Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Review of the Epidemiology, Immunopathogenesis, Diagnosis, and Treatment of Pleural TB in HIV- Infected Patients

Background. High HIV burden countries have experienced a high burden of pleural TB in HIV-infected patients. Objective. To review the epidemiology, immunopathogenesis, diagnosis, and treatment of pleural TB in HIV-infected patients. Methods. A literature search from 1950 to June 2011 in MEDLINE was conducted. Results. Two-hundred and ninety-nine studies were identified, of which 30 met the inclusion criteria. The immunopathogenesis as denoted by cells and cytokine profiles is distinctly different between HIV and HIV-uninfected pleural TB disease. Adenosine deaminase and interferon gamma are good markers of pleural TB disease even in HIV-infected patients. HIV-uninfected TB suspects with pleural effusions commonly have a low yield of TB organisms however the evidence suggests that in dually infected patients smear and cultures have a higher yield. The Gene Xpert MTB/RIF assay has significant potential to improve the diagnosis of pleural TB in HIV-positive patients. Conclusions. Pleural TB in HIV-infected patients has a different immunopathogenesis than HIV-uninfected pleural TB and these findings in part support the differences noted in this systematic review. Research should focus on developing an interferon gamma-based point of care diagnostic test and expansion of the role of Gene Xpert in the diagnosis of pleural TB.
Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn5 transposase.

Transposition of Tn5 and IS50 requires the specific binding of transposase (Tnp) to the end inverted repeats, the outside end (OE) and the inside end (IE). OE and IE have 12 identical base-pairs and seven non-identical base-pairs. Previously we described the isolation of a Tnp mutant, EK54, that shows an altered preference for OE versus IE compared to wild-type (wt) Tnp. EK54 enhances OE recognition and decreases IE recognition both in DNA binding and in overall transposition. Here we report that base-pairs 10, 11 and 12 of the OE are critical for the specific recognition by EK54 Tnp. These three adjacent base-pairs act cooperatively; all three must be present in order for EK54 Tnp to interact very favorably with the end DNA. The existence of only one or two of these three base-pairs decreases binding of EK54 Tnp. The combined use of EK54 Tnp and a new OE/IE mosaic end sequence containing the OE base-pairs 10, 11 and 12 gives rise to an extraordinarily high transposition frequency. Just as the Tnp is a multifunctional protein, the nucleotides in the 19 bp Tn5 ends also affect other functions besides Tnp binding. Furthermore, the fact that we were able to isolate end sequence variants that transpose at a higher frequency than the natural ends (OE and IE) with wt Tnp reveals yet another way in which the wt transposition frequency is depressed, i.e. by keeping the end sequences suboptimal.
Native and microwaved bean and pea starch preparations: physiological effects on the intestinal ecosystem, caecal tissue and serum lipids in rats

Dietary beans and peas provide fibre, resistant starch and other nutrients that are often lacking in the human diet. The influence of native starches of beans and peas (and microwaved preparations) on N utilisation, biochemical indices in blood serum and caecal ecosystem state (SCFA, bacterial enzymes, micro-organisms) was studied in vivo. The native pea starch contained more resistant starch compared with its bean counterpart (31 v. 17 %); however, processing decreased these amounts to 25 v. 10 %. N digestibility was found to decrease considerably in all experimental groups. A considerable reduction was observed in glucose and total cholesterol concentration in rat blood serum as a result of feeding both dietary legume starch preparations under microwave treatment. This indicates that starch of bean origin activated glycolytic bacterial enzymes; however, all the analysed starches were found to reduce the activity of β-glucuronidase. In addition, both dietary bean starches significantly induced the formation of SCFA in the caecal digesta. As compared with the control group, a significant decrease in the pH of caecal and colonic digesta was demonstrated for both bean starch preparations. In comparison with the diet with native pea starch, its microwaved preparation reduced the concentrations of acetic, butyric and propionic acids among caecal SCFA and increased the pH of caecal and colonic digesta. The atherogenic index was significantly lower in rats fed microwaved pea starch. All investigated starch preparations increased the population of Bifidobacterium spp. in caecal digesta, but were also good substrates for opportunistic Enterococcus or Escherichia coli.
Effects of agriculture production systems on nitrate and nitrite accumulation on baby-leaf salads

Nitrate and nitrite are widespread contaminants of vegetables, fruits, and waters. The levels of these compounds are increased as a result of using organic wastes from chemical industries, domestic wastes, effluents, nitrogenous fertilizers, and herbicides in agriculture. Therefore, determining the nitrate and nitrite levels in biological, food, and environmental samples is important to protect human health and the environment. In this context, we set this study, in which we report the effect of production system (conventional and organic) on the accumulation of nitrates and nitrites in fresh baby-leaf samples. The average levels of the nitrate () and nitrite () contents in six different baby-leaf salads of a single species (green lettuce, red lettuce, watercress, rucola, chard, and corn salad) produced in organic and conventional agriculture system were evaluated. Spectrophotometric analytical method recently published was validated and used. Nitrates and nitrites were detected in all samples. The nitrates levels from organic production varied between 1.45 and 6.40 mg/kg fresh weight (FW), whereas those from conventional production ranged from 10.5 to 45.19 mg/kg FW. The nitrites content was lower than nitrates and ranged from 0.32 to 1.89 mg/kg FW in organic production system and between 0.14 and 1.41 mg/kg FW in conventional production system. Our results showed that the nitrate content was dependent on the agricultural production system, while for nitrites, this dependency was less pronounced.
Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming

Many sound sources can only be recognised from the pattern of sounds they emit, and not from the individual sound events that make up their emission sequences. Auditory scene analysis addresses the difficult task of interpreting the sound world in terms of an unknown number of discrete sound sources (causes) with possibly overlapping signals, and therefore of associating each event with the appropriate source. There are potentially many different ways in which incoming events can be assigned to different causes, which means that the auditory system has to choose between them. This problem has been studied for many years using the auditory streaming paradigm, and recently it has become apparent that instead of making one fixed perceptual decision, given sufficient time, auditory perception switches back and forth between the alternatives—a phenomenon known as perceptual bi- or multi-stability. We propose a new model of auditory scene analysis at the core of which is a process that seeks to discover predictable patterns in the ongoing sound sequence. Representations of predictable fragments are created on the fly, and are maintained, strengthened or weakened on the basis of their predictive success, and conflict with other representations. Auditory perceptual organisation emerges spontaneously from the nature of the competition between these representations. We present detailed comparisons between the model simulations and data from an auditory streaming experiment, and show that the model accounts for many important findings, including: the emergence of, and switching between, alternative organisations; the influence of stimulus parameters on perceptual dominance, switching rate and perceptual phase durations; and the build-up of auditory streaming. The principal contribution of the model is to show that a two-stage process of pattern discovery and competition between incompatible patterns can account for both the contents (perceptual organisations) and the dynamics of human perception in auditory streaming.
Privacy-preserving multi-keyword ranked search over encrypted cloud data

With the advent of cloud computing, data owners are motivated to outsource their complex data management systems from local sites to the commercial public cloud for great flexibility and economic savings. But for protecting data privacy, sensitive data has to be encrypted before outsourcing, which obsoletes traditional data utilization based on plaintext keyword search. Thus, enabling an encrypted cloud data search service is of paramount importance. Considering the large number of data users and documents in the cloud, it is necessary to allow multiple keywords in the search request and return documents in the order of their relevance to these keywords. Related works on searchable encryption focus on single keyword search or Boolean keyword search, and rarely sort the search results. In this paper, for the first time, we define and solve the challenging problem of privacy-preserving multi-keyword ranked search over encrypted cloud data (MRSE). We establish a set of strict privacy requirements for such a secure cloud data utilization system. Among various multi-keyword semantics, we choose the efficient similarity measure of “coordinate matching”, i.e., as many matches as possible, to capture the relevance of data documents to the search query. We further use “inner product similarity” to quantitatively evaluate such similarity measure. We first propose a basic idea for the MRSE based on secure inner product computation, and then give two significantly improved MRSE schemes to achieve various stringent privacy requirements in two different threat models. Thorough analysis investigating privacy and efficiency guarantees of proposed schemes is given. Experiments on the real-world dataset further show proposed schemes indeed introduce low overhead on computation and communication.
Regulated Mucin Secretion from Airway Epithelial Cells

Secretory epithelial cells of the proximal airways synthesize and secrete gel-forming polymeric mucins. The secreted mucins adsorb water to form mucus that is propelled by neighboring ciliated cells, providing a mobile barrier which removes inhaled particles and pathogens from the lungs. Several features of the intracellular trafficking of mucins make the airway secretory cell an interesting comparator for the cell biology of regulated exocytosis. Polymeric mucins are exceedingly large molecules (up to 3 × 106 Da per monomer) whose folding and initial polymerization in the ER requires the protein disulfide isomerase Agr2. In the Golgi, mucins further polymerize to form chains and possibly branched networks comprising more than 20 monomers. The large size of mucin polymers imposes constraints on their packaging into transport vesicles along the secretory pathway. Sugar side chains account for >70% of the mass of mucins, and their attachment to the protein core by O-glycosylation occurs in the Golgi. Mature polymeric mucins are stored in large secretory granules ∼1 μm in diameter. These are translocated to the apical membrane to be positioned for exocytosis by cooperative interactions among myristoylated alanine-rich C kinase substrate, cysteine string protein, heat shock protein 70, and the cytoskeleton. Mucin granules undergo exocytic fusion with the plasma membrane at a low basal rate and a high stimulated rate. Both rates are mediated by a regulated exocytic mechanism as indicated by phenotypes in both basal and stimulated secretion in mice lacking Munc13-2, a sensor of the second messengers calcium and diacylglycerol (DAG). Basal secretion is induced by low levels of activation of P2Y2 purinergic and A3 adenosine receptors by extracellular ATP released in paracrine fashion and its metabolite adenosine. Stimulated secretion is induced by high levels of the same ligands, and possibly by inflammatory mediators as well. Activated receptors are coupled to phospholipase C by Gq, resulting in the generation of DAG and of IP3 that releases calcium from apical ER. Stimulated secretion requires activation of the low affinity calcium sensor Synaptotagmin-2, while a corresponding high affinity calcium sensor in basal secretion is not known. The core exocytic machinery is comprised of the SNARE proteins VAMP8, SNAP23, and an unknown Syntaxin protein, together with the scaffolding protein Munc18b. Common and distinct features of this exocytic system in comparison to neuroendocrine cells and neurons are highlighted.
Case Base Engineering for Large Scale Industrial Applications

Case-based reasoning (CBR) has emerged as promising technology for decision support. However, its application to large scale industrial problems has been negligible. We believe that the lack of usable problem-solving cases is the major factor limiting the wide spread use of CBR in complex industrial environment. We propose a framework of methodologies called case base engineering (CBE) that can be used for the development of high quality case bases. The framework is presented in light of our CBE experience in application to plastics extrusion facility and aircraft maintenance. Finally, we identify issues for future research.
Optimal Personalized Filtering Against Spear-Phishing Attacks

To penetrate sensitive computer networks, attackers can use spear phishing to sidestep technical security mechanisms by exploiting the privileges of careless users. In order to maximize their success probability, attackers have to target the users that constitute the weakest links of the system. The optimal selection of these target users takes into account both the damage that can be caused by a user and the probability of a malicious e-mail being delivered to and opened by a user. Since attackers select their targets in a strategic way, the optimal mitigation of these attacks requires the defender to also personalize the e-mail filters by taking into account the users' properties. In this paper, we assume that a learned classifier is given and propose strategic per-user filtering thresholds for mitigating spear-phishing attacks. We formulate the problem of filtering targeted and non-targeted malicious e-mails as a Stackelberg security game. We characterize the optimal filtering strategies and show how to compute them in practice. Finally, we evaluate our results using two real-world datasets and demonstrate that the proposed thresholds lead to lower losses than non-strategic thresholds.
Sprites triggered by negative lightning discharges

High altitude air breakdown, manifested as “red sprites,” is reported in close association with negative cloud‐to‐ground lightning (−CG) on at least two occasions above an unusual storm on August 29, 1998. Data from high speed photometry, low‐light‐level video, and receivers of lightning electromagnetic signatures in the frequency range 10 Hz to 20 kHz are used to establish the association and indicate that the causative −CG discharges effected unusually large vertical charge moment changes (ΔMQv) of up to 1550 C · km in 5 ms. The existence of sprites caused by −CG's, rather than the regularly associated +CG's, has immediate implications for sprite models and observations.
Helminths of Small Mammals (Chiroptera, Insectivora, Lagomorpha) from Mongolia with a Description of a New Species of Schizorchis (Cestoda: Anoplocephalidae)

Abstract Fifty-eight individuals belonging to 10 species of bats, insectivores, and pikas were examined for helminths from 4 collection sites in Mongolia in 1999. Two species of bats (Vespertilio murinus and Eptesicus gobiensis) were infected with a single species of trematode (Plagiorchis vespertilionis), which represents a new record for the country. One individual of E. gobiensis also harbored 1 unidentified filaroid nematode. The acanthocephalan Moniliformis moniliformis was found in the hedgehog Hemiechinus auritus. Cestodes in the genus Catenotaenia and the herein described Schizorchis mongoliensis n. sp. were recovered from pikas belonging to the species Ochotona alpina. Schizorchis mongoliensis n. sp. is distinguished from other members of the genus by shorter strobila length accompanied by earlier maturation of proglottids, as well as a distinct vaginal valve and secondary lateral seminal receptacle.
Distribution and determinants of serum creatinine in the general population: the Hordaland Health Study

Background: Serum creatinine is a well-recognized risk factor for cardiovascular disease (CVD) and is also a rough measure of glomerular filtration rate. The purpose of the present study was to investigate determinants of serum creatinine in the general population. Methods: The participants were recruited as a part of the Hordaland Health Study, and included 6952 men aged 41-49 years, 8218 women aged 41-49 years, 1470 men aged 71-74 years and 1865 women aged 71-74 years. Data on lifestyle factors, medical history and medication were obtained through questionnaires. Body size and blood pressure measurements as well as non-fasting blood samples were obtained during a health examination. Determinants of serum creatinine were identified using multiple linear and logistic regression analyses. Results: Male and older participants had higher levels of serum creatinine than female and middle-aged participants. For older participants, creatinine was associated with serum triglycerides, CVD, upper-arm circumference and use of antihypertensive drugs as well as inversely associated with cigarette smoking. For middle-aged participants, creatinine was associated with upper-arm circumference, serum lipids and physical exercise, as well as inversely associated with smoking and alcohol intake. The associations with CVD risk factors were much stronger for older participants than for middle-aged participants and most associations were significant after adjustments as well as present within the reference range of serum creatinine. Conclusions: In this general population sample, high serum creatinine levels were associated with risk factors for CVD. These associations were stronger in older subjects, whereas in middle-aged subjects lifestyle variables were relatively more important.
Early and Late Loss of the Cytoskeletal Scaffolding Protein, Ankyrin G Reveals Its Role in Maturation and Maintenance of Nodes of Ranvier in Myelinated Axons

The mechanisms that govern node of Ranvier organization, stability, and long-term maintenance remain to be fully elucidated. One of the molecular components of the node is the cytoskeletal scaffolding protein, ankyrin G (AnkG), which interacts with multiple members of the nodal complex. The role of AnkG in nodal organization and maintenance is still not clearly defined as to whether AnkG functions as an initial nodal organizer or whether it functions as a nodal stabilizer after the nodal complex has been assembled. Using a mouse model system, we report here that perinatal and juvenile neuronal ablation of AnkG has differential consequences on nodal stability. Early loss of AnkG creates immature nodes with abnormal morphology, which undergo accelerated destabilization within a month, resulting in rapid voltage-gated sodium (NaV) channel and βIV spectrin loss with reduced effects on neurofascin 186. On the other hand, late ablation of AnkG from established nodal complexes leads to slow but progressive nodal destabilization over 10 months, primarily affecting βIV spectrin, followed by NaV channels, with modest impact on neurofascin 186. We also show that ankyrin R and βI spectrin are not sufficient to prevent nodal disorganization after AnkG ablation. Additionally, nodal disorganization in both early and late AnkG mutants is accompanied by axonal pathology and neurological dysfunction. Together, our results suggest that AnkG plays an indispensable role in the maturation and long-term stabilization of the newly assembled nodal complex, and that loss of AnkG after nodal stabilization does not lead to rapid nodal disassembly but to loss of specific nodal components in a time-dependent manner. SIGNIFICANCE STATEMENT Nodes of Ranvier are the myelin-free gaps along myelinated axons that allow fast communication between neurons and their target cells by propagating action potentials in a saltatory manner. The cytoskeletal scaffolding protein ankyrin G (AnkG) has been thought to play an important role in node formation; however, its precise role in nodal assembly, stability, and maintenance is still not clear. By using spatiotemporal ablation of AnkG, we report its differential role in nodal maturation and stabilization. We show that early AnkG-deficient nodes fail to mature and undergo rapid destabilization. In contrast, nodes that assemble with AnkG are much more stable and undergo gradual disintegration with sequential loss of nodal components in the absence of AnkG.
Altered behavioral rhythms and clock gene expression in mice with a targeted mutation in the Period1 gene

A group of specialized genes has been defined to govern the molecular mechanisms controlling the circadian clock in mammals. Their expression and the interactions among their products dictate circadian rhythmicity. Three genes homologous to Drosophila period exist in the mouse and are thought to be major players in the biological clock. Here we present the generation of mice in which the founding member of the family, Per1, has been inactivated by homologous recombination. These mice present rhythmicity in locomotor activity, but with a period almost 1 h shorter than wild‐type littermates. Moreover, the expression of clock genes in peripheral tissues appears to be delayed in Per1 mutant animals. Importantly, light‐induced phase shifting appears conserved. The oscillatory expression of clock genes and the induction of immediate‐early genes in response to light in the master clock structure, the suprachiasmatic nucleus, are unaffected. Altogether, these data demonstrate that Per1 plays a distinct role within the Per family, as it may be involved predominantly in peripheral clocks and/or in the output pathways of the circadian clock.