm and in limb mesenchyme of 10 and 11 day embryos.
Activity Recognition Using Fusion of Low-Cost Sensors on a Smartphone for Mobile Navigation Application

Low-cost inertial and motion sensors embedded on smartphones have provided a new platform for dynamic activity pattern inference. In this research, a comparison has been conducted on different sensor data, feature spaces and feature selection methods to increase the efficiency and reduce the computation cost of activity recognition on the smartphones. We evaluated a variety of feature spaces and a number of classification algorithms from the area of Machine Learning, including Naive Bayes, Decision Trees, Artificial Neural Networks and Support Vector Machine classifiers. A smartphone app that performs activity recognition is being developed to collect data and send them to a server for activity recognition. Using extensive experiments, the performance of various feature spaces has been evaluated. The results showed that the Bayesian Network classifier yields recognition accuracy of 96.21% using four features while requiring fewer computations.