Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of Nitric Oxide Donor Molsidomine on Skeletal Muscle Damage in a Rat Hind Limb Model of Ischemia-Reperfusion

Background: In this experimental study, we aimed to examine the protective effect of molsidomine (MS), a nitric oxide (NO) donor, against ischemia-reperfusion (I-R) injury in a rat skeletal muscle model. Methods: Ischemia was achieved by application of an elastic rubber band as high as possible on the left thigh of the rats. Group 1: the control group received a sham operation. Group 2: the I-R group received I-R injury to the left hind limbs. Group 3: the I-R/MS group underwent the same model of I-R injury and received MS. Group 4: the I-R/L-NAME (N-ω-nitro-L-arginine-methyl ester) group underwent the same model of I-R injury and received L-NAME, an inhibitor of NO synthase. Results: In groups 2 and 4, malondialdehyde increased significantly when compared to groups 1 and 3. Superoxide dismutase, catalase and glutathione peroxidase increased significantly in group 3 compared to groups 2 and 4. The NO levels were significantly elevated in group 3 compared to groups 2 and 4. In addition, the histopathological score was considerably lower in group 3 than in group 4. The number of necrotic muscle fibers and infiltration of neutrophils were significantly reduced in the MS-treated group. Conclusions: These findings suggest that MS can exert a protective effect against skeletal muscle injury caused by I-R in the rats.
Epithelial-mesenchymal transition as a potential explanation for podocyte depletion in diabetic nephropathy.

BACKGROUND Depletion of glomerular podocytes is an important feature of progressive diabetic nephropathy. Although the most plausible explanation for this podocyte depletion is detachment from the glomerular basement membrane after cellular apoptosis, the mechanism is unclear. Fibroblast-specific protein 1 (FSP1; encoded by the S100A4 gene) is a member of the S100 family of calcium-binding proteins and is constitutively expressed in the cytoplasm of tissue fibroblasts or epithelial cells converted into fibroblasts by means of epithelial-mesenchymal transition. STUDY DESIGN Retrospective cross-sectional analysis. SETTINGS & PARTICIPANTS 109 patients with type 2 diabetes mellitus, of whom 43 (39%) underwent kidney biopsy. PREDICTOR Clinical stage (4 categories) and histological grade (5 categories) of diabetic nephropathy. OUTCOME FSP1 expression in podocytes in urine and glomeruli in kidney biopsy specimens. MEASUREMENTS Immunohistochemistry, real-time polymerase chain reaction, and in situ hybridization. RESULTS 38 of 109 patients (35%) were normoalbuminuric, 16 (15%) had microalbuminuria, 8 (7%) had macroalbuminuria, and 47 (43%) had decreased kidney function. Approximately 95% of podocytes in urine sediment were not apoptotic, and 86% expressed FSP1. The number of FSP1-positive podocytes in urine sediment was significantly larger in patients with macroalbuminuria than in those with normoalbuminuria (P = 0.03). Intraglomerular expression of FSP1 occurred almost exclusively in podocytes from patients with diabetes, and the number of FSP1-positive podocytes was larger in glomeruli showing diffuse mesangiopathy than in those showing focal mesangiopathy (P = 0.01). The number also was larger in glomeruli with nodular lesions than in those without nodular lesions (P < 0.001). FSP1-positive podocytes selectively expressed Snail1 and integrin-linked kinase, a known trigger for epithelial-mesenchymal transition. LIMITATIONS Nonrepresentative study population. CONCLUSIONS These results suggest that the appearance of FSP1 in podocytes of patients with diabetes is associated with more severe clinical and pathological findings of diabetic nephropathy, perhaps because of induction of podocyte detachment through epithelial-mesenchymal transition-like phenomena.
Mucus Layers in Inflammatory Bowel Disease

Abstract:The intestinal epithelium is covered with mucus with the main structural building block being the densely O-glycosylated MUC2 mucin. The intestinal epithelium is exposed to ingested material, our digestive machinery, and large amounts of microorganisms. Mucus is the first line of defense and aids to limit exposure to all these threats to the epithelium. In the small intestine, mucus acts as a matrix, which contains antimicrobial products, such as defensins and immunoglobulin A that limit epithelial exposure to the luminal bacteria. In the colon, the stratified inner mucus layer acts as a physical barrier excluding bacteria from the epithelium. Bacterial penetration of this normally restricted zone is observed in many colitis models and also in patients with ulcerative colitis. Mucus defects that allow bacteria to reach the epithelium and to stimulate an immune system response can lead to the development of intestinal inflammation. The current state of our knowledge concerning the function of the mucus layers and the main mucin component, MUC2, in inflammatory bowel disease is described in this review.
Parallel Evolution in Streptococcus pneumoniae Biofilms

Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.
Research on effect of the quantity and aspect ratio of steel fibers on compressive and flexural strength of SIFCON

SIFCON (Slurry Infiltrated Fiber Reinforced Concrete) is a composite which occur hardening of the matrix phase, consists of cement, water, mineral additives, fine sand, water reducing plasticizer, and reinforced with high volume fiber (5–20%). The main difference from the high strength concrete (HSC) is the ductile behaviour at failure. However, the brittleness increases with the strength increase in HSC, SIFCON has a ductile behaviour because of the high volume fiber content, low permeability, high durability. Despite fiber content is 2-3% in fiber reinforced concrete, fiber content may be ten times more in SIFCON and ductility is gained. This concrete is suggested to be used in military buildings against explosion, industrial grounds, airports, and bridge feet. In this study, in order to investigate the compressive and flexural strengths of SIFCON, the aspect ratio and fiber volume of steel fibers were chosen as variable and the effects of these parameters on compressive and flexural strengths were investigated. In the study, steel fibers with aspect ratio of 40, 55, 65, and 80 were used in 0, 4, 8 and 12% ratios. The water/binder ratio was kept constant at 0.35. Silica fume is used 10% and water-reducing plasticizer is used 1.5% of cement by weight. 7 and 28 days cured samples were subjected to compressive and flexural tests and the results were compared. As a result of the tests carried out, increases in both the compressive and flexural strengths of SIFCON specimens were determined with increasing fiber volume up to 8%. Strength reductions were observed at higher ratios. In cases where the fiber volume is too high, it has been seen that the strengths were decreased. The reason of strength reduction can be explained by the difficulty of passing ability of mortar between the fibers. The highest strengths were obtained from fibers with the aspect ratio of 80. Increase in the aspect ratio as well as increases in compressive and flexural strengths have been found.
Minimal Pleural Effusion in Small Cell Lung Cancer: Proportion, Mechanisms, and Prognostic Effect.

PURPOSE To determine the frequency and investigate possible mechanisms and prognostic relevance of minimal (<10-mm thickness) pleural effusion in patients with small cell lung cancer (SCLC). MATERIALS AND METHODS The single-center retrospective study was approved by the institutional review board of the hospital, and informed consent was waived by the patients. A cohort of 360 consecutive patients diagnosed with SCLC by using histologic analysis was enrolled in this study. Based on the status of pleural effusion on chest computed tomographic (CT) scans at diagnosis, patients were classified into three groups: no pleural effusion, minimal pleural effusion, and malignant pleural effusion. Eighteen variables related to patient, environment, stage, and treatment were included in the final model as potential confounders. RESULTS Minimal pleural effusion was present in 74 patients (20.6%) and malignant pleural effusion in 83 patients (23.0%). Median survival was significantly different in patients with no, minimal, or malignant pleural effusion (median survival, 11.2, 5.93, and 4.83 months, respectively; P < .001, log-rank test). In the fully adjusted final model, patients with minimal pleural effusion had a significantly increased risk of death compared with those with no pleural effusion (adjusted hazard ratio, 1.454 [95% confidence interval: 1.012, 2.090]; P = .001). The prognostic effect was significant in patients with stage I-III disease (adjusted hazard ratio, 2.751 [95% confidence interval: 1.586, 4.773]; P < .001), but it disappeared in stage IV disease. An indirect mechanism representing mediastinal lymphadenopathy was responsible for the accumulation in all but one patient with minimal pleural effusion. CONCLUSIONS Minimal pleural effusion is a common clinical finding in staging SCLC. Its presence is associated with worse survival in patients and should be considered when CT scans are interpreted.
Visible light photocatalytic activity of BiFeO3 nanoparticles for degradation of methylene blue

This study reports on the photocatalytic activity of BiFeO3 nanoparticles on the degradation of cationic dye methylene blue (MB). BiFeO3 prepared by using carrageenan as a biotemplating method were characterised using XRD, SEM and EDX analysis. The effect of different parameters such as catalyst dosage, initial concentration of dye, reaction time, pH, and regeneration study on the removal efficiency were investigated. It was found that 12.79 mmol/L BiFeO3 exhibited 96% degradation of methylene blue at basic pH (pH 8 and pH 10) in 180 min. The catalysts were found to be negatively charged in alkaline medium hence the electrostatic charge attracted more cationic dye towards the catalytic site. Kinetic studies showed the degradation can be described according to Langmuir-Hinshelwood expression.
Investigation of Magnetic Nanoparticle Motion under a Gradient Magnetic Field by an Electromagnet

Finite element numerical simulations were carried out in 2D geometry to calculate the magnetic force on magnetic nanoparticles under a specially fabricated electromagnet. The particle motion was modeled by a system of ordinary differential equations. The snapshots of trajectories of 4000 MNPs with and without magnetic field were analyzed and qualitatively found to be in agreement with camera visualizations of MNP movement in a container. The results of the analysis could be helpful for the design of electromagnetic field and motion analysis of magnetic particles for the delivery of magnetic materials in biomedical applications.
The Twilight Envelope: A User-Centered Approach to Describing Roadway Illumination at Night

Visual recognition functions, such as acuity and contrast sensitivity, deteriorate rapidly over the declining luminances found during civil twilight. Thus civil twilight, a critical part of the transition between daylight and darkness, represents lighting conditions that may be useful to describe artificial illumination. Automotive headlamps project a three-dimensional beam that ranges from illumination levels comparable to daylight at the vehicle to the dark limit of civil twilight (3.3 lx) at some distance ahead. This twilight envelope is characterized as a distance beyond which foveal visual functions are severely impaired, and thus it provides a general, functional description of the useful extent of the headlamp beam. This user-centered approach to describing illumination is useful for characterizing visibility when driving at night or in other artificially lit environments. This paper discusses the twilight envelope approach and its application to intervehicle variations in headlamp systems. Actual or potential applications of this research include user-centered description of artificial illumination and driver/pedestrian safety education
Exotic behavior and crystal structures of calcium under pressure

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc → bcc → simple cubic → Ca-IV → Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The β-tin (I41/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33–71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching approximately 20 K at 120 GPa, in good agreement with experiment.
Epidemiology of sickle cell disease in Saudi Arabia

Sickle cell disease (SCD) is an autosomal recessive disorder characterized by production of abnormal hemoglobin S and is associated with high morbidity and mortality. Information about the prevalence of SCD in Saudi Arabia is patchy and probably underestimated, but studies have reported that SCD is a relatively common genetic disorder in this part of the world. The prevalence of SCD in Saudi Arabia varies significantly in different parts of the country, with the highest prevalence is in the Eastern province, followed by the southwestern provinces. The reported prevalence for sickle-cell trait ranges from 2% to 27%, and up to 2.6% will have SCD in some areas. Clinical and hematological variability exists in SCD in Saudi Arabia with two major phenotypes: a mild phenotype and a severe phenotype. Further studies on the prevalence, molecular and clinical epidemiology of SCD may help predict disease severity and risk stratification of patients to determine whether to receive early intensive care or continued symptomatic care.
CryptoLib: Cryptography in Software

With the capacity of communications channels increasing at the current rates and with the kinds of electronic services becoming more varied and multidimensional, there is also coming a greater tendency to store and forward sensitive, semi-private or very private information. With this tendency there is an increasing interest in protecting the privacy and security of communications channels and sensitive information. Many protocols have been devised which provide varying levels of security and which have overhead associated with them roughly proportional to the level of that security. These protocols make use of cryptosystems which may be divided roughly into two groups: private key and public key. It is generally assumed that efficient implementations of these systems are possible only in hardware or at least coded in very nonportable assembly language for particular processors. CryptoLib is a very portable and efficient library of routines necessary for the aforementioned cryptosystems. It written entirely in C and exists under UNIX.
Micromarkers 2.0: an update on the role of microRNAs in cancer diagnosis and prognosis

The identification of reliable diagnostic or prognostic biomarkers is one of the most pressing goals in oncological research. MicroRNAs have proven to be very promising cancer biomarkers because they are resistant to degradation in many tissue types (including FFPE specimens and body fluids), easily measured and, most importantly, their amount correlates with the presence of the tumor or with clinically relevant cancer features. In addition, our knowledge of microRNA genetic alterations in familial and sporadic cancer has recently improved. This review presents an update on cancer diagnostic and prognostic microRNAs, discusses novel tools for prognostic microRNAs identification and evaluates the possible translation of these discoveries to the clinic.
Unreliable Evidence: 2 Sources of Uncertainty During Perceptual Choice

Perceptual decisions often involve integrating evidence from multiple concurrently available sources. Uncertainty arises when the integrated (mean) evidence fails to support one alternative over another. However, evidence heterogeneity (variability) also provokes uncertainty. Here, we asked whether these 2 sources of uncertainty have independent behavioral and neural effects during choice. Human observers undergoing functional neuroimaging judged the average color or shape of a multielement array. The mean and variance of the feature values exerted independent influences on behavior and brain activity. Surprisingly, BOLD signals in the dorsomedial prefrontal cortex (dmPFC) showed polar opposite responses to the 2 sources of uncertainty, with the strongest response to ambiguous tallies of evidence (high mean uncertainty) and to homogenous arrays (low variance uncertainty). These findings present a challenge for models that emphasize the role of the dmPFC in detecting conflict, errors, or surprise. We suggest an alternative explanation, whereby evidence is processed with increased gain near the category boundary.
238U/235U Variations in Meteorites: Extant 247Cm and Implications for Pb-Pb Dating

How to Get a Date Radiometric dating relies on measuring the abundance of a radioactive isotope and/or its decay products. By knowing a decay rate and an isotopic starting abundance—both assumed to be constant—an age is determined. Using high-resolution mass spectrometry, Brennecka et al. (p. 449, published online 31 December; see the Perspective by Connelly) show that the known starting abundance of 238U and 235U isotopes in meteorites, which decay into 206Pb and 207Pb, respectively, is actually quite variable. Trace amounts of 247Cm in the early solar system may have unexpectedly contributed additional 235U, skewing the ratio. Pb-Pb dating, the method commonly used to date early solar system materials, may thus need a correction of up to 5 million years. Variable abundances of meteorite isotopes may require correcting the lead-based age of the solar system by 5 million years. The 238U/235U isotope ratio has long been considered invariant in meteoritic materials (equal to 137.88). This assumption is a cornerstone of the high-precision lead-lead dates that define the absolute age of the solar system. Calcium-aluminum–rich inclusions (CAIs) of the Allende meteorite display variable 238U/235U ratios, ranging between 137.409 ± 0.039 and 137.885 ± 0.009. This range implies substantial uncertainties in the ages that were previously determined by lead-lead dating of CAIs, which may be overestimated by several million years. The correlation of uranium isotope ratios with proxies for curium/uranium (that is, thorium/uranium and neodymium/uranium) provides strong evidence that the observed variations of 238U/235U in CAIs were produced by the decay of extant curium-247 to uranium-235 in the early solar system, with an initial 247Cm/235U ratio of approximately 1.1 × 10−4 to 2.4 × 10−4.
Early crest animals and the insight they provide into the evolutionary origin of craniates

The Cristozoa (also known as crest animals) are established as representing the animals containing neural crest and its derivatives, constituting all known craniates and their immediate precraniate precursors. The precraniate crest animals all are extinct and preserved only in Early Cambrian strata of Yunnan (southwestern China). Fine anatomical details of Haikouella and the slightly more advanced species Yunnanozoon exhibit many characters unique to vertebrates, but they lack a skull and most other elaborated placodal and neural crest derivations, throwing novel light onto the previously missing history at the very beginning of cristozoan evolution. Comparative study with the cephalochordate amphioxus suggests that precraniate evolution is marked by a series of innovations including: muscular ventilation with gill‐bearing and jointed brachial arches, paired head sensorial organs including paired eyes and nostrils, relatively large, slightly differentiated brain, protovertebrae, and some derivatives of neural crest cells. But, they lack ears, a clear telencephalon, and a skull. Furthermore, comparison of the brains of amphioxus and craniates suggests that the tripartite brain with telencephalon was not an older structure but a novelty of the craniates. genesis 46:623–639, 2008. © 2008 Wiley‐Liss, Inc.
Anatomical feasibility of transferring supinator motor branches to the posterior interosseous nerve in C7-T1 brachial plexus palsies. Laboratory investigation.

OBJECT In C7-T1 palsies of the brachial plexus, shoulder and elbow function is preserved, but finger motion is absent. Finger flexion has been reconstructed using tendon or nerve transfers. Finger extension has been restored ineffectively by attaching the extensor tendons to the distal side of the dorsal radius (that is, tenodesis). In these types of nerve palsy, supinator muscle function is preserved because innervation stems from the C-6 root. In the present study, the authors investigated the anatomy and the feasibility of transferring the supinator motor branches to the posterior interosseous nerve. Sacrifice of the supinator motor branches does not abolish supination because biceps muscle function is preserved in lower-type injuries of the brachial plexus. METHODS The posterior interosseous nerve was dissected in 20 formalin-fixed forearms. Through posterior forearm access, the posterior interosseous nerve and its motor branches to the supinator muscle were dissected. Specimens were removed for histological study. RESULTS In the vicinity of the supinator muscle's proximal margin (that is, the Frohse arcade), 2 nerve branches arose laterally and medially from the posterior interosseous nerve to innervate the superficial and deep heads of the supinator muscle, respectively. The supinator motor nerves, when divided, could be coapted directly to the posterior interosseous nerve. The number of myelinated fibers in the supinator motor branches corresponded to 70% that of the posterior interosseous nerve. CONCLUSIONS The supinator motor nerves can be transferred directly to the posterior interosseous nerve to restore thumb and finger extension in patients with C7-T1 brachial plexus lesions.