Miracle-dz/UniFAR-FTUs huggingface dataset:
Adherence epitopes of Mycoplasma genitalium adhesin.

The adherence-mediating sites of the 153 kDa adhesin of Mycoplasma genitalium (MgPa-protein) were characterized at the amino acid sequence level using six monoclonal anti-MgPa antibodies which showed adherence-inhibiting activity. For characterization of the regions to which antibody bound, three segments of the adhesin (N-terminal region, a D1-domain located approximately in the middle of the molecule and a D2-domain located near to the C-terminus) were synthesized as overlapping octapeptides. These regions were chosen in analogy to the three domains of Mycoplasma pneumoniae that are involved in the adhesion process. Whereas two monoclonal antibodies (mAb 5B11 and mAb 6F3) bound exclusively to an epitope in the N-region, mAb 3B7 and mAb 6A2 reacted with two distinct epitopes of the D2-domain only. Binding to short synthetic peptides of different regions was analysed for mAb 3A12 (N-region and D1-region) and mAb 2B6 (N-region and D2-region). Close proximity of the N-region and the D2-region in the native MgPa-protein of M. genitalium was indicated in a competitive ELISA test, using freshly harvested M. genitalium cells. Epitope mapping and competition experiments with monoclonal anti-MgPa antibodies revealed interesting differences in the adherence-mediating sites of MgPa and the adhesin (P1-protein) of M. pneumoniae. Whereas a three-dimensional arrangement of protein loops is suggested for both native adhesins, the MgPa-protein and the P1-protein adherence-mediating epitopes are located in non-homologous regions of these two related proteins. (ABSTRACT TRUNCATED AT 250 WORDS)
MPGL: An Efficient Matching Pursuit Method for Generalized LASSO

Unlike traditional LASSO enforcing sparsity on the variables, Generalized LASSO (GL) enforces sparsity on a linear transformation of the variables, gaining flexibility and success in many applications. However, many existing GL algorithms do not scale up to high-dimensional problems, and/or only work well for a specific choice of the transformation. We propose an efficient Matching Pursuit Generalized LASSO (MPGL) method, which overcomes these issues, and is guaranteed to converge to a global optimum. We formulate the GL problem as a convex quadratic constrained linear programming (QCLP) problem and tailor-make a cutting plane method. More specifically, our MPGL iteratively activates a subset of nonzero elements of the transformed variables, and solves a subproblem involving only the activated elements thus gaining significant speed-up. Moreover, MPGL is less sensitive to the choice of the trade-off hyper-parameter between data fitting and regularization, and mitigates the long-standing hyper-parameter tuning issue in many existing methods. Experiments demonstrate the superior efficiency and accuracy of the proposed method over the state-of-the-arts in both classification and image processing tasks.
The path from the choroid plexus to the subventricular zone: go with the flow!

In adult mammals, under physiological conditions, neurogenesis, the process of generating new functional neurons from precursor cells, occurs mainly in two brain areas: the subgranular zone in the dentate gyrus of the hippocampus, and the subventricular zone (SVZ) lining the walls of the brain lateral ventricles. Taking into account the location of the SVZ and the cytoarchitecture of this periventricular neural progenitor cell niche, namely the fact that the slow dividing primary progenitor cells (type B cells) of the SVZ extend an apical primary cilium toward the brain ventricular space which is filled with cerebrospinal fluid (CSF), it becomes likely that the composition of the CSF can modulate both self-renewal, proliferation and differentiation of SVZ neural stem cells. The major site of CSF synthesis is the choroid plexus (CP); quite surprisingly, however, it is still largely unknown the contribution of molecules specifically secreted by the adult CP as modulators of the SVZ adult neurogenesis. This is even more relevant in light of recent evidence showing the ability of the CP to adapt its transcriptome and secretome to various physiologic and pathologic stimuli. By giving particular emphasizes to growth factors and axonal guidance molecules we will illustrate how CP-born molecules might play an important role in the SVZ niche cell population dynamics.
Development and recent evaluation of the MT_CKD model of continuum absorption

Water vapour continuum absorption is an important contributor to the Earth's radiative cooling and energy balance. Here, we describe the development and status of the MT_CKD (MlawerTobinCloughKneizysDavies) water vapour continuum absorption model. The perspective adopted in developing the MT_CKD model has been to constrain the model so that it is consistent with quality analyses of spectral atmospheric and laboratory measurements of the foreign and self continuum. For field measurements, only cases for which the characterization of the atmospheric state has been highly scrutinized have been used. Continuum coefficients in spectral regions that have not been subject to compelling analyses are determined by a mathematical formulation of the spectral shape associated with each water vapour monomer line. This formulation, which is based on continuum values in spectral regions in which the coefficients are well constrained by measurements, is applied consistently to all water vapour monomer lines from the microwave to the visible. The results are summed-up (separately for the foreign and self) to obtain continuum coefficients from 0 to 20 000 cm−1. For each water vapour line, the MT_CKD line shape formulation consists of two components: exponentially decaying far wings of the line plus a contribution from a water vapour molecule undergoing a weak interaction with a second molecule. In the MT_CKD model, the first component is the primary agent for the continuum between water vapour bands, while the second component is responsible for the majority of the continuum within water vapour bands. The MT_CKD model should be regarded as a semi-empirical model with strong constraints provided by the known physics. Keeping the MT_CKD continuum consistent with current observational studies necessitates periodic updates to the water vapour continuum coefficients. In addition to providing details on the MT_CKD line shape formulation, we describe the most recent update to the model, MT_CKD_2. 5, which is based on an analysis of satellite- and ground-based observations from 2385 to 2600 cm−1 (approx. 4 μm).
Update on current management of chronic kidney disease in patients with HIV infection

The prevalence of HIV-associated chronic kidney disease (CKD) varies geographically and depends on the definition of CKD used, ranging from 4.7% to 38% globally. The incidence, however, has decreased with the use of effective combined antiretroviral therapy (cART). A wide variety of histological patterns are seen in HIV-associated kidney diseases that include glomerular and tubulointerstitial pathology. In resource-rich settings, there has been a plateau in the incidence of end-stage renal disease secondary to HIV-associated nephropathy (HIVAN). However, the prevalence of end-stage renal disease in HIV-positive individuals has risen, mainly due to increased longevity on cART. There is a disparity in the occurrence of HIVAN among HIV-positive individuals such that there is an 18- to 50-fold increased risk of developing kidney disease among HIV-positive individuals of African descent aged between 20 and 64 years and who have a poorer prognosis compared with their European descent counterparts, suggesting that genetic factors play a vital role. Other risk factors include male sex, low CD4 counts, and high viral load. Improvement in renal function has been observed after initiation of cART in patients with HIV-associated CKD. Treatment with an angiotensin-converting enzyme inhibitor/angiotensin receptor blocker is recommended, when clinically indicated in patients with confirmed or suspected HIVAN or clinically significant albuminuria. Other standard management approaches for patients with CKD are recommended. These include addressing other cardiovascular risk factors (appropriate use of statins and aspirin, weight loss, cessation of smoking), avoidance of nephrotoxins, and management of serum bicarbonate and uric acid, anemia, calcium, and phosphate abnormalities. Early diagnosis of kidney disease by screening of HIV-positive individuals for the presence of kidney disease is critical for the optimal management of these patients. Screening for the presence of kidney disease upon detection of HIV infection and annually thereafter in high-risk populations is recommended.
Light Location Influences the Perceived Locations of Internal Sounds

Numerous studies have shown that visual stimuli can bias the perceived location of auditory stimuli. Here, we sought to determine if a visual stimulus can also bias the perceived location of multiple internal auditory stimuli. Fifty subjects were presented with a train of eight binaural click-pairs over headphones while a single flash of light was presented either to the left or to the right side of a central fixation point on an otherwise black CRT screen. A no-flash baseline was also implemented, as was a no-fixation control. The subjects used a rating scale to indicate the perceived location of each of the eight click-pairs within their heads. The results showed that the flash of light significantly influenced the perceived location of the click-pairs, biasing them in the same direction as the flash of light. This suggests that, even without perceptual correspondence, cross-modal interactions can occur.
“Eppur si muove” (yet it moves)

In the 17th century, the problem of the relative movement of the Earth with respect to the sun was an issue of central importance, and in fact, the man who has been considered responsible for the birth of modern science was committed to house arrest for defending the heliocentric hypothesis. Four centuries after the (never-confirmed) legend of Galileo Galilei's rebellious phrase, a problem of relative motion, now between the protein and substrate in enzyme catalyzed reactions, is once again a hot topic in the scientific community. In this regard, Warshel and coworkers’ study in PNAS (1) reports a very interesting study on the relationship between enzyme catalysis and protein conformational motions.
Neural Activity in Macaque Parietal Cortex Reflects Temporal Integration of Visual Motion Signals during Perceptual Decision Making

Decision-making often requires the accumulation and maintenance of evidence over time. Although the neural signals underlying sensory processing have been studied extensively, little is known about how the brain accrues and holds these sensory signals to guide later actions. Previous work has suggested that neural activity in the lateral intraparietal area (LIP) of the monkey brain reflects the formation of perceptual decisions in a random dot direction-discrimination task in which monkeys communicate their decisions with eye-movement responses. We tested the hypothesis that decision-related neural activity in LIP represents the time integral of the momentary motion “evidence. ” By briefly perturbing the strength of the visual motion stimulus during the formation of perceptual decisions, we tested whether this LIP activity reflected a persistent, integrated “memory” of these brief sensory events. We found that the responses of LIP neurons reflected substantial temporal integration. Brief pulses had persistent effects on both the monkeys' choices and the responses of neurons in LIP, lasting up to 800 ms after appearance. These results demonstrate that LIP is involved in neural time integration underlying the accumulation of evidence in this task. Additional analyses suggest that decision-related LIP responses, as well as behavioral choices and reaction times, can be explained by near-perfect time integration that stops when a criterion amount of evidence has been accumulated. Temporal integration may be a fundamental computation underlying higher cognitive functions that are dissociated from immediate sensory inputs or motor outputs.
Nedd2 Is Required for Apoptosis after Trophic Factor Withdrawal, But Not Superoxide Dismutase (SOD1) Downregulation, in Sympathetic Neurons and PC12 Cells

Activation of cysteine aspartases (caspases) seems to be a required element of apoptotic death in many paradigms. We have shown previously that general inhibitors of cysteine aspartases block apoptosis of PC12 cells and sympathetic neurons evoked by either trophic factor (nerve growth factor and/or serum) deprivation or superoxide dismutase (SOD1) downregulation. Moreover, activation of a caspase family member similar or equivalent to the interleukin-1β-converting enzyme (ICE) was implicated for death caused by SOD1 downregulation, but not withdrawal of trophic support. The experiments presented here demonstrate that diminished expression of the cysteine aspartase Nedd2 in PC12 cells and sympathetic neurons induced by an appropriate vector peptide-linked antisense oligonucleotide rescues them from death caused by trophic factor deprivation without inhibiting apoptosis in the same cell types evoked by SOD1 downregulation. Neither the level (as revealed by Western immunoblotting) nor the cellular distribution (as revealed immunohistochemically) of Nedd2 was altered demonstrably by trophic factor deprivation. However, evidence for proteolytic processing of Nedd2 (consistent with commencement of activation) was observed in PC12 cells after withdrawal of trophic support. These findings indicate that neuronal death triggered by different initial causes may be mediated by distinct members of the cysteine aspartase family.
An Enhanced Secured FPGA based DES

In this paper we demonstrate an efficient and compact reconfigurable hardware implementation of the Data Encryption Standard (DES) algorithm. Our design was implemented on FPGA of device VirtexEXCV400e. As a strategy to reduce the associated design critical path, we utilized a parallel structure that allowed us to compute all the eight DES S-boxes simultaneously. The testing of theimplemented design shows that it is possible to generate data in 16 clock cycles when non-pipelined approach is employed. Whenpipelined approach is employed on the other hand, 17 clocksignals are required for the initial phase only
Postoperative Complications in Pediatric Inflammatory Bowel Disease: A Population-based Study

Background:We describe, in a population-based cohort, the incidence of and factors associated with postoperative complications (POCs) in pediatric-onset inflammatory bowel disease. Methods:Using the pediatric population-based EPIMAD Cohort (1988–2004), among 692 incident inflammatory bowel disease cases, 128 patients with Crohn's disease (CD) and 25 with ulcerative colitis (UC) (22%) had undergone at least 1 major abdominal surgery at a median age of 16 years [interquartile range, Q1–Q3 = 14–17]. Factors associated with POC were assessed using Cox models. Results:After a median postoperative follow-up of 8 years (3–12), 76 (49.7%) patients had experienced at least 1 POC with a total of 113 complications. The frequency of severe POC (grade >2) was similar in CD and UC (28% of all complications versus 27%, P = 0.95). A total of 64 early POCs (within 30 d of surgery) were observed in 47 patients (31%), with 33 being infectious and 31 noninfectious, higher in UC than in CD (25% of patients with CD versus 60% of patients with UC, P < 0.001). Forty-nine late POCs (≥30 d) were observed in 37 patients (24%). The occurrence of late POC was similar in UC and CD. The cumulative probability of POC was 31% (95% confidence interval, 24–39) at 1 month, 46% (38–54) at 1 year, and 48% (41–57) at 5 years. Multivariate analysis found that the UC type was the only factor associated with early POC (hazard ratio = 2.9; 95% confidence interval, 1.6–5.4). Conclusions:One-half of the children with inflammatory bowel disease had experienced at least 1 POC. Only UC relative to CD was significantly associated with an increased risk of early POC.
Oxidative modification of tropomyosin and myocardial dysfunction following coronary microembolization.

AIMS We addressed a potential mechanism of myocardial dysfunction following coronary microembolization at the level of myofibrillar proteins. METHODS AND RESULTS Anaesthetized pigs underwent intracoronary infusion of microspheres. After 6 h, the microembolized areas (MEA) had decreased systolic wall thickening to 38 +/- 7% of baseline and a 2.62 +/- 0.40-fold increase in the formation of disulphide cross-bridges (DCB) in tropomyosin relative to that in remote areas. The impairment in contractile function correlated inversely with DCB formation (r = -0.68; P = 0.015) and was associated with increased TNF-alpha content. DCB formation was reflected by increased tropomyosin immunoreactivity and abolished in vitro by dithiothreitol. Ascorbic acid prevented contractile dysfunction as well as increased DCB and TNF-alpha. In anaesthetized dogs, 8 h after intracoronary microspheres infusion, contractile function was reduced to 8+/-10% of baseline and DCB in MEA was 1.48+/-0.12 higher than that in remote areas. In conscious dogs, 6 days after intracoronary microspheres infusion, myocardial function had returned to baseline and DCB was no longer different between remote and MEA. Again contractile function correlated inversely with DCB formation (r = -0.83; P = 0.005). CONCLUSION Myofibrillar protein oxidation may represent a mechanistic link between inflammation and contractile dysfunction following coronary microembolization.
Prognostic significance of D-dimer, natural anticoagulants and routine coagulation parameters in acute pancreatitis.

AIM This study was conducted to assess the predictive value of coagulation abnormalities in determining disease severity and prognosis of acute pancreatitis (AP). METHODS Patients of AP and 25 healthy volunteers were included in this prospective observational study. The final outcomes were disease severity assessed by Computed Tomography Severity Index, Acute Physiological Assessment and Chronic Health Evaluation--II, presence of organ failure and mortality. Prothrombin time (PT), partial thromboplastin time (PTT), thrombin time (TT), fibrinogen, antithrombin-III (AT-III), protein-C, and protein-S levels were assessed on day 0, 3 and 7 of admission. RESULTS Of the 38 patients included, 13 died. Mean PT and TT were similar between patients and controls on any given day. PTT showed elevation on day 3 and 7 (p = 0.001) compared to controls, although fibrinogen and D-dimer were significantly higher in patients on all days. Protein C and AT-III were significantly lower in patients and more so in non survivors ( (p = 0.001)) than controls. Multiple logistic regression analysis revealed D-dimer levels > or = 400 - 800 ng/ml and AT- III level of < 71% at admission were associated with high mortality (OR 11.2, AUROC 0.70 and OR 16.6, AUROC 0.82 respectively) as well as predicted organ failure. CONCLUSION Serum D-dimer and antithrombin-III levels can be used to assess disease severity and predict outcome of patients with acute pancreatitis.
Adult and Immature Stages of the New Species of the Genus Demodex (Acariformes: Demodecidae) with Data on Parasitism, Topography, and Topical Specificity of Demodecid Mites in the Yellow-Necked Mouse, Apodemus flavicollis (Rodentia: Muridae)

Abstract Demodex mollis n. sp. is described from the yellow-necked mouse, Apodemus flavicollis (Melchior, 1834), from Poland. It is a medium-sized demodecid mite (adult stages are, on average, 249 μm long) observed in the skin of the eyelid area. This new species is most similar to two other species occupying similar a microhabitat in hosts of the same genus—Demodex lacrimalis Lukoschus and Jongman, 1974 from Apodemus sylvaticus Linnaeus, 1758 and Demodex huttereri Mertens, Lukoschus and Nutting, 1983 from Apodemus agrarius (Pallas, 1771)—but it differs in the following features: the terminal palpi are equipped with 3 spines, including 1 large claw-like spine and 1 single spine; subgnathosomal setae (setae n) are situated on both sides of the anterior side of the pharyngeal bulb; claws on the leg tarsi are bifurcated and each is equipped with large subterminal spur and proximal pointed projection; the opisthosoma is soft and flexible; and the male aedeagus has a different shape and localization. The differences also relate to sexual dimorphism. Males are more robust and stocky, epimeral plates I and IV are connected at the midline part of the podosoma, and epimeral plates II and III are separated. Females are slender, epimeral plates I–III are connected at the midline of the podosoma, and epimeral plate IV ia fused in 1 plate. The new species was noted in 22.5% of mice, with a mean intensity of 7.0 parasites per host. The topography of demodecid mites was also analyzed in the skin of A. flavicollis, and also Demodex corniculatus Izdebska, 2012 was observed in the hairy skin of the bodies of all the examined mice.
Containment of Simian Immunodeficiency Virus Infection: Cellular Immune Responses and Protection from Rechallenge following Transient Postinoculation Antiretroviral Treatment

ABSTRACT To better understand the viral and host factors involved in the establishment of persistent productive infection by primate lentiviruses, we varied the time of initiation and duration of postinoculation antiretroviral treatment with tenofovir {9-[2-(R)-(phosphonomethoxy)propyl]adenine}while performing intensive virologic and immunologic monitoring in rhesus macaques, inoculated intravenously with simian immunodeficiency virus SIVsmE660. Postinoculation treatment did not block the initial infection, but we identified treatment regimens that prevented the establishment of persistent productive infection, as judged by the absence of measurable plasma viremia following drug discontinuation. While immune responses were heterogeneous, animals in which treatment resulted in prevention of persistent productive infection showed a higher frequency and higher levels of SIV-specific lymphocyte proliferative responses during the treatment period compared to control animals, despite the absence of either detectable plasma viremia or seroconversion. Animals protected from the initial establishment of persistent productive infection were also relatively or completely protected from subsequent homologous rechallenge. Even postinoculation treatment regimens that did not prevent establishment of persistent infection resulted in downmodulation of the level of plasma viremia following treatment cessation, compared to the viremia seen in untreated control animals, animals treated with regimens known to be ineffective, or the cumulative experience with the natural history of plasma viremia following infection with SIVsmE660. The results suggest that the host may be able to effectively control SIV infection if the initial exposure occurs under favorable conditions of low viral burden and in the absence of ongoing high level cytopathic infection of responding cells. These findings may be particularly important in relation to prospects for control of primate lentiviruses in the settings of both prophylactic and therapeutic vaccination for prevention of AIDS.