Miracle-dz/UniFAR-FTUs huggingface dataset:
Testicular structure and spermatogenesis of Amazonian freshwater cururu stingray Potamotrygon cf. histrix

Summary The cururu stingray Potamotrygon cf. histrix, a new and endemic Amazonian freshwater species, presents appropriate characteristics for fish keeping and is exploited from its natural environment. The present study identified the testicular structure and spermatogenesis of this species. Gonads from adult male specimens were dissected, fixed and processed for histological analysis. The testes were of testicular/epigonial type. The presence of germinal papillae was observed in the upper portion of organ with primordial germ cells and Sertoli cell precursors. The testis was lobular with zonal organization and cystic gametogenesis, with the occurrence of spermatoblasts. The Sertoli cells underwent morphological modifications over the course of gamete formation. The spermatozoids had long heads and were spiraled on their own axis. Information on the reproductive biology will serve as basis for studies on the reproduction and phylogeny of this peculiar group of cartilaginous fish.
A Cytoplasmic Structure Resembling Large Protein Aggregates Induced by Interferons

IFP 35 is an interferon (IFN)-regulated leucine zipper protein, expression of which is observed in a variety of cell types including monocytes/macrophages, epithelial cells and fibroblasts. Using immunofluorescence studies, we demonstrate that IFP 35 is found in characteristic punctate cytoplasmic structures after IFN treatment. Co-localization experiments using double immunofluorescence and confocal laser scanning microscopy failed to show association of IFP 35 with known organelles (mitochondria, peroxisomes, endoplasmic reticulum, lysosomes, endosomes, Golgi complex), ribosomes, or actin filaments. Subcellular fractionation to separate membrane-associated from cytoplasmic proteins demonstrated that IFP 35 localizes to the cytoplasm. Separation of postnuclear supernatant from HeLa cells by gel filtration revealed that IFP 35 eluted at a molecular mass of 200-440 kD, suggesting that IFP 35 is part of protein complexes. Electron microscopic studies showed cytoplasmic clusters of a few aggregates of IFP 35 in IFN-treated cells which were neither associated with nor surrounded by a membrane. A combination of immunoprecipitation and immunofluorescence studies of cells transfected with a hemagglutinin epitopetagged IFP 35 expression construct demonstrated complex formation and co-localization of endogenous and transfected IFP 35. Taken together, our studies demonstrate that IFP 35 associates with unique cytoplasmic structures that are distinct from known organelles and resemble large protein aggregates.
Usage behavior of a large-scale scientific archive

Archival storage systems for scientific data have been growing in both size and relevance over the past two decades, yet researchers and system designers alike must rely on limited and obsolete knowledge to guide archival management and design. To address this issue, we analyzed three years of filelevel activities from the NCAR mass storage system, providing valuable insight into a large-scale scientific archive with over 1600 users, tens of millions of files, and petabytes of data. Our examination of system usage showed that, while a subset of users were responsible for most of the activity, this activity was widely distributed at the file level. We also show that the physical grouping of files and directories on media can improve archival storage system performance. Based on our observations, we provide suggestions and guidance for both future scientific archival system designs as well as improved tracing of archival activity.
Evaluation of Balanced Ultrasound Breast Imaging Under Three Density Profile Assumptions

A balanced inverse scattering algorithm for ultrasonic breast imaging is developed to simultaneously reconstruct quantitative images of the breast's ultrasonic properties. These properties are the inhomogeneous compressibility, attenuation, and density. Three scenarios are considered for this inversion algorithm. First, all the properties are assumed to be independent. The assumption of a linear relation between the contrast of compressibility and inverse density is then considered in the second scenario, whereas the density variation is neglected in the third scenario. The image corresponding to the attenuation is of particular importance because breast tumors can be better identified using this property in comparison with compressibility and density images. However, this contrast is often poorly reconstructed because the magnitude of this contrast in the mathematical formulation of the problem is generally smaller than the magnitude of the contrasts of the other two properties. To overcome this problem, a novel balancing method is applied to all these three inversion algorithms so as to enhance the reconstruction results. Using synthetic data from MRI-based breast models, it is demonstrated that the use of the proposed balancing scheme enhances the reconstruction results of all these algorithms and, in particular, enhances their reconstructed images corresponding to the attenuation profile.
Organization of lamprey variable lymphocyte receptor C locus and repertoire development

Jawless vertebrates are pivotal representatives for studies of the evolution of adaptive immunity due to their unique position in chordate phylogeny. Lamprey and hagfish, the extant jawless vertebrates, have an alternative lymphocyte-based adaptive immune system that is based on somatically diversifying leucine-rich repeat (LRR)-based antigen receptors, termed variable lymphocyte receptors (VLRs). Lamprey T-like and B-like lymphocyte lineages have been shown to express VLRA and VLRB types of anticipatory receptors, respectively. An additional VLR type, termed VLRC, has recently been identified in arctic lamprey (Lethenteron camtschaticum), and our analysis indicates that VLRC sequences are well conserved in sea lamprey (Petromyzon marinus), L. camtschaticum, and European brook lamprey (Lampetra planeri). Genome sequences of P. marinus were analyzed to determine the organization of the VLRC-encoding locus. In addition to the incomplete germ-line VLRC gene, we have identified 182 flanking donor genomic sequences that could be used to complete the assembly of mature VLRC genes. Donor LRR cassettes were classifiable into five basic structural groups, the composition of which determines their order of use during VLRC assembly by virtue of sequence similarities to the incomplete germ-line gene and to one another. Bidirectional VLRC assembly was predicted by comparisons of mature VLRC genes with the sequences of donor LRR cassettes and verified by analysis of partially assembled intermediates. Biased and repetitive use of certain donor LRR cassettes was demonstrable in mature VLRCs. Our analysis provides insight into the unique molecular strategies used for VLRC gene assembly and repertoire diversification.
The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins

Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
Characterization of ameboid microglia isolated from developing mammalian brain

Ameboid microglia are isolated from the cerebral tissue of neonatal rat by selective cell adhesion to plastic. Histochemical markers show that the microglial preparations are homogeneous (95 +/- 3%) and represent a 10% yield from starting cultures. Isolated ameboid microglia contain nonspecific esterase activity, the macrophage surface antigens MAC-1 and MAC-3, and acetylated low-density lipoprotein receptors. Ameboid cells have functional properties similar to those of macrophages, including the ability to engulf 5 micron latex beads, to secrete Interleukin-1 (IL-1) and to release superoxide anion. Unlike monocytes and adherent spleen cells, ameboid microglia do not show peroxidase activity by histochemical stain. Unlike resident peritoneal macrophages, ameboid microglia proliferate in vitro. Scanning electron microscopy shows that ameboid cells have short, spinous processes that can be distinguished from the ruffled surfaces of body macrophages. Our observations suggest that ameboid microglia are a distinct class of mononuclear phagocytic cells. Retinoic acid and dimethyl sulfoxide, agents known to accelerate differentiation in vitro, stimulate ameboid cells to develop thin processes several hundred microns in length. These “process-bearing” microglia eventually lose the capacity to engulf latex beads and to proliferate. They also show reductions in nonspecific esterase activity and in the binding of acetylated low- density lipoprotein. We suggest that in vitro ameboid microglia differentiate into nonphagocytic cells similar to ramified microglia found in normal adult brain. The isolation techniques described here provide the opportunity to study the composition and function of different microglial subpopulations during the development of the CNS.
Why Men Matter: Mating Patterns Drive Evolution of Human Lifespan

Evolutionary theory predicts that senescence, a decline in survival rates with age, is the consequence of stronger selection on alleles that affect fertility or mortality earlier rather than later in life. Hamilton quantified this argument by showing that a rare mutation reducing survival is opposed by a selective force that declines with age over reproductive life. He used a female-only demographic model, predicting that female menopause at age ca. 50 yrs should be followed by a sharp increase in mortality, a “wall of death. ” Human lives obviously do not display such a wall. Explanations of the evolution of lifespan beyond the age of female menopause have proven difficult to describe as explicit genetic models. Here we argue that the inclusion of males and mating patterns extends Hamilton's theory and predicts the pattern of human senescence. We analyze a general two-sex model to show that selection favors survival for as long as men reproduce. Male fertility can only result from matings with fertile females, and we present a range of data showing that males much older than 50 yrs have substantial realized fertility through matings with younger females, a pattern that was likely typical among early humans. Thus old-age male fertility provides a selective force against autosomal deleterious mutations at ages far past female menopause with no sharp upper age limit, eliminating the wall of death. Our findings illustrate the evolutionary importance of males and mating preferences, and show that one-sex demographic models are insufficient to describe the forces that shape human senescence.
Individual and social network predictors of the short-term stability of bullying victimization in the United Kingdom and Germany.

BACKGROUND There is still relatively little research on the social context within which bullying develops and remains stable. AIM This study examined the short-term stability of bullying victimization among primary school students in the United Kingdom and Germany (mean age, 8.9 years) and the individual and social network factors that contributed to remaining a victim of bullying. SAMPLE The sample consisted of 454 children (247 males and 207 females). METHODS Participants completed questionnaires on bullying victimization at three assessment points over a 9-week period. Other measures consisted of self-reported demographic, peer, and family relationship characteristics. Social network indices of density, reciprocity, and hierarchy were constructed using friendship and peer acceptance nominations. RESULTS Relative risk analyses indicated a six-fold increased risk of remaining a victim at consequent follow-ups, compared to a child not victimized at baseline becoming a victim over the follow-up period. Individual characteristics explained substantially more variance in the stability of bullying victimization than class-level factors. Hierarchical logistic regression analyses revealed that being victimized by siblings and being rejected by peers predicted remaining a victim over a 9-week period. CONCLUSIONS Bullying victimization among primary school students proved moderately stable over a 9-week period. Individual characteristics were more influential in predicting the stable victim role than class-level factors. Our findings have implications for the identification of stable victims in primary school and early preventative bullying programs.
Evaluation of countermeasures for red light running by traffic simulator–based surrogate safety measures

ABSTRACT Objective: The conflicts among motorists entering a signalized intersection with the red light indication have become a national safety issue. Because of its sensitivity, efforts have been made to investigate the possible causes and effectiveness of countermeasures using comparison sites and/or before-and-after studies. Nevertheless, these approaches are ineffective when comparison sites cannot be found, or crash data sets are not readily available or not reliable for statistical analysis. Considering the random nature of red light running (RLR) crashes, an inventive approach regardless of data availability is necessary to evaluate the effectiveness of each countermeasure face to face. Method: The aims of this research are to (1) review erstwhile literature related to red light running and traffic safety models; (2) propose a practical methodology for evaluation of RLR countermeasures with a microscopic traffic simulation model and surrogate safety assessment model (SSAM); (3) apply the proposed methodology to actual signalized intersection in Virginia, with the most prevalent scenarios—increasing the yellow signal interval duration, installing an advance warning sign, and an RLR camera; and (4) analyze the relative effectiveness by RLR frequency and the number of conflicts (rear-end and crossing). Results: All scenarios show a reduction in RLR frequency (−7.8, −45.5, and −52.4%, respectively), but only increasing the yellow signal interval duration results in a reduced total number of conflicts (−11.3%; a surrogate safety measure of possible RLR-related crashes). An RLR camera makes the greatest reduction (−60.9%) in crossing conflicts (a surrogate safety measure of possible angle crashes), whereas increasing the yellow signal interval duration results in only a 12.8% reduction of rear-end conflicts (a surrogate safety measure of possible rear-end crash). Conclusions: Although increasing the yellow signal interval duration is advantageous because this reduces the total conflicts (a possibility of total RLR-related crashes), each countermeasure shows different effects by RLR-related conflict types that can be referred to when making a decision. Given that each intersection has different RLR crash issues, evaluated countermeasures are directly applicable to enhance the cost and time effectiveness, according to the situation of the target intersection. In addition, the proposed methodology is replicable at any site that has a dearth of crash data and/or comparison sites in order to test any other countermeasures (both engineering and enforcement countermeasures) for RLR crashes.
Intratympanic Dexamethasone for Sudden Sensorineural Hearing Loss After Failure of Systemic Therapy

Objective: Intratympanic steroids are increasingly used in the treatment of inner ear disorders, especially in patients with sudden sensorineural hearing loss (SNHL) who have failed systemic therapy. We reviewed our experience with intratympanic steroids in the treatment of patients with sudden SNHL to determine overall success, morbidity, and prognostic factors.
On seeing the trees and the forest: Single‐signal and multisignal analysis of periictal intracranial EEG

Purpose: Epileptic seizures are associated with a dysregulation of electrical brain activity on many different spatial scales. To better understand the dynamics of epileptic seizures, that is, how the seizures initiate, propagate, and terminate, it is important to consider changes of electrical brain activity on different spatial scales. Herein we set out to analyze periictal electrical brain activity on comparatively small and large spatial scales by assessing changes in single intracranial electroencephalography (EEG) signals and of averaged interdependences of pairs of EEG signals.
Evaluation of gastric emptying in patients with chronic renal failure on continuous ambulatory peritoneal dialysis using 99mTc-solid meal.

BACKGROUND Continuous ambulatory peritoneal dialysis (CAPD) is an alternative to the hemodialysis mode of terminal renal failure treatment. Nutritional status impairment is common among patients with end-stage renal disease, and its laboratory surrogates predict increased morbidity and mortality risk in patients on chronic haemodialysis or peritoneal dialyses. The aetiology of malnutrition is multifactorial and delayed gastric emptying is also considered to be a significant factor. The aim of this study was to estimate the direct influence of indwelled dialysate in the peritoneal cavity on gastric emptying in patients treated with CAPD. MATERIAL AND METHODS the study group included 20 patients (9 males, 11 females) aged 50,1 +/- 11 years (range: 39-75 years) with chronic renal failure treated with CAPD for 18.4 +/- 14.7 months. All patients were non-diabetic and had no other than chronic uraemia co-morbidity known to influence autonomic nervous system function and gastric motility. The control group included 15 healthy volunteers matched by age, sex and body weight. Dialysis adequacy parameters were calculated based on 24-hour urine and dialysate collections. Gastric emptying was estimated with dynamic abdominal scintigraphy. We compared the results of gastric emptying tests performed in dialysed patients with and without dialysate liquid in the peritoneal cavity and related the values to those of the control subjects. RESULTS In the study group, weekly values of dialysis parameters were within the ranges considered satisfactory in terms of uraemia control. All parameters of gastric emptying were significantly delayed and prolonged in terminal renal failure patients, but the results have shown no significant differences between those with and without indwelling dialysate. CONCLUSIONS Based on the results we conclude that gastric emptying in subjects with chronic renal failure treated with CAPD is markedly delayed compared to healthy subjects. There was no significant effect of indwelling dialysate in the peritoneal cavity on gastric emptying rates found, based on the observation that its removal was not associated with any noticeable improvement of gastric emptying. The data strongly contraindicate the theory of peritoneal dialysate volume being the cause of this reversible disorder and indicate that the role of other possible factors leading to the development of gastropathy in those patients should be investigated.
THE MECHANISM OF DNA REPLICATION AND GENETIC RECOMBINATION IN PHAGE.

Preliminary kinetic studies on virucidal activity of human serum suggest that more than one factor may limit the reaction. In view of the multicomponent nature of C', experiments-were performed to determine whether a C' component as well as properdin is a limiting factor. Accordingly, a constant volume of Rp, which contains C' components, was added to increasing quantities of serum. The virucidal activity of these mixtures was significantly less than that of serum alone, suggesting inhibition by high concentrations of serum constituents. Experiments are now being carried out using phage labeled with p32 or S15, in order to elucidate the mechanism of phage neutralization by the properdin system. Summary. -The phage-neutralizing action of fresh human serum is heat labile and is dependent on the four recognized components of complement, on properdin, and on a divalent cation(s). Phage neutralization by fresh serum may be of use in assaying properdin.
Autocrine TGF-β and stromal cell-derived factor-1 (SDF-1) signaling drives the evolution of tumor-promoting mammary stromal myofibroblasts

Much interest is currently focused on the emerging role of tumor-stroma interactions essential for supporting tumor progression. Carcinoma-associated fibroblasts (CAFs), frequently present in the stroma of human breast carcinomas, include a large number of myofibroblasts, a hallmark of activated fibroblasts. These fibroblasts have an ability to substantially promote tumorigenesis. However, the precise cellular origins of CAFs and the molecular mechanisms by which these cells evolve into tumor-promoting myofibroblasts remain unclear. Using a coimplantation breast tumor xenograft model, we show that resident human mammary fibroblasts progressively convert into CAF myofibroblasts during the course of tumor progression. These cells increasingly acquire two autocrine signaling loops, mediated by TGF-β and SDF-1 cytokines, which both act in autostimulatory and cross-communicating fashions. These autocrine-signaling loops initiate and maintain the differentiation of fibroblasts into myofibroblasts and the concurrent tumor-promoting phenotype. Collectively, these findings indicate that the establishment of the self-sustaining TGF-β and SDF-1 autocrine signaling gives rise to tumor-promoting CAF myofibroblasts during tumor progression. This autocrine-signaling mechanism may prove to be an attractive therapeutic target to block the evolution of tumor-promoting CAFs.
Laser in situ Keratomileusis Retreatment for Residual Myopia and Astigmatism

A ll surgical procedures have the potential for side effects and complications, and refractive surgery is no exception. 1 Laser in situ ker-atomileusis (LASIK) may be the corneal refractive procedure with the fewest complications. Although the predictability of LASIK is high and better than other refractive procedures, the nature of surgery upon living tissue is such that accurate prediction of refractive outcome is not entirely possible. Fortunately, with the current excimer laser algorithms , overcorrection rarely occurs after LASIK performed for correction of myopia and myopic astigmatism. However, undercorrection and/or regression of the achieved correction of myopia or astigmatism are inevitable in some eyes. 417 LASIK procedures were performed by the author at Almana General Hospital in Dammam for correction of myopia ranging from-1.00 to-17.00 diopters (D). The surgical technique and results of the first 157 consecutive eyes were reported. Forty-six of 417 eyes (11.0%) were undercorrected by 1.00 D or more. In eleven eyes, patients were satisfied with their results and decided not to have additional treatment. Overcorrection did not exceed +0.50 D in any eye. This study reports the results of LASIK retreat-ment performed on 35 eyes of 23 patients for correction of residual myopia, with or without astigma-tism. All these patients had undergone LASIK for correction of myopia (and astigmatism), and after at least 3 months from their primary LASIK procedure, they still had 1.00 D or more of residual myopia, with or without residual astigmatism.