Miracle-dz/UniFAR-FTUs huggingface dataset:
Management of severe community-acquired pneumonia of children in developing and developed countries

Childhood community-acquired pneumonia (CAP) is common, and recent data have shown that the number of children with severe CAP is increasing worldwide. Regardless of geographical area, severe cases are those at the highest risk of hospitalisation, prolonged hospitalisation and death, and therefore require prompt identification and the most effective treatment in order to reduce CAP-related morbidity and mortality. This review evaluates the available data concerning the diagnosis and treatment of severe and/or complicated cases of paediatric CAP in developed and developing countries. It also underlines the fact that any evidence-based recommendations require more research in various areas, including the aetiology of severe cases and the reasons for the complications, the better definition of first-choice antibiotic treatment and when surgery may be useful, and the role of chest physiotherapy.
Plasmodium falciparum possesses two GRASP proteins that are differentially targeted to the Golgi complex via a higher- and lower-eukaryote-like mechanism

Plasmodium falciparum, the causative agent of malaria, relies on a complex protein-secretion system for protein targeting into numerous subcellular destinations. Recently, a homologue of the Golgi re-assembly stacking protein (GRASP) was identified and used to characterise the Golgi organisation in this parasite. Here, we report on the presence of a splice variant that leads to the expression of a GRASP isoform. Although the first GRASP protein (GRASP1) relies on a well-conserved myristoylation motif, the variant (GRASP2) displays a different N-terminus, similar to GRASPs found in fungi. Phylogenetic analyses between GRASP proteins of numerous taxa point to an independent evolution of the unusual N-terminus that could reflect unique requirements for Golgi-dependent protein sorting and organelle biogenesis in P. falciparum. Golgi association of GRASP2 depends on the hydrophobic N-terminus that resembles a signal anchor, leading to a unique mode of Golgi targeting and membrane attachment.
Adherence of pilus- Opa+ gonococci to epithelial cells in vitro involves heparan sulfate

Neisseria gonorrhoeae attaches to host epithelial cells via pili and opacity-associated (Opa) outer membrane proteins. Pilus- gonococci (Gc) of strain MS11 adhere to both human and nonhuman cells, but only when particular Opa proteins are expressed; OpaA+ variants adhere best, OpaC+ variants are next best, and the seven other Opa+ variants adhere poorly or not at all. The adherence of OpaA+ Gc to Chinese hamster ovary (CHO) cells is inhibited by heparin or heparan sulfate (HS), but not by chondroitin sulfate. OpaA+ Gc do not adhere to CHO cells devoid of HS proteoglycans; low concentrations of heparin restore OpaA+ Gc adherence to these HS-deficient CHO cells and high concentrations inhibit it. 3H-heparin binding to whole Gc parallels their adherence abilities (OpaA+ > OpaC+ > OpaH+ >> Opas B, D, E, F, G, I = Opa- = 0). Opa proteins separated by SDS-PAGE also bind 3H-heparin. These data suggest that adherence of pilus-, Opa+ Gc involves HS-proteoglycan of eukaryotic cells.
Caffeine Decreases Topiramate Levels in Zebrafish Larvae in a Pentylenetetrazol-Induced Seizure Model

Epilepsy ranks as the second-most prevalent neurological disease, and is characterized by seizures resulting in neurobiological and behavioral impairment. Naturally occurring in coffee beans or tea leaves, the alkaloid caffeine (CAF) is the most prevalent global stimulant. Caffeine has been observed to influence epileptic seizures and the efficacy of antiepileptic medications, with a notable impact on topiramate (TPM). This study aimed to explore the influence of CAF on TPM’s anticonvulsant effects in zebrafish larvae within a PTZ-induced seizure model, concurrently determining TPM concentrations through a sophisticated analytical approach based on ultrahigh-performance liquid chromatography and subsequent mass spectrometric detection. Zebrafish larvae four days post-fertilization were incubated for 18 h with varying doses of TPM or combinations of CAF + TPM, and locomotor activity was then assessed. Seizures were induced by introducing a PTZ solution to achieve a final concentration of 20 mM. Utilizing liquid chromatography–mass spectrometry (LC–MS/MS), TPM levels in the larvae were quantified. CAF co-administration (especially in higher doses) with TPM caused a decrease in the average locomotor activity in the larvae compared to TPM alone. Moreover, CAF decreased TPM levels in the larvae at all investigated doses. In conclusion, these findings offer a novel perspective on the interplay between CAF and TPM, shedding light on previously unexplored facets. The potential impact of CAF consumption in assisting with epileptic seizure control, unless proven otherwise, suggests a noteworthy consideration for future research and clinical practices.
Nimesulide-Induced Fixed Drug Eruption Followed by Etoricoxib-Induced Fixed Drug Eruption: An Unusual Case Report and Review of the Literature

Fixed drug eruption (FDE) is a well-recognized, non-immediate, drug hypersensitivity reaction, often attributed to the use of various medications, most commonly non-steroidal anti-inflammatory drugs (NSAIDs) and antibiotics. Cross-reactivity between related NSAIDs in FDE has been reported, but among chemically unrelated NSAIDs, is rare. Herein, we present a rare well-documented case where a patient initially displayed tolerance to etoricoxib after experiencing a nimesulide-induced FDE. Subsequently, the patient developed an etoricoxib-induced FDE, accompanied by the development of bullous lesions. This case report and the literature review on comparable FDE occurrences shed light on the intricate nature of FDEs, suggesting the possibility of cross-reactivity between chemically related and unrelated NSAIDs or the emergence of new drug-specific T cells without cross-reactivity after multiple exposures to a drug in a susceptible patient. Our case underscores the importance of increased awareness and vigilance among both physicians and patients in the realm of personalized medicine. Further research is needed to unravel the intricate mechanisms behind these drug eruptions, improve diagnostic approaches, and enhance patient care.
Neopolyploidy and pathogen resistance

Despite the well-documented historical importance of polyploidy, the mechanisms responsible for the establishment and evolutionary success of novel polyploid lineages remain unresolved. One possibility, which has not been previously evaluated theoretically, is that novel polyploid lineages are initially more resistant to pathogens than the diploid progenitor species. Here, we explore this possibility by developing and analysing mathematical models of interactions between newly formed polyploid lineages and their pathogens. We find that for the genetic mechanisms of pathogen resistance with the best empirical support, newly formed polyploid populations of hosts are expected to be more resistant than their diploid progenitors. This effect can be quite strong and, in the case of perennial species with recurrent polyploid formation, may last indefinitely, potentially providing a general explanation for the successful establishment of novel polyploid lineages.
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

Structural genomics is an international effort to determine the three‐dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the “Pfam5000” strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These strategies include complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss‐Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at the European Bioinformatics Institute (EBI). Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68% of all prokaryotic proteins (covering 59% of residues) and 61% of eukaryotic proteins (40% of residues). More fine‐grained coverage that would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example, to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: A significant fraction (about 30–40% of the proteins and 40–60% of the residues) of each proteome is classified in small families, which may have little overlap with other species of interest. Random selection of targets from one or more genomes is similar to the Pfam5000 strategy in that proteins from larger families are more likely to be chosen, but substantial effort would be spent on small families. Proteins 2005. © 2004 Wiley‐Liss, Inc.
A Graph-Based Meta-Data Model for DevOps: Extensions to SSP and SysML2 and a Review on the DCP standard

Computer simulation has become a vital tool for modeling complex systems. However, the development and deployment of simulation models often involve multiple stages, tools, and teams, which can lead to significant challenges in maintaining quality, reliability, and efficiency. DevOps, a set of practices that combines software development and IT operations, has emerged as a promising approach to streamline the simulation development. However, most system engineers are not DevOps specialists and there are a lot of manual steps involved when writing build pipelines and configurations of simulations. For this purpose, an abstract graph-based meta-data model was presented in previous work to provide an automation framework for DevOps with simulations. In this work we want to continue our investigations by expanding and harmonizing this approach to better work with established standards like SSP, SysML2 and DCP and demonstrating it's application on real-life use cases.
Practical Linguistic Steganography using Contextual Synonym Substitution and a Novel Vertex Coding Method

Linguistic steganography is concerned with hiding information in natural language text. One of the major transformations used in linguistic steganography is synonym substitution. However, few existing studies have studied the practical application of this approach. In this article we propose two improvements to the use of synonym substitution for encoding hidden bits of information. First, we use the Google n-gram corpus for checking the applicability of a synonym in context, and we evaluate this method using data from the SemEval lexical substitution task and human annotated data. Second, we address the problem that arises from words with more than one sense, which creates a potential ambiguity in terms of which bits are represented by a particular word. We develop a novel method in which words are the vertices in a graph, synonyms are linked by edges, and the bits assigned to a word are determined by a vertex coding algorithm. This method ensures that each word represents a unique sequence of bits, without cutting out large numbers of synonyms, and thus maintains a reasonable embedding capacity.
Hand-held microsurgical forceps with force-feedback for micromanipulation

This paper presents a hand-held microsurgical forceps design with force-feedback capabilities designed for micromanipulation tasks. The device uses a customized force sensor that measures grasping forces over a range of 0-300mN and uses an actuator to exert amplified forces back on to the operator's fingertip in a mechanically-ungrounded setup. This allows perception of low force levels that are otherwise imperceptible to human touch. A customized force sensor design for the forceps grasping measurement is presented and a calibration experiment was conducted to validate its linearity and repeatability. A bench test of the device was conducted to demonstrate its intrinsic force-amplifying capabilities, with amplification factors of up to ×50 reported. A user study was conducted to confirm that the device could significantly improve human perception of grasping forces compared to conventional microsurgical forceps with the results demonstrating an order-of-magnitude improvement in force perception.
Unlocking the Uterine Code: Microbiota, Immune Cells, and Therapy for Recurrent Reproductive Failure

The uterine microbiota has been the subject of increasing study, but its interaction with the local immune system remains unclear. Successful embryo implantation relies on endometrial receptivity, which is pivotal for immunological tolerance to fetal antigens and precise regulation of inflammatory mediators. Emerging data suggest a dynamic interplay between endometrial microflora and the immune system, making dysbiosis a potential determinant of pregnancy outcomes. Imbalances in the regulation of immune cells in the endometrium and decidua have been associated with infertility, miscarriage, and obstetric complications. A thorough comprehension of the immune system in the female reproductive tract shows potential for improving women’s health and pregnancy outcomes. The objective of this study was to evaluate the patterns of endometrial microbiota in patients with recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL) and to explore their implications for endometrial immune cells and chronic endometritis (CE). Immune cells in biopsies from 107 RIF and 93 RPL patients were examined using flow cytometry. The endometrial microbial composition was analyzed using real-time polymerase chain reaction (RT-PCR). The research uncovered disrupted endometrial microbiota in most women with RIF and RPL, which was often associated with significant effects on lymphocytes, T cells, and uNK cells.
Evolution in the Treatment of Delayed Postpancreatectomy Hemorrhage: Surgery to Interventional Radiology

Objectives We summarized a single center's evolution in the management of postpancreatectomy hemorrhage (PPH) from surgical toward endovascular management. Methods Between 2003 and 2013, 337 patients underwent Whipple procedures. Using the International Study Group of Pancreatic Surgery (ISGPS) consensus definition, patients with PPH were identified and retrospectively analyzed for the presentation of hemorrhage, type of intervention, and 90-day mortality outcome measures. Results Management evolved from operative intervention alone, to combined operative and on-table angiographic intervention, to endovascular intervention alone. The prevalence of PPH was 3.0%. Delayed PPH occurred with a mean of 13.8 days. On angiography, visceral arteries affected were the gastroduodenal artery, hepatic artery, jejunal branches of the superior mesenteric artery, pancreaticoduodenal artery, and inferior phrenic artery. Ninety-day mortality for PPH was 20%. From early to recent experience, the mortality rate was 100% for operative intervention alone, 25% for combined operative and on-table angiographic intervention, and 0% for endovascular intervention alone. Conclusions Our 10-year experience supports current algorithms in the management of PPH. Key considerations include the recognition of the sentinel bleed, the presence of a pancreatic fistula, and the initial operative role of a long gastroduodenal artery stump with radiopaque marker for safe and effective embolization should PPH occur.
Influence of religiosity on HIV risk behaviors in active injection drug users

Abstract Previous studies have shown a positive relationship between religiosity and the practice or adoption of protective health behaviors, including reduction of illicit drug use among hard-core injecting drug users (IDUs). The purpose of this study was to examine the role of religiosity in predicting HIV high-risk drug and sexual practices among a sample of IDUs in Chicago, USA. We hypothesized that high religiosity would be associated with a lower likelihood of IDUs engaging in risky behaviors for HIV transmission. Snowball sampling techniques were used to recruit 1,095 active IDUs for HIV testing, counseling and partner notification. Data were analyzed from 880 subjects who self-identified with one of three religions, Christianity, Islam or Judaism. Logistic regression was used to examine the relationship between religiosity (based on self-reports of personal strength of religious belief: very strong; somewhat strong; not at all), independent of specific religion, and HIV risk behaviors (defined as 12 unsafe sex- and drug-related practices) as well as HIV serostatus. Contrary to our hypothesis, subjects with stronger religiosity were more likely to engage in four risk behaviors related to sharing injection paraphernalia. Compared to those who self-reported having no religiosity, subjects who stated that their lives were strongly influenced by religious beliefs were significantly more likely to share injection outfits, cookers, cotton and water. The association of certain HIV risk behaviors with higher religiosity has implications for HIV prevention and warrants further research to explore IDUs’ interpretation of religious teachings and the role of religious education in HIV prevention programs.
Combinatorial Pure Exploration of Multi-Armed Bandits

We study the combinatorial pure exploration (CPE) problem in the stochastic multi-armed bandit setting, where a learner explores a set of arms with the objective of identifying the optimal member of a decision class, which is a collection of subsets of arms with certain combinatorial structures such as size-K subsets, matchings, spanning trees or paths, etc. The CPE problem represents a rich class of pure exploration tasks which covers not only many existing models but also novel cases where the object of interest has a non-trivial combinatorial structure. In this paper, we provide a series of results for the general CPE problem. We present general learning algorithms which work for all decision classes that admit offline maximization oracles in both fixed confidence and fixed budget settings. We prove problem-dependent upper bounds of our algorithms. Our analysis exploits the combinatorial structures of the decision classes and introduces a new analytic tool. We also establish a general problem-dependent lower bound for the CPE problem. Our results show that the proposed algorithms achieve the optimal sample complexity (within logarithmic factors) for many decision classes. In addition, applying our results back to the problems of top-K arms identification and multiple bandit best arms identification, we recover the best available upper bounds up to constant factors and partially resolve a conjecture on the lower bounds.
Random walks in Weyl chambers and crystals

We use Kashiwara crystal basis theory to associate a random walk 𝒲 to each irreducible representation V of a simple Lie algebra. This is achieved by endowing the crystal attached to V with a (possibly non‐uniform) probability distribution compatible with its weight graduation. We then prove that the generalized Pitman transform defined for similar random walks with uniform distributions yields yet another Markov chain. When the representation is minuscule, and the associated random walk has a drift in the Weyl chamber, we establish that this Markov chain has the same law as 𝒲 conditioned to never exit the cone of dominant weights. For the defining representation V of 𝔤𝔩n, we notably recover the main result of O’Connell [Trans. Amer. Math. Soc. 355 (2003) 3669–3697]. At the heart of our proof is a quotient version of a renewal theorem which holds for a general random walk on a lattice. This theorem also has applications in representation theory since it permits the behaviour of some outer multiplicities for large dominant weights to be described.
Helicobacter pylori specific nested PCR assay for the detection of 23S rRNA mutation associated with clarithromycin resistance

Background—Clarithromycin is one of the most important antibiotics for Helicobacter pylori eradication. However, 5–10% of strains are reported to be resistant. It has been shown that one point mutation in the 23S rRNA gene is associated with resistance to clarithromycin. Aims—To establish a polymerase chain reaction (PCR) system which amplifies a segment of the 23S rRNA gene containing the mutation points with primers specific forH pylori, so that H pylori infection and the mutation associated with clarithromycin resistance can be examined simultaneously. Methods—To detectH pylori infection and the mutation simultaneously, primers specific for the H pylori 23S rRNA gene were designed based on sequence conservation among H pylori strains and sequence specificity as compared with other bacteria. DNA from 57 cultured strains and from 39 gastric juice samples was amplified in the seminested 23S rRNA PCR. Clinical applicability was evaluated in 85 patients. Results—DNA samples from 57 cultured strains were all amplified. The novel assay and the urease A PCR agreed in 37/39 gastric juice samples with no false positives. The assay did not amplify the DNA of bacteria other thanH pylori. Eight of 85 samples had the mutation before treatment. In clarithromycin based treatment, eradication was achieved in 2/5 (40%) with the mutation and 29/34 (85%) without the mutation. Conclusion—The assay using gastric juice is quick (within 12 hours) and non-invasive (endoscopy not required), enabling rapid initiation of appropriate antibiotic treatment.
FINE STRUCTURE OF THE NOTOCHORD OF AMPHIOXUS

The protochordate amphioxus has been a favorite object of study for over a century. Early workers gave particular attention to the notochord of this remarkable animal because of its unique position and structure and its evolutionary significance (1). Modern advances in microscopy have opened the way for new research on the chorda dorsalis. Tenbaum (2) recently examined it under the polarizing microscope, and we present here observations made with the electron microscope.