Miracle-dz/UniFAR-FTUs huggingface dataset:
Henipavirus RNA in African Bats

Background Henipaviruses (Hendra and Nipah virus) are highly pathogenic members of the family Paramyxoviridae. Fruit-eating bats of the Pteropus genus have been suggested as their natural reservoir. Human Henipavirus infections have been reported in a region extending from Australia via Malaysia into Bangladesh, compatible with the geographic range of Pteropus. These bats do not occur in continental Africa, but a whole range of other fruit bats is encountered. One of the most abundant is Eidolon helvum, the African Straw-coloured fruit bat. Methodology/Principal Findings Feces from E. helvum roosting in an urban setting in Kumasi/Ghana were tested for Henipavirus RNA. Sequences of three novel viruses in phylogenetic relationship to known Henipaviruses were detected. Virus RNA concentrations in feces were low. Conclusions/Significance The finding of novel putative Henipaviruses outside Australia and Asia contributes a significant extension of the region of potential endemicity of one of the most pathogenic virus genera known in humans.
Microuli, a family of miniature subterminal inverted-repeat transposable elements (MSITEs): transposition without terminal inverted repeats.

The ﬁrst Microuli element, Microuli-Aa1, was discovered as a 209-bp insertion in the 5 (cid:57) long terminal repeat of a retrotransposon named Mosqcopia-Aa2 (un-published data, GenBank AY009101) in the yellow fever mosquito, Aedes aegypti. As shown in ﬁgure 1 A, the Microuli insertion resulted in a TTAA target duplication, indicating past mobility of the element. To further characterize this mobile element, we screened an A. aegypti genomic library, using a digoxigenin-labeled single-stranded DNA probe generated by asymmetric PCR using the entire Microuli-Aa1 as the template. The library construction, probe labeling, and library screening pro-cedures were as previously described (Tu 2000). The ﬁnal washing stringency was 0.5 (cid:51) SSC with 0.1% SDS at 55 (cid:56) C, which allows approximately 15%–25% mis-match (Meinkoth and Wahl 1984). Because 462 positive plaques were identiﬁed among 64,000 total plaques screened, it was estimated using a previously described calculation method (Tu 2000) that there were approximately 3,000 copies of Microuli per haploid genome. The entire inserts of three positive genomic clones iso-lated during the above screening experiment were sequenced and deposited in GenBank (AY009102– AY009104). The boundaries of Microuli elements were deduced based on sequence comparisons between the four genomic clones.
Passive and active protection against disorders of the gut.

Abstract The large surface area of mucosal surfaces, particularly of the gastrointestinal tract, is protected against microorganisms and environmental antigens by various innate factors (e.g., mucins, lactoferrin, and others) and specific antibodies which are of IgA, or in some species, IgG Isotypes. Passive protection provided by effective prenatal transplacental transport of maternal antibodies and/or post-natal consumption of milk antibodies in breastfed newborns, is essential for the survival of neonates. Passive protection of mucosal surfaces by pre-formed antibodies in non-breast juveniles or adults is currently used only on an experimental basis: IgA-enriched preparations of gamma-globulin have been successfully given to children, and antibodies specific for several gastrointestinal pathogens have been isolated from immunized cows' milk, hens' eggs, or transgenic plants. Systemic administration of pre-formed antibodies is effective for protection against intestinal pathogens in species (e.g., mice, rats) endowed with efficient hepato-biliary transport of IgA into the gut lumen. However, this route of antibody administration is of limited efficiency in other species, including humans, in which almost all intestinal antibodies are produced locally by plasma cells in the gut mucosa and are not derived to a significant degree from the circulation. Active immunization is preferable for long-lasting protection. The site of immunization and presence of lymphoid tissues with inductive potential play an essential role in generating humoral immune responses in mucosal secretions. The relative efficiency of immunization routes (e.g., oral, nasal, rectal or genital) in the induction of preferential antibody responses in the intestinal secretion has not been studied extensively. Furthermore, suitable antigen delivery systems for achieving this goal must also be considered.
An appraisal of selection criteria for dynamic psychotherapies and implications for setting time limits.

Practitioners of short-term dynamic psychotherapies commonly hold the working assumption that through rigorous selection procedures the progress to be expected in a specified length of time can be predicted. We question this assumption and draw upon relevant findings from the psychotherapy research literature, as well as from our own clinical and research experiences, to support our skepticism. Without minimizing the demonstrated effectiveness of short-term therapies, we propose that setting prearranged time limits be either replaced or supplemented by the implementation of a "time limited attitude. " We further propose that this attitude can contribute to more efficiently conducted treatment, regardless of length. The concept of a time-limited attitude is defined, and the suggestion is made to arrange therapy in defined but flexible durations of treatment rather than by either setting initial termination dates or leaving the time open-ended. Finally, we suggest that the initially proposed length of treatment be determined by the clarity with which a treatment focus can be established. Clinical vignettes are provided to illustrate the relationship between clarity of focus and initially proposed length of treatment.
Methods for Studying Rodent Intestinal Lipoprotein Production and Metabolism

Lipid absorption begins with the digestion of dietary triacylglycerol and ultimately results in the secretion of triacylglycerol in chylomicrons into the lymphatics. Additionally, the intestine also secretes numerous proteins and peptides involved in lipid and lipoprotein metabolism in response to food. Ultimately, chylomicrons and these proteins, peptides, and hormones are found in lymph. The lymph fistula rat model has traditionally been used to study this intestinal absorption of nutrients, especially lipids, but recently, this model has also been used for studying the secretion of hormones by the small intestine. The protocols described in this unit include the lymph fistula rat and mouse model, as well as in vivo chylomicron metabolism studies. These experimental models are helpful for the study of metabolic phenotypes, the characterization of intestinal lipid absorption and transport, and determining peripheral metabolism of intestinally derived lipoproteins. Curr. Protoc. Mouse Biol. 2:219‐230 © 2012 by John Wiley & Sons, Inc.
SPARSE REPRESENTATIONS FOR LIMITED DATA TOMOGRAPHY By Hstau

In limited data tomography, with applications such as electron microscopy and medical imaging, the scanning views are within an angular range that is often both limited and sparsely sampled. In these situations, standard algorithm s produce reconstructions with notorious artifacts. We show in this paper that a sparsity image representation principle, based on learning dictionaries for sparse representations of ima ge patches, leads to significantly improved reconstructions o f the unknown density from its limited angle projections. The pre sentation of the underlying framework is complemented with illustrative results on artificial and real data.
Docetaxel, estramustine and prednisone for hormone-refractory prostate cancer: a single-center experience.

BACKGROUND The results of chemotherapy in patients with advanced, hormone-refractory prostate cancer (HRPC) have been disappointing. Mitoxantrone has been used in the past for palliation, but it does not prolong survival. It was recently demonstrated that docetaxel is able to improve median survival as compared to mitoxantrone. We, therefore, wanted to evaluate a docetaxel-based regimen, with regard to efficacy and tolerability, in men with HRPC at our institution. PATIENTS AND METHODS Patients with progressive HRPC (new metastatic lesions or PSA progression) and no prior cytotoxic chemotherapy received the following treatment administered in 21-day cycles: 280 mg estramustine three times daily on days 1 to 5 and 7 to 11, 70 mg docetaxel per square meter of body surface area on day 2, and 10 mg prednisone once daily throughout the course. After four cycles, the patients were re-evaluated via PSA, blood counts, CT and bone scans. If no progression had occurred, two more cycles were given. Objective response rates, post-treatment declines in serum PSA levels, as well as side-effects, were recorded. RESULTS Thirty-nine patients with HRPC (age range 43-79 years, average 65 years) were enrolled after informed consent. The median PSA in this cohort was 144 (1.5-3030) ng/ml. The percentage of patients with bone and lymph node metastases was 82% and 61.5%, respectively. During an average follow-up period of 11 months, 20 patients (64.5%) showed a response to therapy, including a complete (CR), partial (PR) or mixed (MR) response, stable disease (SD) of metastatic lesions, or a PSA response. A post-therapeutic decrease of serum PSA levels of >25%, >50% and >75% occurred in 26.1%, 21.7% and 26.1% of patients, respectively. Lymph node metastases responded better to therapy (73%) than bone metastases (42%). Regarding toxicity, the regimen was generally well tolerated. Only three patients showed adverse events (one grade 4 neutropenia, one dermatological and one as a result of pain), which led to therapy withdrawal. Minor adverse events included nausea, alopecia and fatigue. No cardiovascular events were reported. CONCLUSION Although the patients included in the present study had advanced disease, responses were promising and toxicity was tolerable. These preliminary data support the findings of recently published studies and suggest that docetaxel-based chemotherapy is going to play an important role as a regimen for patients with HRPC.
Modulation of glycosylation and transport of viral membrane glycoproteins by a sodium ionophore

Analysis of viral glycoprotein expression on surfaces of monensin- treated cells using a fluorescence-activated cell sorter (FACS) demonstrated that the sodium ionophore completely inhibited the appearance of the vesicular stomatitis virus (VSV) G protein on (Madin- Darby canine kidney) MDCK cell surfaces. In contrast, the expression of the influenza virus hemagglutinin (HA) glycoprotein on the surfaces of MDCK cells was observed to occur at high levels, and the time course of its appearance was not altered by the ionophore. Viral protein synthesis was not inhibited by monensin in either VSV- or influenza virus-infected cells. However, the electrophoretic mobilities of viral glycoproteins were altered, and analysis of pronase-derived glycopeptides by gel filtration indicated that the addition of sialic acid residues to the VSV G protein was impaired in monensin-treated cells. Reduced incorporation of fucose and galactose into influenza virus HA was observed in the presence of the ionophore, but the incompletely processed HA protein was cleaved, transported to the cell surface, and incorporated into budding virus particles. In contrast to the differential effects of monensin on VSV and influenza virus replication previously observed in monolayer cultures of MDCK cells, yields of both viruses were found to be significantly reduced by high concentrations of monensin in suspension cultures, indicating that cellular architecture may play a role in determining the sensitivity of virus replication to the drug. Nigericin, an ionophore that facilitates transport of potassium ions across membranes, blocked the replication of both influenza virus and VSV in MDCK cell monolayers, indicating that the ion specificity of ionophores influences their effect on the replication of enveloped viruses.
Comportement à la corrosion des alliages TiNi et TA6V4 dans la salive artificielle et performance d’usure

Ce travail porte sur l’etude du comportement tribologique sans lubrification et electrochimique dans la salive artificielle des alliages TiNi (50/50) et TA6V4 pour les applications en orthodontie (implants dentaires). L'alliage TiNi (50/50) a ete prepare dans un four a induction sous vide alors que l'alliage commercial TA6V4 sera utilise comme materiau de reference. L’analyse microstructurale et la composition chimique des deux alliages TiNi et TA6V4 a ete realisee par microscopie electronique a balayage (MEB) couplee a l’EDS. Les resultats montrent que l'alliage TiNi presente une meilleure resistance a l'usure par glissement a sec (1,327x10 -4 mm 3 /Nm) par comparaison avec l'alliage TA6V4 (9,506x10 -4 mm 3 /Nm). Les mecanismes d’usure ont ete clairement identifies pour les deux alliages et sont principalement bases sur une usure abrasive et adhesive pour l'alliage TiNi, et une usure abrasive associee a une oxydation, pour l’alliage TA6V4. L'etude electrochimique a revele que les deux alliages presentent un caractere passif avec une resistance elevee a la corrosion. Mots cles: Alliages de titane- Microstructure- Comportement a l'usure- Resistance a la corrosion- Impedance. Corrosion Behavior of TiNi and TA6V4 Alloys in Artificial Saliva and Wear Performance This work aims to study the tribological performance in dry conditions and electrochemical behavior, in the artificial saliva of TiNi (50/50) alloys in comparison with TA6V4 alloys in the focus to use them for dental applications. The TiNi alloy was prepared in a vacuum induction melting furnace whileTA6V4 commercial alloy should be used as a reference material. The TiNi alloy (50/50) was prepared in a vacuum induction melting furnace while the TA6V4 commercial alloy will be used as a reference material. The microstructural analysis and chemical composition of the two TiNi and TA6V4 alloys was determined by scanning electron microscopy (SEM) coupled to EDS. Results showed that TiNi alloy exhibits a better wear resistance in dry sliding mode (1.327x10 -4 mm 3 / Nm) when compared to the alloy TA6V4 (9,506x10 -4 mm 3 / Nm). The wear mechanisms of both alloys have been clearly established. It can be retained that NiTi alloy degradation is governed by an adhesive and abrasive wear mechanism, but for the TA6V4 alloy, abrasive and oxidative wear mechanisms are determined. Electrochemical studies reveal a passive behavior character and higher resistance against corrosion. Key words : Titanium alloys- Microstructure- Wear behavior- Corrosion resistance- Impedance.
Global Loss of Bmal1 Expression Alters Adipose Tissue Hormones, Gene Expression and Glucose Metabolism

The close relationship between circadian rhythm disruption and poor metabolic status is becoming increasingly evident, but role of adipokines is poorly understood. Here we investigated adipocyte function and the metabolic status of mice with a global loss of the core clock gene Bmal1 fed either a normal or a high fat diet (22% by weight). Bmal1 null mice aged 2 months were killed across 24 hours and plasma adiponectin and leptin, and adipose tissue expression of Adipoq, Lep, Retn and Nampt mRNA measured. Glucose, insulin and pyruvate tolerance tests were conducted and the expression of liver glycolytic and gluconeogenic enzyme mRNA determined. Bmal1 null mice displayed a pattern of increased plasma adiponectin and plasma leptin concentrations on both control and high fat diets. Bmal1 null male and female mice displayed increased adiposity (1.8 fold and 2.3 fold respectively) on the normal diet, but the high fat diet did not exaggerate these differences. Despite normal glucose and insulin tolerance, Bmal1 null mice had increased production of glucose from pyruvate, implying increased liver gluconeogenesis. The Bmal1 null mice had arrhythmic clock gene expression in epigonadal fat and liver, and loss of rhythmic transcription of a range of metabolic genes. Furthermore, the expression of epigonadal fat Adipoq, Retn, Nampt, AdipoR1 and AdipoR2 and liver Pfkfb3 mRNA were down-regulated. These results show for the first time that global loss of Bmal1, and the consequent arrhythmicity, results in compensatory changes in adipokines involved in the cellular control of glucose metabolism.
Incidence of cancer among persons with schizophrenia and their relatives.

BACKGROUND It has repeatedly been reported that the risk for cancer in patients with schizophrenia is different from that of the general population, specifically a lower risk for lung cancer despite increased smoking. Confirmation of these associations could lead to hypotheses on shared risk or protective factors, either genetic or environmental. METHODS From Finland's National Hospital Discharge and Disability Pension registers, Helsinki, we identified a cohort of 26 996 individuals born between 1940 and 1969 and treated for schizophrenia between 1969 and 1991. They were followed up for cancer from 1971 to 1996 by record linkage with the Finnish Cancer Registry, yielding 446 653 person-years at risk, and standardized incidence ratios (SIRs) were calculated. Likewise, 39 131 parents and 52 976 siblings of the patients with schizophrenia were followed up to explore familial genetic hypotheses on deviations in cancer risk. RESULTS In patients with schizophrenia, an increased overall cancer risk was found (724 cases observed vs 619 expected; SIR, 1.17; 95% confidence interval [CI], 1.09-1.25). Half of the excess cases were attributable to lung cancer (SIR, 2.17; 95% CI, 1.78-2.60), and the strongest relative increase in risk was in pharyngeal cancer (SIR, 2.60; 95% CI, 1.25-4.77). Cancer incidence in siblings (SIR, 0.89; 95% CI, 0.83-0.94) and parents (SIR, 0.91; 95% CI, 0.89-0.93) was consistently lower than that in the general population. CONCLUSION Although specific lifestyle factors, particularly tobacco smoking and alcohol consumption, probably account for the increased cancer risk in patients with schizophrenia, the decreased risk in relatives would be compatible with a postulated genetic risk factor for schizophrenia offering selective advantage to unaffected relatives.
Securing Java through software watermarking

An important advantage of Java is its portability due to its use of bytecode. However the use of bytecode allows decompilation of Java programs to gain access to their source code. This makes it easier to pirate Java programs, infringing their copyright. This is a disadvantage of Java in comparison with programming languages that compile to native object code.Software watermarking is a relatively new approach to the problem of copyright protection that involves embedding ownership information in an executable program. Watermarking has been extensively researched in the context of multimedia and significant progress has been made toward the development of robust and secure techniques. In this paper we investigate a new software watermarking scheme. This is derived from signal detection theory which is used in multimedia watermarking.
Antiglycating potential of Zingiber officinalis and delay of diabetic cataract in rats

Purpose Advanced glycation end products (AGE) are associated in the development of several pathophysiologies including diabetic cataract. Earlier we have reported that some common dietary agents have antiglycating activity and ginger (Zingiber officinalis) was one of the few prominent agents that effectively prevented AGE formation in vitro. In this study we investigated the potential of ginger to prevent diabetic cataract in rats. Methods Diabetes was induced in Wistar-NIN rats by intraperitoneal injection of streptozotocin (35 mg/kg bodyweight) and the control rats received vehicle alone. While a set of diabetic animals received AIN-93 diet, another set received either 0.5 or 3% ginger in their diet for a period of two months. Cataract progression was monitored by slit-lamp biomicroscope. At the end of two months, the animals were sacrificed to evaluate non-enzymatic glycation and osmotic stress in the eye lens. Results Slit-lamp examination revealed that feeding of ginger not only delayed the onset but also the progression of cataract in rats. Molecular analyses indicated that feeding of ginger significantly inhibited the formation of various AGE products including carboxymethyl lysine in the eye lens. In addition, ginger also countered hyperglycemia-induced osmotic stress in the lens. Conclusions The results indicated that ginger was effective against the development of diabetic cataract in rats mainly through its antiglycating potential and to a lesser extent by inhibition of the polyol pathway. Thus, ingredients of dietary sources, such as ginger, may be explored for the prevention or delay of diabetic complications.
Attention without awareness

Judging by introspection and intuition, most of us would agree that the we become conscious of events in the external physical world when we pay attention to them and things we notice (i.e., become conscious of) are the ones that attract our attention. A long tradition of investigations in psychology and neuroscience also confirm that attention and awareness go hand in hand. Recently, however, the validity of this intuition has been questioned. This thesis addresses the hypothesis that attention and awareness might be disentangled at behavioural and neurobiological levels. Two main questions were: (1) does allocation / withdrawal of attention to / from unconscious stimuli affect the contents of subconscious processing and if so, could one demonstrate such modulations at the perceptual levels of processing? (2) What are the neural substrates of attentional selection of unconscious perception? In order to address these questions I adopted the framework of Load Theory combined with a recently developed technique called Continuous Flash Suppression (which combines binocular rivalry with dichoptic masking allowing for prolonged periods of unconscious exposure to visual stimuli). In 7 behavioural experiments I demonstrated (1) orientation-specific adaptation to unconscious gratings (rendered invisible by CFS); (2) such subconscious orientation processing was modulated by attentional load in a concurrent orthogonal foveal task as well as by sustained spatial attention. Finally, using functional magnetic resonance imaging (fMRI) I showed that human primary visual cortex (Vl) response to invisible stimuli was also modulated by attentional load. My findings join a-number of recent works in challenging the traditional view that attention and awareness are one and the same as well as the idea that attention acts as the gate-keeper to awareness. They also support the suggestion that neither the availability of attentional capacity for stimulus processing nor allocation of spatial attention can be a sufficient condition for awareness.
Supporting Constructive Learning with a Feedback Planner

A promising approach to constructing more effective computer tutors is implementing tutorial strategies that extend over multiple turns. This means that computer tutors must deal with (1) failure, (2) interruptions, (3) the need to revise their tactics, and (4) basic dialogue phenomena such as acknowledgment. To deal with these issues, we need to combine ITS technology with advances from robotics and computational linguistics. We can use reactive planning techniques from robotics to allow us to modify tutorial plans, adapting them to student input. Computational linguistics will give us guidance in handling communication management as well as building a reusable architecture for tutorial dialogue systems. A modular and reusable architecture is critical given the difficulty in constructing tutorial dialogue systems and the many domains to which we would like to apply them. In this paper, we propose such an architecture and discuss how a reactive planner in the context of this architecture can implement multi-turn tutorial strategies.