Miracle-dz/UniFAR-FTUs huggingface dataset:
Abnormal Cortical Development after Premature Birth Shown by Altered Allometric Scaling of Brain Growth

Background We postulated that during ontogenesis cortical surface area and cerebral volume are related by a scaling law whose exponent gives a quantitative measure of cortical development. We used this approach to investigate the hypothesis that premature termination of the intrauterine environment by preterm birth reduces cortical development in a dose-dependent manner, providing a neural substrate for functional impairment. Methods and Findings We analyzed 274 magnetic resonance images that recorded brain growth from 23 to 48 wk of gestation in 113 extremely preterm infants born at 22 to 29 wk of gestation, 63 of whom underwent neurodevelopmental assessment at a median age of 2 y. Cortical surface area was related to cerebral volume by a scaling law with an exponent of 1.29 (95% confidence interval, 1.25–1.33), which was proportional to later neurodevelopmental impairment. Increasing prematurity and male gender were associated with a lower scaling exponent (p < 0.0001) independent of intrauterine or postnatal somatic growth. Conclusions Human brain growth obeys an allometric scaling relation that is disrupted by preterm birth in a dose-dependent, sexually dimorphic fashion that directly parallels the incidence of neurodevelopmental impairments in preterm infants. This result focuses attention on brain growth and cortical development during the weeks following preterm delivery as a neural substrate for neurodevelopmental impairment after premature delivery.
MRI of Rectal Cancer: An Overview and Update on Recent Advances.

OBJECTIVE MRI is the modality of choice for rectal cancer staging. The high soft-tissue contrast of MRI accurately assesses the extramural tumor spread and relation to mesorectal fascia and the sphincter complex. This article reviews the role of MRI in the staging and treatment of rectal cancer. The relevant anatomy, MRI techniques, preoperative staging, post-chemoradiation therapy (CRT) imaging, and tumor recurrence are discussed with special attention to recent advances in knowledge. CONCLUSION MRI is the modality of choice for staging rectal cancer to assist surgeons in obtaining negative surgical margins. MRI facilitates the accurate assessment of mesorectal fascia and the sphincter complex for surgical planning. Multiparametric MRI may also help in the prediction and estimation of response to treatment and in the detection of recurrent disease.
A novel double antibody sandwich-lateral flow immunoassay for the rapid and simple detection of hepatitis C virus

The objective of this study was to screen for antigens of the hepatitis C virus (HCV) to establish a new double antibody sandwich-lateral flow immunoassay (DAS-LFIA) method for testing the presence of anti-HCV antibodies in human serum or plasma. A series of different recombinant HCV proteins in Escherichia coli cells were constructed, expressed, purified and the new DAS-LFIA strip was developed. The sensitivity and specificity of new the DAS-LFIA strip were evaluated by detecting 23 HCV-positive sera, a set of quality control references for anti-HCV detection that contain known amounts of anti-HCV antibodies, and 8 HCV-negative sera. A total of 300 clinical serum samples was examined by both the new DAS-LFIA strip and enzyme-linked immunosorbent assay (ELISA). Data were analyzed using SPSS 11.5 software. The sensitivity and specificity of the new DAS-LFIA strip were 100%. The lowest test line of the HCV DAS-LFIA strips was 2 NCU/ml. Additionally, the concordance between the new DAS-LFIA strip and ELISA methods was 94.33%. In conclusion, our new testing method is rapid, simple, sensitive and specifically detects the presence of anti-HCV antibodies in human serum or plasma. Therefore, it may be used for monitoring HCV.
Characterization of Ocular Methicillin-Resistant Staphylococcus epidermidis Isolates Belonging Predominantly to Clonal Complex 2 Subcluster II

ABSTRACT Staphylococcus epidermidis is an abundant member of the microbiota of the human skin and wet mucosa, which is commonly associated with sight-threatening infections in eyes with predisposing factors. Ocular S. epidermidis has become notorious because of its capability to form biofilms on different ocular devices and due to the evolving rates of antimicrobial resistance. In this study, the molecular epidemiology of 30 ocular methicillin-resistant S. epidermidis (MRSE) isolates was assessed using multilocus sequence typing (MLST). Antimicrobial resistance, accessory gene-regulator and staphylococcal cassette chromosome mec (SCCmec) types, biofilm formation, and the occurrence of biofilm-associated genes were correlated with MLST clonal complexes. Sequence types (STs) frequently found in the hospital setting were rarely found in our collection. Overall, 12 different STs were detected with a predominance of ST59 (30%), ST5 and ST6 (13.3% each). Most of the isolates (93.3%) belonged to the clonal complex 2 (CC2) and grouped mainly within subcluster CC2-II (92.9%). Isolates grouped within this subcluster were frequently biofilm producers (92.3%) with a higher occurrence of the aap (84.5%) and bhp (46.1%) genes compared to icaA (19.2%). SCCmec type IV (53.8%) was predominant within CC2-II strains, while 38.4% were nontypeable. In addition, CC2-II strains were frequently multidrug resistant (80.7%) and demonstrated to be particularly resistant to ciprofloxacin (80.8%), ofloxacin (77%), azithromycin (61.5%), and gentamicin (57.7%). Our findings demonstrate the predominance of a particular MRSE cluster causing ocular infections, which was associated with high rates of antimicrobial resistance and particularly the carriage of biofilm-related genes coding for proteinaceous factors implicated in biofilm accumulation.
Studies on the host–parasite interface of strigeoid trematodes

The adhesive organ of Apatemon gracilis minor Yamaguti, 1933, consists of two lobes lying in a cup-shaped fore-body. The cytoplasmic tegument covering the apposing faces of the lobes is different from that covering their outer surfaces. The covering of the outer surface corresponds to the general tegument present on the rest of the body, whereas that on the inner surfaces is finely pitted and in certain regions is elevated to form a coarse reticulum. This specialized surface is covered externally by a plasma membrane and is in continuity with nucleated cell bodies lying below the basement layer. The cell bodies contain large quantities of granular endoplasmic reticulum as well as several Golgi complexes and numerous mitochondria. Masses of secretion bodies are present and these also occur in the extensions to the external tegument as well as within the external tegument of the lobes. When the parasite is attached the inner faces of the lobes come into contact with the vascular lamina propria of the host. The possible biological role of this specialized host–parasite interface is discussed and it is suggested that this surface specialization may form a morphological basis for the ‘placental’ function suggested for the adhesive organ by earlier workers. The author wishes to acknowledge the research grant provided by the S.R. C. for the purchase of a vacuum coating unit and an AEI EM 6 electron microscope. The progress of this study was greatly facilitated by the excellent assistance of Mr T. Davies and Miss C. Green. The Stereoscan micrographs are published by permission of the Cambridge Instrument Company.
Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces

Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat samples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition.
Reconstruction of audio waveforms from spike trains of artificial cochlea models

Spiking cochlea models describe the analog processing and spike generation process within the biological cochlea. Reconstructing the audio input from the artificial cochlea spikes is therefore useful for understanding the fidelity of the information preserved in the spikes. The reconstruction process is challenging particularly for spikes from the mixed signal (analog/digital) integrated circuit (IC) cochleas because of multiple non-linearities in the model and the additional variance caused by random transistor mismatch. This work proposes an offline method for reconstructing the audio input from spike responses of both a particular spike-based hardware model called the AEREAR2 cochlea and an equivalent software cochlea model. This method was previously used to reconstruct the auditory stimulus based on the peri-stimulus histogram of spike responses recorded in the ferret auditory cortex. The reconstructed audio from the hardware cochlea is evaluated against an analogous software model using objective measures of speech quality and intelligibility; and further tested in a word recognition task. The reconstructed audio under low signal-to-noise (SNR) conditions (SNR < –5 dB) gives a better classification performance than the original SNR input in this word recognition task.
Probing the Pareto Frontier for Basis Pursuit Solutions

The basis pursuit problem seeks a minimum one-norm solution of an underdetermined least-squares problem. Basis pursuit denoise (BPDN) fits the least-squares problem only approximately, and a single parameter determines a curve that traces the optimal trade-off between the least-squares fit and the one-norm of the solution. We prove that this curve is convex and continuously differentiable over all points of interest, and show that it gives an explicit relationship to two other optimization problems closely related to BPDN. We describe a root-finding algorithm for finding arbitrary points on this curve; the algorithm is suitable for problems that are large scale and for those that are in the complex domain. At each iteration, a spectral gradient-projection method approximately minimizes a least-squares problem with an explicit one-norm constraint. Only matrix-vector operations are required. The primal-dual solution of this problem gives function and derivative information needed for the root-finding method. Numerical experiments on a comprehensive set of test problems demonstrate that the method scales well to large problems.
MicroRNA-1291 promotes endometrial fibrosis by regulating the ArhGAP29-RhoA/ROCK1 signaling pathway in a murine model

Intrauterine adhesions (IUAs) are caused by endometrial damage and are associated with a poor pregnancy prognosis including infertility, oligomenorrhea and recurrent pregnancy loss. Understanding the pathogenesis of IUAs may help prevent and treat this condition more effectively. The aim of the current study was to investigate the function of microRNA-1291 (miR-1291) during the development of IUAs following endometrial damage and elucidate the potential molecular mechanisms involved. The expression of Rho GTPase activating protein 29 (ArhGAP29), a putative target mRNA of miR-1291, was determined by immunohistochemical staining of human endometrial tissue from patients with IUAs and compared with normal endometrial tissues. ArhGAP29 expression was significantly decreased in endometrial tissues with IUAs compared with normal endometrium. Additionally, a murine IUAs model was developed and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) demonstrated that miR-1291 levels were significantly increased in the uterine tissue and plasma of the IUAs group compared with the normal mice. Furthermore, an miR-1291 antagomir was injected into the uterine cavity of experimental IUAs mice to block miR-1291. Hematoxylin and eosin and Masson's stain revealed that blocking miR-1291 significantly ameliorated endometrial fibrosis. Furthermore, levels of epithelial mesenchymal transition (EMT)-associated proteins, and ArhGAP29-RhoA/Rho-associated coiled coil containing protein kinase 1 (ROCK1) were measured in uterine tissue by western blot, RT-qPCR analysis and immunofluorescence staining. Levels of the mesenchymal marker proteins, vimentin and N-cadherin, were increased in the IUAs group mice, accompanied by a relative decrease in the epithelial marker proteins, cytokeratin and E-cadherin compared with normal murine endometrium. miR-1291 inhibition decreased RhoA/ROCK1 expression in the EMT pathway, but increased ArhGAP29 expression. Taken together, the findings indicate that miR-1291 acts upstream of ArhGAP29 to negatively regulate the RhoA/ROCK1 EMT pathway, ultimately leading to endometrial fibrosis. These studies may provide new potential therapeutic options and pave the way to use circulating miR-1291 as a clinical biomarker of endometrial fibrosis.
TNFα blockade prevents the development of inflammatory bowel disease in HLA-B27 transgenic rats

Rats transgenic for HLA‐B27 and human β2microglobulin (B27TR) develop a multi‐systemic disease resembling inflammatory bowel disease (IBD) and spondyloarthritis. TNFα has a crucial role in chronic inflammation. Our objective was to evaluate the effect of anti‐TNFα treatment on spontaneous IBD in B27TR. Nine‐week‐old B27TR received monoclonal anti‐TNFα or an isotypic IgG2a,k up to age of 18 weeks. A second group was monitored up to 18 weeks and then randomly assigned to anti‐TNFα or IgG2 a,k treatment. Each rat was monitored for clinical IBD manifestations. After sacrifice, the colon was examined for pathological changes. TNFα receptors (TNF‐R1, TNF‐R2), Fas/Fas‐L expression and apoptosis were evaluated. IgG2a,k‐treated and untreated B27TR presented signs of IBD at 11 weeks, whereas in anti‐TNFα‐treated B27TR no IBD signs were detected. In the late treatment, IBD signs improved after 1 week. Histopathological analysis of IgG2a,k‐treated B27TR colon showed inflammatory signs that were widely prevented by early anti‐TNFα treatment. Late treatment did not significantly reduce inflammation. TNF‐R1 was weakly expressed in intestinal epithelial cells of IgG2a,k‐treated B27TR, while it was comparable to controls in anti‐TNFα‐treated animals. TNF‐R2 immunopositivity was strongly evident in IgG2a,k‐treated B27TR, whereas was absent in anti‐TNFα‐treated rats. RT‐PCR confirmed these results. IgG2a,k‐treated B27TR showed, at 18 weeks, few Fas‐positive cells and an increase of Fas‐L‐positive cells. At 27 weeks, Fas‐/Fas‐L‐positive cell number was significantly low. Anti‐TNFα treatment increased Fas‐L expression, whereas Fas increased only with the early treatment. TNFα blockade is effective in preventing inflammation in early phase of IBD, maintaining the homeostatic balance of apoptosis.
Challenges of Highly Adaptable Information Systems

In other words, information systems in these domains must be highly adaptable if they are to satisfy users’ complex and rapidly evolving requirements. This position paper identifies four current research areas in software engineering that are critical success factors for the development of highly adaptable information systems. The e-learning domain is used as a running example. Section 2 introduces some background material and related work in the areas of information system architecture, software evolution and e-learning. Section 3 outlines the issues that define this research programme. Section 4 relates these concerns to current research in the Applied Software Engineering Research Group at the University of Reading.
Boundary Layer Oscillations from Thunderstorms at Sydney Airport

Abstract Analyses of wind velocity and air pressure data, acquired by a set of low-level anemometers at Sydney Airport, Australia, indicate the passage of a set of three remarkably smooth atmospheric boundary layer oscillations that traveled ahead of a thunderstorm on 27 December 1991. The oscillations were probably generated by a nearby thunderstorm outflow, propagating into a stably stratified atmospheric layer. It is likely that the phenomenon was initiated by the degenerating of an outflow gravity current into a family of amplitude-ordered solitary waves. Although reasonable agreement can be obtained on the propagation speed using a linear theory, the weakness of the trapping mechanism for this solution and an overestimation of the weakly nonlinear wave half-width leads to a conclusion that the waves fully nonlinear.
Conditional Reduction of Adult Born Doublecortin-Positive Neurons Reversibly Impairs Selective Behaviors

Adult neurogenesis occurs in the adult mammalian subventricular zone (SVZ) along the walls of the lateral ventricles and the subgranular zone (SGZ) of the hippocampal dentate gyrus. While a burgeoning body of research implicates adult neurogenesis in olfactory bulb (OB)- and hippocampal-related behaviors, the precise function continues to elude. To further assess the behavioral importance of adult neurogenesis, we herein generated a novel inducible transgenic mouse model of adult neurogenesis reduction where mice with CreERT2 under doublecortin (DCX) promoter control were crossed with mice where diphtheria toxin A (DTA) was driven by the Rosa26 promoter. Activation of DTA, through the administration of tamoxifen (TAM), results in a specific reduction of DCX+ immature neurons in both the hippocampal dentate gyrus and OB. We show that the decrease of DCX+ cells causes impaired social discrimination ability in both young adult (from 3 months) and middle aged (from 10 months) mice. Furthermore, these animals showed an age-independent altered coping behavior in the Forced Swim Test without clear changes in anxiety-related behavior. Notably, these behavior changes were reversible on repopulating the neurogenic zones with DCX+ cells on cessation of the TAM treatment, demonstrating the specificity of this effect. Overall, these results support the notion that adult neurogenesis plays a role in social memory and in stress coping but not necessarily in anxiety-related behavior.
The Representation of Tool Use in Humans and Monkeys: Common and Uniquely Human Features

Though other species of primates also use tools, humans appear unique in their capacity to understand the causal relationship between tools and the result of their use. In a comparative fMRI study, we scanned a large cohort of human volunteers and untrained monkeys, as well as two monkeys trained to use tools, while they observed hand actions and actions performed using simple tools. In both species, the observation of an action, regardless of how performed, activated occipitotemporal, intraparietal, and ventral premotor cortex, bilaterally. In humans, the observation of actions done with simple tools yielded an additional, specific activation of a rostral sector of the left inferior parietal lobule (IPL). This latter site was considered human-specific, as it was not observed in monkey IPL for any of the tool videos presented, even after monkeys had become proficient in using a rake or pliers through extensive training. In conclusion, while the observation of a grasping hand activated similar regions in humans and monkeys, an additional specific sector of IPL devoted to tool use has evolved in Homo sapiens, although tool-specific neurons might reside in the monkey grasping regions. These results shed new light on the changes of the hominid brain during evolution.
Aerobic bacterial flora of the normal conjunctiva at high altitude area of Shimla Hills in India: a hospital based study.

AIM To study the normal aerobic conjunctival flora in lower to mid Himalayan region of Shimla Hills. METHODS Samples from normal conjunctiva of 200 individuals above the age of 13 years who visited Indira Gandhi Medical College Hospital Shimla for refraction or cataract surgery were taken by anaesthetising the conjunctival sac with sterile 4% Xylocaine solution. Samples were obtained by gently rubbing lower fornix with a sterile cotton wool swab moistened with normal saline and keeping the eye lids wide apart to avoid contamination from lid margins. It was immediately inoculated in Brain Heart infusion and subjected to standard aerobic culture and identification techniques. RESULTS Totally, 72 eyes (36%) conjunctival sacs were sterile. Predominant aerobes isolated were Staphylococcus spp. in 120 (60%) followed by Haemophilus in 16 (8%), diphtheroids in 10 (5%), and Escherichia.coli (E. coli) in 4 (2%). A single aerobe was isolated from 98 eyes (49%) while 30 eyes (15%) yielded more than 1 aerobe. Staphylococcus epidermidis (S. epidermidis) was the most common bacterium, found alone in 58 eyes (29%) and in combination with another aerobe in 30 eyes (15%), followed by Staphylococcus aureus (S. aureus) in 18 (9%) and 10 eyes (5%) respectively. CONCLUSION S. epidermidis is the most common commensal organism followed by Haemophilus species. diphtheroids occupied the third position which otherwise are found more abundantly in literature. Pathogens like S. aureus, Staphylococcus citreus and E. coli were also found. Therefore, preoperative administration of topical broad spectrum antibiotics is extremely important in prophylaxis against ocular infection. The variation in microflora of normal conjunctiva in this part of world can be attributed to geographical, climatic and ethnic characteristics of the population under study.
In Utero Hepatocellular Transplantation in Rats

This work represents a step forward in the experimental design of an in utero hepatocellular transplantation model in rats. We focused on the enrichment optimization of isolated fetal hepatocytes suspension, arranging the surgery methodology of in utero transplantation, monitoring the biodistribution of the transplanted hepatocytes, and assessing the success of the transplants. Rat fetuses have been transplanted at the 17th embryonic day (ED17) with fetal hepatocytes isolated from rats at the end of pregnancy (ED21). We assessed possible differences between lymphocyte population, CD4 positive, CD8 positive, double-positive T-cells, and anti-inflammatory cytokines interleukins 4 and 10 (IL4 and IL10) as well. Cellular viability reached the rates of 90–95%. Transplanted groups had a limited success. Transplanted hepatocytes were not able to pass through the hematoplacental barrier. The hepatocytes injected were primarily located in the liver. There was an upward trend in the whole amount of T CD4 and T CD8 cells. There was an increased IL4 in the transplanted groups observed in the pregnant rats. The possibility to induce tolerance in fetuses with a hepatocyte transplant in utero could be a key point to avoid the immunosuppression treatments which must be undergone by transplanted patients.
A real‐time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution

Aims: To develop a quantitative, real‐time PCR assay to detect the nifH gene of Methanobrevibacter smithii. Methanobrevibacter smithii is a methanogenic archaea found in the intestinal tract of humans that may be a useful indicator of sewage pollution in water.