Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions of Methicillin Resistant Staphylococcus aureus USA300 and Pseudomonas aeruginosa in Polymicrobial Wound Infection

Understanding the pathology resulting from Staphylococcus aureus and Pseudomonas aeruginosa polymicrobial wound infections is of great importance due to their ubiquitous nature, increasing prevalence, growing resistance to antimicrobial agents, and ability to delay healing. Methicillin-resistant S. aureus USA300 is the leading cause of community-associated bacterial infections resulting in increased morbidity and mortality. We utilized a well-established porcine partial thickness wound healing model to study the synergistic effects of USA300 and P. aeruginosa on wound healing. Wound re-epithelialization was significantly delayed by mixed-species biofilms through suppression of keratinocyte growth factor 1. Pseudomonas showed an inhibitory effect on USA300 growth in vitro while both species co-existed in cutaneous wounds in vivo. Polymicrobial wound infection in the presence of P. aeruginosa resulted in induced expression of USA300 virulence factors Panton-Valentine leukocidin and α-hemolysin. These results provide evidence for the interaction of bacterial species within mixed-species biofilms in vivo and for the first time, the contribution of virulence factors to the severity of polymicrobial wound infections.
In∗bug: Visual analytics of bug repositories

Bug tracking systems are used to track and store the defects reported during the life of software projects. The underlying repositories represent a valuable source of information used for example for defect prediction and program comprehension. However, bug tracking systems present the actual bugs essentially in textual form, which is not only cumbersome to navigate, but also hinders the understanding of the intricate pieces of information that revolve around software bugs. We present in*Bug, a web-based visual analytics platform to navigate and inspect bug repositories. in*Bug provides several interactive views to understand detailed information about the bugs and the people that report them. The tool can be downloaded at http://inbug.inf. usi.ch
Analysis of the Safety and Efficacy of Intra-Arterial Thrombolytic Therapy in Ischemic Stroke

Background and Purpose— Intra-arterial thrombolytic therapy (IAT) may be a treatment option for patients with ischemic stroke. We analyzed the safety and efficacy of IAT on the basis of published data. Methods— We searched computerized databases for studies using IAT in ≥10 patients with ischemic stroke. Some studies had control patients for comparison. Data were collected on age, stroke territory, time to treatment, medication, site of arterial occlusion and recanalization on angiogram, outcomes, and symptomatic intracranial hemorrhage (SICH). Results— The analysis included 27 studies with 852 patients who received IAT and 100 control subjects. There were more favorable outcomes in the IAT than in the control group (41.5% versus 23%, P =0.002), with a lower mortality rate for IAT (IAT, 27.2%; control group, 40%, P =0.004). The IAT group had an odds ratio of 2.4 (95% CI, 1.45 to 3.85) for favorable outcome. SICH was more frequent in the IAT group compared with the control group (9.5% versus 3%, P =0.046). The subgroup of patients receiving a combination of intravenous thrombolytic therapy and IAT had more favorable outcomes than the IAT alone subgroup, but this trend did not reach statistical significance (53.6% versus 41.5%, P =0.1). Among the patients treated with IAT, those who had supratentorial strokes were more likely to have favorable outcomes than those with infratentorial strokes (42.2% versus 25.6%;P =0.001; odds ratio, 2.0; 95% CI, 1.33 to 3.0). Conclusions— IAT for ischemic stroke appears efficacious but carries an increased risk of SICH. Further prospective studies are needed to prove the safety and efficacy of IAT in stroke.
Genetic features of Lynch syndrome in the Israeli population

Diagnosis of Lynch syndrome (LS) may be complex. Knowledge of mutation spectrum and founder mutations in specific populations facilitates the diagnostic process. Aim of the study is to describe genetic features of LS in the Israeli population and report novel and founder mutations. Patients were studied at high‐risk clinics. Diagnostics followed a multi‐step process, including tumor testing, gene analysis and testing for founder mutations. LS was defined by positive mutation testing. We diagnosed LS in 242 subjects from 113 families coming from different ethnicities. We identified 54 different mutations; 13 of them are novel. Sixty‐seven (59%) families had mutations in MSH2, 20 (18%) in MSH6, 19 (17%) in MLH1 and 7 (6%) in PMS2; 27% of the MSH2 mutations were large deletions. Seven founder mutations were detected in 61/113 (54%) families. Constitutional mismatch repair deficiency (CMMR‐D) was identified in five families. Gene distribution in the Israeli population is unique, with relatively high incidence of mutations in MSH2 and MSH6. The mutation spectrum is wide; however, 54% of cases are caused by one of seven founder mutations. CMMR‐D occurs in the context of founder mutations and consanguinity. These features should guide the diagnostic process, risk estimation, and genetic counseling.
ISSN 2249-9709 Original Article Kolaviron and L-Ascorbic acid Ameliorates Chlorambucil -Induced Hepatic and Renal Toxicity in Rat

Chlorambucil, (4-(4-(Bis (2-chloroethyl) amino) phenyl) butanoic acid), is a well-established bifunctional alkylating agent indicated in chronic leukemia. Kolaviron (KV), a biflavonoid from Garcinia kola and L-ascorbic acid (ASA) are known to offer protection against oxidative damage in vivo. This study was designed to investigate the protective role of KV and ASA on chlorambucil (CLB)-induced toxicity in rat. Twenty male Wistar rats (180-200g) were randomized into four groups. Group-I animals served as control, Group-II received chlorambucil (0.2mg/kg b.w. p.o.), Group III (0.2mg/kg chlorambucil and 100mg/kg kolaviron p.o.), and Group IV (0.2mg/kg chlorambucil and 100mg/kg L-ascorbic acid p.o.) respectively for 14 days. Chlorambucil induced marked renal and liver damage as evident by a significant increase in plasma bilirubin, urea, and creatinine by 233%, 74% and 174% respectively (p˂0.05). Similarly, plasma ALP, ALT, and AST rose significantly by 103%, 43%, and 59% respectively (p˂0.05). However, co-treatment with KV and ASA caused reduction in the levels of urea, creatinine, bilirubin, ALP, ALT, and AST relative to chlorambucil rats. Also, hepatic malondialdehyde content of chlorambucil-treated rats increased significantly by 113% (p˂0.05). However, co-treatment with KV and ASA significantly attenuated chlorambucil-induced alteration in hepatic lipid peroxidation. Moreover, chlorambucil treatment caused a marked depletion in antioxidant status as hepatic vitamin C, GSH, GST, SOD and catalase activities by were significantly reduced 33%, 39%, 48.2%, 47.2%; and 55.8% respectively (p˂0.05). Co-treatment with KV and ASA however, significantly ameliorated the chlorambucil-induced reduction in vitamin C, GSH, GST, SOD and catalase levels. Overall, kolaviron and L-ascorbic acid protected against chlorambucil-induced damages in the liver and kidney of the rat.
Familial combined hyperlipidemia is associated with alterations in the cholesterol synthesis pathway.

OBJECTIVE Familial combined hyperlipidemia (FCH) is a common familial lipid disorder characterized by increases in plasma total cholesterol, triglyceride, and apolipoprotein B-100 levels. In light of prior metabolic and genetic research, our purpose was to ascertain whether FCH cases had significant abnormalities of plasma markers of cholesterol synthesis and absorption as compared to unaffected kindred members. METHODS AND RESULTS Plasma levels of squalene, desmosterol, and lathosterol (cholesterol synthesis markers) and campesterol, sitosterol, and cholestanol (cholesterol absorption markers) were measured by gas-liquid chromatography in 103 FCH patients and 240 normolipidemic relatives (NLR). Squalene, desmosterol, and lathosterol levels were 6% (0.078), 31%, (P<0.001) and 51% (P<0.001) higher in FCH as compared to NLR, and these differences were especially pronounced in women. An interaction with obesity was also noted for a subset of these markers. We did not observe any apparent differences for the cholesterol absorption markers among FCH patients and NLR. CONCLUSIONS Our data indicate that both men and women with FCH have alterations in the cholesterol synthesis pathway, resulting in 51% higher levels of lathosterol (and additionally desmosterol in women). Plasma levels of the cholesterol precursor sterol squalene were only slightly increased (6%), suggesting enhanced conversion of squalene to lathosterol in this disorder.
Performance Bounds for Maximum Likelihood Detection of Single Carrier FDMA

Single Carrier FDMA (SC-FDMA) plays an important role in modern wireless communications as an alternative to OFDM mainly since it exhibits low peak-to-average power ratio. Accordingly, SC-FDMA is employed as the uplink scheme for the 3GPP long term evolution (LTE). In the presence of multipath, the SC-FDMA signal may arrive at the receiver perturbed by inter-symbol-interference, which renders the single-tap frequency-domain equalization suboptimal. Optimum maximum likelihood detection for SC-FDMA is often prohibitively complex, and hence useful mostly as a performance bound for suboptimal detection schemes. In this work, the optimum-detector performance is analyzed in detail; the analysis can be easily applied to any SC frequency-domain equalization scheme. Closed form bounds on the achievable bit error rate are provided for low and high SNR regimes in correlated and uncorrelated Rayleigh fading channels. The bounds reveal that the diversity order at high SNR is significantly smaller than in the low SNR regime. Moreover, error rate flaring behavior is demonstrated under optimum detection of SC-FDMA. The analytical results are verified by simulations.
Interplay of environmental signals and progenitor diversity on fate specification of cortical GABAergic neurons

Cortical GABAergic interneurons constitute an extremely diverse population of cells organized in a well-defined topology of precisely interconnected cells. They play a crucial role regulating inhibitory-excitatory balance in brain circuits, gating sensory perception, and regulating spike timing to brain oscillations during distinct behaviors. Dysfunctions in the establishment of proper inhibitory circuits have been associated to several brain disorders such as autism, epilepsy, and schizophrenia. In the rodent adult cortex, inhibitory neurons are generated during the second gestational week from distinct progenitor lineages located in restricted domains of the ventral telencephalon. However, only recently, studies have revealed some of the mechanisms generating the heterogeneity of neuronal subtypes and their modes of integration in brain networks. Here we will discuss some the events involved in the production of cortical GABAergic neuron diversity with focus on the interaction between intrinsically driven genetic programs and environmental signals during development.
(2-Hydroxyethyl)(propyl)azanium 2-[(2-carboxyphenyl)disulfanyl]benzoate monohydrate

With the exception of the terminal hydroxy group [N—C—C—O = 53.8 (5)°], the cation of the title salt hydrate, C5H14NO+·C14H9O4S2 −. H2O, is a straight chain. A twisted conformation is found for the anion [C—S—S—C = −87.44 (16)°]. In the crystal, the anions self-assemble into a helical supramolecular chain via charge-assisted O—H⋯Oc hydrogen bonds. These chains are connected into a three-dimensional network via N—H⋯Oc, N—H⋯Ow, Oh—H⋯Ocb, and Ow—H⋯Oc hydrogen-bonding interactions (c = carboxylate, w = water, h = hydroxy and cb = carbonyl).
The aging human lens: structure, growth, and physiological behaviour

The aging human lens has been the subject of intense research over the past 20 years, for a number of quite disparate reasons. The fact that the incidence of cataract rises exponentially with age after 50 years1 provides the driving influence for much of the effort, but the unique accessibility, homogeneity, and basic simplicity of structure of the organ itself makes it a fruitful system for fundamental studies of tissue growth, development, and differentiation.2-4 Images of the whole human lens in vivo have been available for detailed analysis since the introduction of the quantitative slit lamp (or Scheimpflug) camera (Fig 1). This has been invaluable in providing an understanding of the changes in shape and optical properties both of the ‘normal’ and cataractous aging lens.5-7 The lens is also accessible as an in vitro system of study through the provision of donor eyes for corneal transplant and general research. Since the lens has no direct blood supply, it survives well both in the globe itself and in organ culture media.8-10 Whole cataractous lenses were also once routinely available before the advent of extracapsular cataract extraction (ECCE) with intraocular lens implantation and in the past there have been combined slit lamp and in vitro studies which have correlated changes in light scatter and absorbance with specific alterations in ion and protein levels (Fig 1 and Marcantonio et al 11 and Hockwin et al 12). Figure 1 Images of normal human lenses (A, B, and C), posterior polar cataract (D, E, F), and pure nuclear cataract (G, H, I). Note that slit lamp camera images (A, D, G) all have a scattering reflect artefact (small white rectangle). The normal subject (A) was 40 years of age and the accompanying in vitro grid photographs (B) and polarising images (C) were …
Covariance in Unsupervised Learning of Probabilistic Grammars

Probabilistic grammars offer great flexibility in modeling discrete sequential data like natural language text. Their symbolic component is amenable to inspection by humans, while their probabilistic component helps resolve ambiguity. They also permit the use of well-understood, general-purpose learning algorithms. There has been an increased interest in using probabilistic grammars in the Bayesian setting. To date, most of the literature has focused on using a Dirichlet prior. The Dirichlet prior has several limitations, including that it cannot directly model covariance between the probabilistic grammar's parameters. Yet, various grammar parameters are expected to be correlated because the elements in language they represent share linguistic properties. In this paper, we suggest an alternative to the Dirichlet prior, a family of logistic normal distributions. We derive an inference algorithm for this family of distributions and experiment with the task of dependency grammar induction, demonstrating performance improvements with our priors on a set of six treebanks in different natural languages. Our covariance framework permits soft parameter tying within grammars and across grammars for text in different languages, and we show empirical gains in a novel learning setting using bilingual, non-parallel data.
Retroviral expression of connexins in embryonic chick lens.

PURPOSE To develop an in vivo model system in which exogenous proteins can be expressed in embryonic chick lens and to further understand the function of connexin-mediated gap junction intercellular communication in lens cell biology. METHODS RCAS(A) is a replication-competent chicken retrovirus that infects dividing cells. Retroviral constructs were prepared containing alkaline phosphatase (AP) and FLAG-tagged connexins. Chick lenses were infected in situ by injecting virus into the lumen of lens vesicles at stage 18, cultures were taken at various periods. The lenses were then dissected, and the expressed proteins were visualized by AP histochemical examination and immunostaining. RESULTS Twenty-four hours after infection, alkaline phosphatase could be seen in epithelia and fibers. As lens fiber maturation progressed, however, the alkaline phosphatase staining was lost as the fibers matured, presumably because of the proteolytic removal of the enzyme. By 72 hours, alkaline phosphatase staining could still be observed in epithelial cells and in differentiating fibers in the bow region but not in the mature lens fibers. FLAG-tagged exogenous lens connexins were also abundantly expressed by viral infection. The exogenous connexins were localized at the cell surfaces in junctional maculae and showed the same cell-type specific distribution as that of their endogenous connexin counterparts. CONCLUSIONS An in vivo model system has been developed in the chick that provides opportunities to study the expression of wild-type and mutant proteins during lens differentiation. Expression of wild-type connexins has revealed that the characteristic distribution of the three different lens connexins is maintained even when expression is driven by a viral promoter.
Topic Models for Word Sense Disambiguation and Token-Based Idiom Detection

This paper presents a probabilistic model for sense disambiguation which chooses the best sense based on the conditional probability of sense paraphrases given a context. We use a topic model to decompose this conditional probability into two conditional probabilities with latent variables. We propose three different instantiations of the model for solving sense disambiguation problems with different degrees of resource availability. The proposed models are tested on three different tasks: coarse-grained word sense disambiguation, fine-grained word sense disambiguation, and detection of literal vs. non-literal usages of potentially idiomatic expressions. In all three cases, we outperform state-of-the-art systems either quantitatively or statistically significantly.
Automated Wildlife Monitoring Using Self-Configuring Sensor Networks Deployed in Natural Habitats

To understand the complex interactions among animals within an ecosystem, biologists need to be able to track their location and social interactions. There are a variety of factors that make this difficult. We propose using adaptive, embedded networked sensing technologies to develop an efficient means for wildlife monitoring. This paper surveys our research; we demonstrate how a self-organizing system can efficiently conduct real-time acoustic source detection and localization using distributed embedded devices.
Influence of high-resistance and high-velocity training on sprint performance.

The purpose of this study is to analyze the effect of high-resistance (HR) and high-velocity (HV) training on the different phases of 100-m sprint performance. Two training groups (HR and HV) were compared with two control groups (RUN and PAS). The HR (N = 22) and HV group (N = 21) trained 3 d.wk-1 for 9 wk: two strength training sessions (HR or HV) and one running session. There was a run control group (RUN, N = 12) that also participated in the running sessions (1 d.wk-1) and a passive control group (PAS, N = 11). Running speed over a 100-m sprint was recorded every 2 m. By means of a principal component analysis on all speed variables, three phases were distinguished: initial acceleration (0-10 m), building-up running speed to a maximum (10-36 m), and maintaining maximum speed in the second part of the run (36-100 m). HV training resulted in improved initial acceleration (P < 0.05 compared with RUN, PAS, and HR), a higher maximum speed (P < 0.05 compared with PAS), and a decreased speed endurance (P < 0.05 compared to RUN and PAS). The HV group improved significantly in total 100 m time (P < 0.05 compared with the RUN and PAS groups). The HR program resulted in an improved initial acceleration phase (P < 0.05 compared with PAS).
Search by shape examples: modeling nonrigid deformation

We describe our work on shape-based image database search using the technique of modal matching. Modal matching employs a deformable shape decomposition that allows users to select example objects and have the computer efficiently sort the set of objects based on the similarity of their shape. Shapes are compared in terms of the types of nonrigid deformations (differences) that relate them. The modal decomposition provides deformation "control knobs" for flexible matching and thus allows for selecting weighted subsets of shape parameters that are deemed significant for a particular category or context. We demonstrate the utility of this approach for shape comparison in 2-D image databases; however the general formulation is applicable to signals of any dimensionality. <<ETX>>
Ab-initio Investigation of Hydrogen Trap State by Cementite in bcc-Fe

Hydrogen trap state by cementite in ferrite was investigated by ab-initio calculations. The calculated trap energy at cementite interstitial was 33 kJ/mol and that at the interface of cementite/ferrite was 39 kJ/mol. The calculated activation energy of the migration over the stable interstitial sites is 55 kJ/mol. Considering calculated zero point vibration energy, the trap energy at cementite interstitial becomes 41 kJ/mol and the activation energy becomes at least 59 kJ/mol. The low temperature peak at about 400 K in Thermal Desorption Spectrum (TDS) of cementite reported by other researchers is considered to correspond to the trap site at the cementite/ferrite interface. Since the interstitial trap site in cementite is not effective because of the high diffusion barrier at low temperature, the higher temperature peak at about 500 K in the TDS is considered to correspond to the migration energy from the defects such as grain boundaries in cementite introduced by deformation.
FITE-TRT: a high quality translation technique for OOV words

We devised a novel statistical technique for the identification of the translation equivalents of source words obtained by transformation rule based translation (TRT). The effectiveness of the devised FITE (frequency-based identification of translation equivalents) technique was tested using biological and medical cross-lingual spelling variants and OOV words in Spanish-English and Finnish-English TRT. For Spanish-English, translation recall was 89.2%-91.0% and for Finnish-English 71.9%-72.9%. For both language pairs FITE-TRT achieved high translation precision, i.e., 97.0%-98.8%. The technique also reliably identified native source language words, i.e., source words that cannot be correctly translated by TRT. Dictionary-based CLIR augmented with FITE-TRT performed substantially better than dictionary-based CLIR where OOV keys were kept intact.
Superinfection of an amoebic abscess by Salmonella enteritidis.

Hepatic abscess can be a difficult diagnosis in the evaluation of a fever of unknown origin. Recently an unusual example of superinfection of an amoebic abscess by Salmonella enteritidis was admitted to this hospital. This existence of concurrent infection by two such unusual and unrelated organisms provides another example of the enigma of Salmonella infections in general and demonstrates the ability of this organism to appear unexpectedly in areas of decreased host resistance in an otherwise healthy individual. Patient Summary The patient was a 20-year-old Negro man, admitted to the medical service, with fever of three weeks' duration. Three weeks prior to admission to Barnes Hospital, he attempted to prevent a friend from falling down some stairs by leaning over a bannister and taking hold of his leg. The bannister pressed against the epigastrium and right upper quadrant of the patient's body, and for several moments he sustained the full