Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell envelope proteins of Staphylococcus epidermidis grown in vivo in a peritoneal chamber implant

Staphylococcus epidermidis was grown in vivo in chambers implanted intraperitoneally in rats. The cell wall and cytoplasmic membrane protein profiles of the in vivo-grown organisms were compared with those of S. epidermidis grown in vitro in nutrient broth (NB), in iron-restricted NB, or in pooled human peritoneal dialysate (HPD). Compared with growth in broth and in common with growth in HPD, growth in vivo in chambers resulted in the repression of many S. epidermidis wall proteins, with proteins of 27, 42, 54, and 70 kDa predominating. Growth in vivo also resulted in the induction of two iron-repressible cytoplasmic membrane proteins of 32 and 36 kDa, which were also present in staphylococci grown in HPD and in iron-restricted NB. Immunoblotting experiments revealed that in sera taken 21 days after inoculation of the intraperitoneal chambers, the predominant antibody response to cell envelope proteins was directed against the 32- and 36-kDa iron-repressible membrane proteins.
The ratio of albumin synthesis to total protein synthesis in normal rat liver, in host liver, and in Morris hepatoma 9121.

Summary Radioactive leucine was injected into the caval vein of normal and Morris hepatoma 9121-bearing rats. Livers and hepatomas were removed 12 min later. Within this time, no newly synthesized radioactive protein had left the liver, since labeled protein appeared in the blood no earlier than 15 min after injection. Albumin was purified from livers and hepatomas to constant specific radioactivity. The specific radioactivity of albumin purified from normal liver was 100 times higher than that of albumin from tumor. In normal liver, the radioactivity incorporated into albumin was 3.7% of that found in total protein. In host liver, 2.8% of total protein radioactivity was found in albumin, and in hepatoma only 0.36% of labeled leucine incorporated into protein was measured in albumin. The protein turnover is slower in Morris hepatoma 9121 than in liver; hence, albumin synthesis is strongly decreased in Morris hepatoma 9121 as compared to liver.
Acclimation of mechanical and hydraulic functions in trees: impact of the thigmomorphogenetic process

The secondary xylem (wood) of trees mediates several functions including water transport and storage, mechanical support and storage of photosynthates. The optimal structures for each of these functions will most likely differ. The complex structure and function of xylem could lead to trade-offs between conductive efficiency, resistance to embolism, and mechanical strength needed to count for mechanical loading due to gravity and wind. This has been referred to as the trade-off triangle, with the different optimal solutions to the structure/function problems depending on the environmental constraints as well as taxonomic histories. Thus, the optimisation of each function will lead to drastically different anatomical structures. Trees are able to acclimate the internal structure of their trunk and branches according to the stress they experience. These acclimations lead to specific structures that favor the efficiency or the safety of one function but can be antagonistic with other functions. Currently, there are no means to predict the way a tree will acclimate or optimize its internal structure in support of its various functions under differing environmental conditions. In this review, we will focus on the acclimation of xylem anatomy and its resulting mechanical and hydraulic functions to recurrent mechanical strain that usually result from wind-induced thigmomorphogenesis with a special focus on the construction cost and the possible trade-off between wood functions.
Complement plays a central role in Candida albicans‐induced cytokine production by human PBMCs

In experimental studies, the role of complement in antifungal host defense has been attributed to its opsonizing capability. In this study, we report that in humans an activated complement system mainly augments Candida albicans‐induced host proinflammatory cytokine production via C5a‐C5aR signaling, while phagocytosis and intracellular killing of Candida are not influenced. By blocking the C5a‐C5aR signaling pathway, either with anti‐C5a antagonist antibodies or with the C5aR antagonist W‐54001, C. albicans‐induced IL‐6 and IL‐1β levels were significantly reduced. Recombinant C5a augmented cytokine production. In addition, using serum from patients with various complement deficiencies, we demonstrated a crucial role of C5, but not C6 or the membrane attack complex, in C. albicans‐induced IL‐6 and IL‐1β production in monocytes. These findings reveal a central role of anaphylatoxin C5a in augmenting host proinflammatory cytokine production upon contact with C. albicans, and define the role of the complement system in anti‐Candida host defense in humans.
High retention in care among HIV-infected patients entering care with CD4 levels >350 cells/μL under routine program conditions in Uganda.

BACKGROUND In Africa, human immunodeficiency virus (HIV)-infected patients who present to care with CD4 levels >350 cells/µL (ie, current antiretroviral treatment thresholds) are often thought to be poorly retained in care, but most estimates do not account for outcomes among patients lost to follow-up. METHODS We evaluated HIV-infected adults who had made a visit in the last 2.5 years in a program in Uganda. We identified a random sample of patients lost to follow-up (9 months without a visit). Ascertainers sought patients in the community in this sample and outcomes were incorporated into revised survival estimates of mortality and retention for the clinic population using a probability weight. RESULTS Of 6473 patients, (29% male, median age 29 years, median CD4 count 550 cells/µL), 1294 (20%) became lost to follow-up over 2.5 years. Two hundred seven (16%) randomly selected lost patients were sought, and in 175 (85%) vital status was ascertained. In 19 of 175 (11%), the patient had died. Of the 156 (89%) alive, 74 (47%) were interviewed in person, and 38 of 74 (51%) reported HIV care elsewhere, whereas 36 of 74 (49%) were not in care. Application of weights derived from sampling found that at 2.5 years, retention among patients who enrolled with CD4 levels >350 cells/µL was 88.2% and mortality was 2.5%. Lower income, unemployment, and rural residence were associated with failure to be retained. CONCLUSIONS Retention in patients entering care with high CD4 counts under routine program conditions in Africa is high in a Ugandan care program and may be systematically underestimated in many other settings.
Autonomous learning of robust visual object detection and identification on a humanoid

In this work we introduce a technique for a humanoid robot to autonomously learn the representations of objects within its visual environment. Our approach involves an attention mechanism in association with feature based segmentation that explores the environment and provides object samples for training. These samples are learned for further object identification using Cartesian Genetic Programming (CGP). The learned identification is able to provide robust and fast segmentation of the objects, without using features. We showcase our system and its performance on the iCub humanoid robot.
Effect of Fly Ash on Properties of Self-Compacting High Strength Lightweight Concrete

As known, fillers directly affect the properties of self-compacting concrete. Fly ash is one of the common fillers used in production of SCC. Using lightweight concrete is extremely important for reducing the self-weight of structures, especially in heavy ones, like high rise buildings. It enables to decrease additional loads in case of renovation or/strengthening of existing structures. Moreover, self-compaction avoids using vibrations for compaction of concrete in existing structures. Therefore the present study is aimed at investigating the effect of change in fly ash content on the properties of self-compacting lightweight concrete (SCLWC). For this reason slump flow test, J-Ring test, L-Box test and V-funnel test were conducted to find workability of the fresh concrete mixture. Further compressive strength, splitting tensile strength, modulus of elasticity and flexural strength of the hardened concrete were obtained. Three concrete mixes of SCLWC with different fly ash contents were prepared to find the best workability and hardened concrete properties. The results of this study form a basis for proportioning of effective concrete mixtures suitable for repairing existing structures and elements.
AL 3 (BH 261): A New Globular Cluster in the Galaxy

AL 3 (BH 261), previously classified as a faint open cluster candidate, is shown to be a new globular cluster in the Milky Way, by means of B, V, and I color-magnitude diagrams. The main feature of AL 3 is a prominent blue extended horizontal branch. Its color-magnitude diagrams match those of the intermediate-metallicity cluster M5. The cluster is projected in a rich bulge field, also contaminated by the disk main sequence. The globular cluster is located in the Galactic bulge at a distance from the Sun d☉ = 6.0 ± 0.5 kpc. The reddening is E(B - V) = 0.36 ± 0.03, and the metallicity is estimated to be [Fe/H] ≈ -1.3 ± 0.25. AL 3 is probably one of the least massive globular clusters of the Galaxy.
Odontogenic Maxillofacial Infections: A Ten-Year Retrospective Analysis.

BACKGROUND To analyze treatment modalities and results in patients with severe odontogenic maxillofacial infections during a 10-y period. METHODS Medical records of 1,077 patients hospitalized because of severe odontogenic maxillofacial infections during 2003-2012 were reviewed. The sample consisted of the records that matched inclusion criteria. For each patient the following data were collected: Age, gender, presence of systemic diseases, length of hospital stay, causal tooth, location of inflammation, treatment, results of bacteriologic sampling, and anti-bacterial susceptibility. RESULTS Male to female ratio was 1.4:1. Two or more anatomic spaces were involved in 42.9% of cases, 37.3% of which involved the floor of the mouth. Penicillin in combination with gentamicin or metronidazole was prescribed in 69% of cases. Sixty-two different micro-organism species were identified with predominance of Streptococcus haemolyticus (42.9%). The microbial analysis showed the highest susceptibility of predominant micro-organisms to penicillin was 76.9% and the highest resistance was to metronidazole (27.9%). CONCLUSIONS The frequency of odontogenic maxillofacial infection remained almost unchanged during a 10-y period. Single-space infections were more common (57.1%) than infections involving two or more spaces. Susceptibility to penicillin remains relatively high; therefore, penicillin can remain part of the armamentarium for treatment of odontogenic maxillofacial infections.
The antisocial brain: psychopathy matters.

CONTEXT The population of men who display persistent antisocial and violent behavior is heterogeneous. Callous-unemotional traits in childhood and psychopathic traits in adulthood characterize a distinct subgroup. OBJECTIVE To identify structural gray matter (GM) differences between persistent violent offenders who meet criteria for antisocial personality disorder and the syndrome of psychopathy (ASPDP) and those meeting criteria only for ASPD (ASPD-P). DESIGN Cross-sectional case-control structural magnetic resonance imaging study. SETTING Inner-city probation services and neuroimaging research unit in London, England. PARTICIPANTS Sixty-six men, including 17 violent offenders with ASPDP, 27 violent offenders with ASPD-P, and 22 healthy nonoffenders participated in the study. Forensic clinicians assessed participants using the Structured Clinical Interview for DSM-IV and the Psychopathy Checklist-Revised. MAIN OUTCOME MEASURES Gray matter volumes as assessed by structural magnetic resonance imaging and volumetric voxel-based morphometry analyses. RESULTS Offenders with ASPDP displayed significantly reduced GM volumes bilaterally in the anterior rostral prefrontal cortex (Brodmann area 10) and temporal poles (Brodmann area 20/38) relative to offenders with ASPD-P and nonoffenders. These reductions were not attributable to substance use disorders. Offenders with ASPD-P exhibited GM volumes similar to the nonoffenders. CONCLUSIONS Reduced GM volume within areas implicated in empathic processing, moral reasoning, and processing of prosocial emotions such as guilt and embarrassment may contribute to the profound abnormalities of social behavior observed in psychopathy. Evidence of robust structural brain differences between persistently violent men with and without psychopathy adds to the evidence that psychopathy represents a distinct phenotype. This knowledge may facilitate research into the etiology of persistent violent behavior.
Via placement for minimum interconnect delay in three-dimensional (3D) circuits

The propagation delay of interlayer 3D interconnects is investigated in this paper. For RC interconnects connecting two circuits located on different physical planes, the interconnect delay is minimized by optimally placing the non-stacked interlayer vias. The problem of determining this optimum via locations under the Elmore delay model is described as a geometric program. Simulations indicate delay improvements of up to 26% for relatively short interconnect. The proposed approach is also compared with a wire sizing algorithm. Timing-driven via placement exhibits better results both in terms of delay and power consumption
Yersinia pseudotuberculosis Virulence Determinants Invasin, YopE, and YopT Modulate RhoG Activity and Localization

ABSTRACT The Yersinia pseudotuberculosis surface protein invasin binds to multiple β1 integrins with high affinity, leading to misregulation of Rac1 activity. Upon host cell binding, alteration of Rho GTPase activity results from the action of several Yersinia outer proteins (Yops) that are translocated into the cytoplasm. We report here that three virulence determinants encoded by Y. pseudotuberculosis manipulate the Rho GTPase RhoG. Y. pseudotuberculosis binding to cells caused robust recruitment of RhoG to the site of attachment, which required high-affinity invasin-β1 integrin association. Furthermore, inactivation of RhoG significantly reduced the efficiency of invasin-mediated bacterial internalization. To investigate the activation state of RhoG, a fluorescence resonance energy transfer-based activation biosensor was developed and used to show distinct spatial activation of RhoG at the site of bacterial attachment. The biosensor was also used to show efficient RhoG inactivation by Y. pseudotuberculosis YopE, a potent Rho GTPase activating protein. Additionally, RhoG mislocalization by the prenylcysteine endoprotease YopT was demonstrated by two independent assays. Functional bacterial uptake experiments demonstrated that RhoG activation can bypass a deficit in Rac1 activity. Interestingly, increasing the size of the particle gave results more consistent with a linear pathway, in which RhoG acts as an upstream activator of Rac1, indicating that increased surface area introduces constraints on the signaling pathways required for efficient internalization. Taken together, these data demonstrate the misregulation of RhoG by multiple Y. pseudotuberculosis virulence determinants. Since RhoG is imperative for proper neutrophil function, this misregulation may represent a unique mechanism by which Yersinia species dampen the immune response.
Usefulness of labial salivary gland biopsy in familial amyloid polyneuropathy Portuguese type

Background. The diagnosis of amyloidosis of all types is definitively made by demonstration of Congo red binding material in the affected tissues. Nerve biopsy was classically used to diagnose amyloid polyneuropathy but less invasive alternative types of biopsies have been proposed including labial salivary gland (LSG) biopsy, a minimally invasive procedure. Method. LSG biopsies were done in 87 subjects with molecular diagnosis of TTRVal30Met mutation. The group includes 76 patients in different stages of familial amyloid polyneuropathy and 11 asymptomatic carriers. They were all submitted to a stomatological and a neurological observation to evaluate oral health problems and to determine the neurological stage of the disease. No major oral health problems were found. Mean age of onset of the symptomatic disease was 32.8 years (±9.69 SD). Conclusions. No significant side effects occurred after the surgical procedure, and adequate material for pathological analysis was always obtained. Amyloid deposition was found in 91% of the patients. Patients with negative biopsies (N = 7) were all in the earlier stage of the disease. Two asymptomatic carriers had biopsies with amyloid deposition. We conclude that LSG biopsy is a useful, sensitive and minimal invasive method to detect amyloid deposition.
The Forgetron: A Kernel-Based Perceptron on a Budget

The Perceptron algorithm, despite its simplicity, often performs well in online classification tasks. The Perceptron becomes especially effective when it is used in conjunction with kernel functions. However, a common difficulty encountered when implementing kernel-based online algorithms is the amount of memory required to store the online hypothesis, which may grow unboundedly as the algorithm progresses. Moreover, the running time of each online round grows linearly with the amount of memory used to store the hypothesis. In this paper, we present the Forgetron family of kernel-based online classification algorithms, which overcome this problem by restricting themselves to a predefined memory budget. We obtain different members of this family by modifying the kernel-based Perceptron in various ways. We also prove a unified mistake bound for all of the Forgetron algorithms. To our knowledge, this is the first online kernel-based learning paradigm which, on one hand, maintains a strict limit on the amount of memory it uses and, on the other hand, entertains a relative mistake bound. We conclude with experiments using real datasets, which underscore the merits of our approach.
Ubiquitin Ligases RGLG1 and RGLG5 Regulate Abscisic Acid Signaling by Controlling the Turnover of Phosphatase PP2CA

Two RING E3 ligases mediate the degradation of the phosphatase PP2CA, a repressor of abscisic acid signaling, thereby modulating the activation of the ABA pathway in Arabidopsis. Abscisic acid (ABA) is an essential hormone for plant development and stress responses. ABA signaling is suppressed by clade A PP2C phosphatases, which function as key repressors of this pathway through inhibiting ABA-activated SnRK2s (SNF1-related protein kinases). Upon ABA perception, the PYR/PYL/RCAR ABA receptors bind to PP2Cs with high affinity and biochemically inhibit their activity. While this mechanism has been extensively studied, how PP2Cs are regulated at the protein level is only starting to be explored. Arabidopsis thaliana RING DOMAIN LIGASE5 (RGLG5) belongs to a five-member E3 ubiquitin ligase family whose target proteins remain unknown. We report that RGLG5, together with RGLG1, releases the PP2C blockade of ABA signaling by mediating PP2CA protein degradation. ABA promotes the interaction of PP2CA with both E3 ligases, which mediate ubiquitination of PP2CA and are required for ABA-dependent PP2CA turnover. Downregulation of RGLG1 and RGLG5 stabilizes endogenous PP2CA and diminishes ABA-mediated responses. Moreover, the reduced response to ABA in germination assays is suppressed in the rglg1 amiR (artificial microRNA)-rglg5 pp2ca-1 triple mutant, supporting a functional link among these loci. Overall, our data indicate that RGLG1 and RGLG5 are important modulators of ABA signaling, and they unveil a mechanism for activation of the ABA pathway by controlling PP2C half-life.
Enumerative Lattice Algorithms in any Norm Via M-ellipsoid Coverings

We give a novel algorithm for enumerating lattice points in any convex body, and give applications to several classic lattice problems, including the Shortest and Closest Vector Problems (SVP and CVP, respectively) and Integer Programming (IP). Our enumeration technique relies on a classical concept from asymptotic convex geometry known as the M-ellipsoid, and uses as a crucial subroutine the recent algorithm of Micciancio and Voulgaris (STOC 2010)for lattice problems in the l2 norm. As a main technical contribution, which may be of independent interest, we build on the techniques of Klartag (Geometric and Functional Analysis, 2006) to give an expected 2^O(n)-time algorithm for computing an M-ellipsoid for any n-dimensional convex body. As applications, we give deterministic 2^O(n)-time and -space algorithms for solving exact SVP, and exact CVP when the target point is sufficiently close to the lattice, on n-dimensional lattices in any (semi-)norm given an M-ellipsoid of the unit ball. In many norms of interest, including all lp norms, an M-ellipsoid is computable in deterministic poly(n) time, in which case these algorithms are fully deterministic. Here our approach may be seen as a derandomization of the â€œAKS sieveâ€for exact SVP and CVP (Ajtai, Kumar, and Siva Kumar, STOC2001 and CCC 2002). As a further application of our SVP algorithm, we derive an expected O(f*(n))^n-time algorithm for Integer Programming, where f*(n) denotes the optimal bound in the so-called â€œflatnesstheorem, â€ which satisfies f*(n) = O(n^(4/3) polylog(n))and is conjectured to be f*(n) = O(n). Our runtime improves upon the previous best of O(n^2)^n by Hildebrand and Koppe(2010).
The invasin protein of Yersinia enterocolitica: internalization of invasin-bearing bacteria by eukaryotic cells is associated with reorganization of the cytoskeleton

Yersinia enterocolitica, a facultative intracellular pathogen of mammals, readily enters (i.e., invades) cultured eukaryotic cells, a process that can be conferred by the cloned inv locus of the species. We have studied the mechanism by which the product of inv, a microbial outer membrane protein termed "invasin," mediates the internalization of bacteria by HEp-2 cells and chicken embryo fibroblasts. Invasin- bearing bacteria initially bound the filopodia and the leading edges of cultured cells. Multiple points of contact between the bacterial surface and the surface of the cell ensued and led to the internalization of the bacterium within an endocytic vacuole; the same multi-step process could be induced by an inert particle coated with invasin-containing membranes. Both adherence and internalization were blocked by an antisera directed against the beta 1 integrin cell- adherence molecule. Ultrastructural studies of detergent-insoluble cytoskeletons from infected cells and immunofluorescence microscopy of phalloidin-labeled cells showed alterations in the structure of the cytoskeleton during the internalization process including the accumulation of polymerized actin around entering bacteria. Bacterial entry was prevented by cytochalasin D indicating that the internalization process requires actin microfilament function. Possible linkages between beta 1 containing integrins and the cytoskeleton were examined during the internalization process through the use of protein- specific antibodies and immunofluorescence microscopy. Like actin, the actin-associated proteins filamin, talin and the beta 1 integrin subunit were also found to accumulate around entering bacteria. These findings suggest that the invasin-mediated internalization process is associated with cytoskeletal reorganization.