Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of ischemia-reperfusion injury on the microcirculation of the steatotic liver of the Zucker rat.

BACKGROUND Much discussion has been focused on the use of steatotic livers for transplantation due to the prevalence of steatosis in the potential donor liver pool (1). The aim of this study was to investigate the possibility that the microcirculation of steatotic liver is more sensitive to the ischemia-reperfusion (IR) injury than normal liver. METHODS The left liver lobe of obese (n=9) and lean Zucker rats (n=9) were subjected to 40 min of warm ischemia followed by 60 min of reperfusion. Fluorescent probes rhodamine 123 (Rh123), bisbenzimide (Bis), and rhodamine 6G (Rh6G) were administered for the identification by intravital fluorescence microscopy (IVFM) of mitochondrial membrane potential, hepatocyte nuclei and leukocytes, respectively before hepatic ischemia and at 15, 30, 45, and 60 min after reperfusion. Blood samples were obtained before and after 60 min of reperfusion. Liver tissue was taken at the end of experiment for histological analysis. RESULTS The liver of the obese rats showed prominent macro- and microvesicular fatty changes (MAFC and MIFC) and hepatocyte swelling. Under IVFM, the obese animals had significantly wider hepatic cords (23.1+/-0.8 microm) than the lean ones (15.9+/-0.5 microm) (P<0.01), whereas no significant difference in sinusoidal diameters was noted. The number of functional sinusoids significantly decreased after 30 min of reperfusion in both groups but no significant change was noted in the nucleus count throughout the experiment. Rh123 fluorescence intensity dropped significantly in the obese group after 60 min of reperfusion but not in the lean rats. Leukocyte adherence showed a significant rise after reperfusion in both groups. Plasma AST and ALT levels were 40- and 24-fold higher respectively for the obese animals after IR compared with their preischemic values, whereas the corresponding increase were 4.2- and 3.4-fold for the lean animals, respectively. CONCLUSIONS Our results indicate that the liver of the obese Zucker rat is steatotic and presents with an abnormal microcirculation manifested by a reduced sinusoidal density. IR led to significantly greater hepatic injury in the steatotic than in the normal liver. This injury was accompanied by a significant reduction in the functional sinusoidal density and mitochondrial membrane potential as assessed by Rh123-associated fluorescence in the steatotic liver. In conclusion, the increased sensitivity of the steatotic liver to IR injury would appear to involve both alterations in blood flow in the microcirculation and to cellular changes.
Inflammation boosts bacteriophage transfer between Salmonella spp.

The parasite of my parasite is my friend? Virulence factors of pathogenic bacteria can be swapped by means of bacterial viruses called phages. In turn, the pathogenic bacteria are under attack by the hosts' immune responses. Diard et al. discovered that SopEϕ, a phage parasite of pathogenic Salmonella species, is encouraged to spread between bacteria by the mouse host's inflammatory responses. Conversely, mucosal vaccination against Salmonella reduced inflammatory responses and curbed the transfer of SopEϕ to naïve bacteria. Science, this issue p. 1211 By reducing inflammation, vaccination inhibits transfer of virulence-promoting phages and limits Salmonella spp. evolution during infections in mice. Bacteriophage transfer (lysogenic conversion) promotes bacterial virulence evolution. There is limited understanding of the factors that determine lysogenic conversion dynamics within infected hosts. A murine Salmonella Typhimurium (S.Tm) diarrhea model was used to study the transfer of SopEΦ, a prophage from S.Tm SL1344, to S.Tm ATCC14028S. Gut inflammation and enteric disease triggered >55% lysogenic conversion of ATCC14028S within 3 days. Without inflammation, SopEΦ transfer was reduced by up to 105-fold. This was because inflammation (e.g., reactive oxygen species, reactive nitrogen species, hypochlorite) triggers the bacterial SOS response, boosts expression of the phage antirepressor Tum, and thereby promotes free phage production and subsequent transfer. Mucosal vaccination prevented a dense intestinal S.Tm population from inducing inflammation and consequently abolished SopEΦ transfer. Vaccination may be a general strategy for blocking pathogen evolution that requires disease-driven transfer of temperate bacteriophages.
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

For most mammalian pathogens, gene expression profiling studies have been limited by technical difficulties to accurately quantify pathogen gene transcripts from infected tissues. Pathogen RNA constitutes a tiny portion of the total RNA isolated from infected tissue samples. Both microarray and RNAseq technologies have difficulties in generating reliable reads for weakly expressed pathogen genes. Mutant pathogen strains with reduced in vivo proliferation pose an even bigger challenge. Here we describe an in vivo gene expression profiling protocol that is very fast, extremely sensitive and highly reproducible. We developed this protocol during our investigation of the fungal pathogen Candida albicans in a murine model of hematogenously disseminated candidiasis. Using this protocol, we have documented time courses of dynamically regulated C. albicans gene expression during kidney infection, and discovered unexpected features of gene expression responses to antifungal drug treatment in vivo.
Blood compatibility evaluations of poly(ethylene glycol)–poly(lactic acid) copolymers

Poly(ethylene glycol)–poly(lactic acid) (PEG–PLA) copolymers have been widely used for various biomedical applications. However, their hemocompatibility has not been clarified, which would lag their developments and clinical applications. In this work, we studied the effect of PEG–PLA copolymers on key human blood components in terms of their structure and bio-functions, including morphology and lysis of red blood cells, fibrinogen structure and conformation, and plasma and blood coagulation. To elucidate a structure–activity relationship, we used diblock PEG–PLA copolymers with different molecular weight, PEG(5 kDa)–PLA(25 kDa) and PEG(2 kDa)–PLA(2 kDa), abbreviated as PEG5k–PLA25k and PEG2k–PLA2k, respectively. The results show that the PEG–PLA copolymers at the concentration range studied in this work neither caused morphological alteration and lysis of red blood cells nor affected the oxygen delivery function and fibrinogen conformation. PEG5k–PLA25k from 10 to 100 mg/mL and PEG2k–PLA2k from 1.5 to 5 mg/mL disturbed the local microenvironments of fibrinogen molecules. PEG5k–PLA25k at up to 0.1 mg/mL did not interfere in the coagulation process of plasma or whole blood, while PEG2k–PLA2k from 0.1 mg/mL significantly interfered in the intrinsic plasma coagulation pathway and impaired whole blood coagulation. The results provide important information for the molecular design and clinical applications of PEG–PLA copolymers.
New sesquiterpene coumarins from the roots of Ferula flabelliloba

Three new sesquiterpene coumarins, namely, farnesiferone B (1), flabellilobin A (2) and flabellilobin B (3), together with nine known compounds, ligupersin A, 7-epi-gamma-eudesmol, persicasulfide A, conferdione, umbelliprenin, conferone, feselol, lehmferin and farnesiferol B were isolated from the roots of Ferula flabelliloba Rech. f. & Aell. (Apiaceae). The structures of these compounds were elucidated by various 1- and 2-D NMR techniques as well as HREIMS.
Attendance monitoring system using facial recognition with audio output and gender classification

Maintaining and taking log of attendance in a class is not much effective through manual process. Since bunking the classes or giving proxies for the absentees become fun and fantasy among the current generation students. Manual entering of attendance in logbooks becomes a difficult task and it can be easily manipulated. Therefore, this paper aims in presenting an automated attendance System — AUDACE. This system automatically detects the student in the class room and marks the attendance by recognizing their face. This system is developed by capturing real time human faces in the class. The detected faces are matched against the reference faces in the dataset and marked the attendance for the attendees. Finally the absentee lists are said aloud through voice conversion system for confirmation. Secondly, the system is trained to classify the gender of the students present in the class.
Lactobacillus plantarum Strains Can Enhance Human Mucosal and Systemic Immunity and Prevent Non-steroidal Anti-inflammatory Drug Induced Reduction in T Regulatory Cells

Orally ingested bacteria interact with intestinal mucosa and may impact immunity. However, insights in mechanisms involved are limited. In this randomized placebo-controlled cross-over trial, healthy human subjects were given Lactobacillus plantarum supplementation (strain TIFN101, CIP104448, or WCFS1) or placebo for 7 days. To determine whether L. plantarum can enhance immune response, we compared the effects of three stains on systemic and gut mucosal immunity, by among others assessing memory responses against tetanus toxoid (TT)-antigen, and mucosal gene transcription, in human volunteers during induction of mild immune stressor in the intestine, by giving a commonly used enteropathic drug, indomethacin [non-steroidal anti-inflammatory drug (NSAID)]. Systemic effects of the interventions were studies in peripheral blood samples. NSAID was found to induce a reduction in serum CD4+/Foxp3 regulatory cells, which was prevented by L. plantarum TIFN101. T-cell polarization experiments showed L. plantarum TIFN101 to enhance responses against TT-antigen, which indicates stimulation of memory responses by this strain. Cell extracts of the specific L. plantarum strains provoked responses after WCFS1 and TIFN101 consumption, indicating stimulation of immune responses against the specific bacteria. Mucosal immunomodulatory effects were studied in duodenal biopsies. In small intestinal mucosa, TIFN101 upregulated genes associated with maintenance of T- and B-cell function and antigen presentation. Furthermore, L. plantarum TIFN101 and WCFS1 downregulated immunological pathways involved in antigen presentation and shared downregulation of snoRNAs, which may suggest cellular destabilization, but may also be an indicator of tissue repair. Full sequencing of the L. plantarum strains revealed possible gene clusters that might be responsible for the differential biological effects of the bacteria on host immunity. In conclusion, the impact of oral consumption L. plantarum on host immunity is strain dependent and involves responses against bacterial cell components. Some strains may enhance specific responses against pathogens by enhancing antigen presentation and leukocyte maintenance in mucosa. In future studies and clinical settings, caution should be taken in selecting beneficial bacteria as closely related strains can have different effects. Our data show that specific bacterial strains can prevent immune stress induced by commonly consumed painkillers such as NSAID and can have enhancing beneficial effects on immunity of consumers by stimulating antigen presentation and memory responses.
A Simplified Method for the Quantitative Bacterial Culture of Urine

they were washed with wet swabs and suspended in 1 ml. of nutrient broth and inoculated on blood agar media and into mice. All tested slides failed to produce either culture or infection. A similar experiment was performed with the same type of slides from which mercuric chloride was removed. Both the medium and mice failed to show the presence of B. anthracis. Because unstained areas round the bacteria may simply be the space between a lightly stained surrounding medium, which retracted from the cells on drying and bacteria, the best way to demonstrate capsules is actually to stain them by some procedure which differentiates them from the cell itself. A modification of Leifson's method (1930) for staining flagella accomplishes this in the case of B. anthracis.
Panda : Verifying and enforcing network paths

We describe a new networking primitive, called a Path Verification Mechanism (PVM). There has been much recent work about how senders and receivers express policies about the paths that their packets take. For instance, users may want to choose providers whom they trust to be discreet, or a receiver may want traffic destined to it to travel through an intrusion detection service. While the ability to express policies has been well-studied, the ability to enforce policies has not. The core challenge is: if we assume an adversarial, decentralized, and high-speed environment, then when a packet arrives at a node, how can the node be sure that the packet followed an approved path? Our solution, Panda, incorporates an optimized cryptographic construction that is compact, and requires negligible configuration state and no PKI. We demonstrate Panda’s plausibility with a NetFPGA hardware implementation. At 86% more costly than an IP router on the same platform, its cost is significant but affordable. Indeed, our evaluation suggests that Panda can scale to backbone speeds.
Developing Camille, a text editor for Rodin

Initially, the Rodin platform for Event‐B did away with a textual representation for models. In this paper, we explain why a textual representation was required after all and we present the semantic‐aware text editor Camille for Rodin. We explain the design choices of Camille, such as splitting the syntax into two‐levels for machine and formula syntax. We also describe the challenges, such as synchronizing the textual representation with the Rodin database, and how they were overcome using an EMF abstraction layer. Copyright © 2011 John Wiley & Sons, Ltd.
Structural and Biophysical Characterization of XIAP BIR3 G306E Mutant: Insights in Protein Dynamics and Application for Fragment‐Based Drug Design

Previous reports describe modulators of X‐linked inhibitor of apoptosis (XIAP)–caspase interaction designed from the AVPI N‐terminal peptide sequence of second mitochondria‐derived activator of caspase. A fragment‐based drug design strategy was initiated to identify therapeutic non‐peptidomimetic antagonists of X‐linked inhibitor of apoptosis protein–protein interactions. Fragments that bind to the AVPI binding site of BIR3 (bacculoviral inhibitory repeat) were identified, and to further localize the fragment binding within the AVPI binding site, a point mutation was designed which alters the dynamics of flexible loops and blocks PI region of the binding cleft, thus enabling definition of weakly bound small molecules in the AV portion of the binding cleft. Nuclear magnetic resonance analysis confirmed the G306E mutation stabilizes the AV pocket. Biophysical characterization of the mutant confirms conformation change within the PI sub‐pocket as evidenced by a significant diminishment in binding affinity of AVPI mimetics, yet the binding affinity of the smaller AV mimetics is maintained or slightly improved in the mutant compared with wild‐type. Additional data from non‐covalent mass spectrometry analysis shows enhanced binding of AV mimetics to the G306E mutant over the wild‐type. The presented data outline a protein engineering strategy that allowed mapping of AV‐replacements with better sensitivity and precision.
Ultraviolet spectrophotometric determination of phenylbutazone in biologic specimens.

A rapid spectrophotometric method for determining phenylbutazone in biologic specimens in the presence of its metabolites and other acid-extractable drugs is described. Extensive separation and extraction of the drug is not required. Alkaline permanganate oxidation of phenylbutazone to azobenzene is the basis for the analytical technique. The strong absorption of azobenzene at 314 mμ makes for a high order of specificity. The method is sufficiently sensitive for the determination of phenylbutazone in blood of patients taking therapeutic amounts of the drug. Data showing the distribution of the drug in the rat are presented.
Amount, position, and age of coarse wood influence litter decomposition in postfire Pinus contorta stands

Spatial variation in vegetation and coarse wood is a major source of forest heterogeneity, yet little is known about how this affects ecosystem processes. In 15-year-old postfire lodgepole pine (Pinus contorta var. latifolia Englem.) stands in Yellowstone National Park, Wyoming, we investigated how the decomposition rate varies with the position of coarse wood and other dominant structures within and among stands. Tongue depressors (TD) (made of birch (Betula sp.)) and litterbags containing herbaceous litter (HL) and needle litter (NL) were deployed for 2 years within 3 burned stands and among 17 burned stands (each 0.25 ha). Within stands, the decomposition rate varied among six microsite treatments (above and below legacy wood, below logs on the ground and elevated logs, below saplings, and on open soil). Two-year mean mass loss from all litter types was least under elevated logs (HL 34.0%, NL 8.6%, TD 3.5%) and greatest under legacy wood (HL 55%, NL 33%, TD 12%). The moisture level was consistently low.
Thomas Aquinas on Human Nature: A Philosophical Study of Summa Theologiae, 1a 75-89

Introduction Part I. Essential Features (QQ75-76) 1. Body and soul 2. The immateriality of soul 3. The unity of body and soul 4. When human life begins Excursus metaphysics: reality as actuality Part II. Capacities (QQ77-83) 5. The soul and its capacities 6. Sensation 7. Desire and freedom 8. Reason and temptation Part III. Functions: (QQ84-89) 9. Mind and image 10. Mind and reality 11. Knowing the mind 12. Life after death Epilogue: Why did God make me?
BinSlayer Accurate Comparison of Binary Executables Martial Bourquin

As the volume of malware inexorably rises, comparison of binary code is of increasing importance to security analysts as a method of automatically classifying new malware samples; purportedly new examples of malware are frequently a simple evolution of existing code, whose differences stem only from a need to avoid detection. This paper presents a polynomial algorithm for calculating the differences between two binaries, obtained by fusing the well-known BinDiff algorithm with the Hungarian algorithm for bi-partite graph matching. This significantly improves the matching accuracy. Additionally a meaningful metric of similarity is calculated, based on graph edit distance, from which an informed comparison of the binaries can be made. The accuracy of this method over the standard approach is demonstrated.
StackMMU: Dynamic stack sharing for embedded systems

Real-time multi-tasking systems may require an individual stack for each task to fulfill all hard real-time requirements. However, these stacks may consume a huge memory space, even if not all stacks are simultaneously fully utilized. Thus, sharing currently unused stack space may improve memory utilization as possible with Memory Management Units (MMUs). However, an MMU introduces temporal jitter to memory accesses, influencing the real-time behavior. In this work, we propose a new concept to share dynamically the complete available stack space across tasks. Thereby, every stack operation executes in a deterministic time, by giving the Microcontroller Unit (MCU) Operating System (OS)-awareness.
Changing atmospheric Δ14C and the record of deep water paleoventilation ages

We propose a new calculation method to better estimate the deep water ventilation age from benthic-planktonic foraminifera ^(14)C ages. Our study is motivated by the fact that changes in atmospheric Δ^(14)C through time can cause contemporary benthic and planktonic foraminifera to have different initial Δ^(14)C values. This effect can cause spurious ventilation age changes to be interpreted from the geologic data. Using a new calculation method, ^(14)C projection ages, we recalculate the data from the Pacific Ocean. Contrary to previous results, we find that the Pacific intermediate and deep waters were about 600 years older than today at the last glacial maximum. In addition, there are possible signals of ventilation age change prior to ice sheet melting and at the Younger Dryas. However, the data are still too sparse to constrain these ventilation transients.
CAVA - A Verified Model Checker

Model checkers like SPIN provide a way to gain certainty about the behavior of programs and protocols. To guarantee that the model checker itself is correct, the CAVA project developed a verified and executable LTL model checker using Isabelle/HOL. This thesis reports on various building blocks of CAVA by presenting the first formalized and executable Promela semantics, a framework for verifying depth-first search based algorithms, and an automata library. As a part thereof, this thesis will detail the development rationale and history of those building blocks.
Evaluación e impacto del fondo en la medida del ángulo de mezcla θ₁₃ en el experimento Double Chooz

En el marco actual de la fisica de particulas en que sabemos que los neutrinos tienen masa, los neutrinos se describen utilizando la base de autoestados de sabor y/o la base de autoestados de masa. Estas bases son diferentes y se relacionan por cuatro parametros, uno de los cuales es el angulo de mezcla θ₁₃ (los otros tres corresponden a los angulos de mezcla θ12 y θ23 y a la fase de violacion CP δCP ). Para determinar estos parametros, se utiliza el fenomeno de la oscilacion de los neutrinos en que se manifiesta la diferencia entre las bases. La primera indicacion de un valor no nulo de θ13 fue llevada a cabo por Double Chooz en 2011[1], a continuacion tambien Daya Bay y RENO publicaron sendas medidas de θ13. La principal dificultad de esta medida es tener que determinar un angulo con una magnitud pequena, a diferencia de θ12 y θ23 que habian sido determinados previamente. La medida de θ13 ha permitido comenzar el desarrollo de experimentos para la medida de la violacion CP, que solo podia ser observada por el fenomeno de la oscilacion si los tres angulos de mezcla θ12, θ23 y θ13 eran distintos de 0. El experimento Double Chooz mide θ13 a partir de la desaparicion de antineutrinos electronicos (νe) emitidos por los reactores nucleares de la central nuclear de Chooz (Francia). Los antineutrinos se observan mediante la coincidencia temporal de la aniquiliacion del positron y la captura del neutron, las particulas que se producen en la desintegracion beta inversa, νe +p → e+ + n. Los detectores de Double Chooz han sido disenados para amplificar la senal de los antineutrinos electronicos manteniendo un nivel bajo de fondo. Se trata de dos detectores identicos, uno de los cuales se situa cerca de los reactores (∼ 400 m) para reducir la incertidumbre en la cantidad de antineutrinos generados, y el otro, lejos (∼ 1050 m), para observar la desaparicion. Ambos son calorimetros de centelleo organico liquido. Los detectores se construyeron de forma escalonada. El detector lejano termino de construirse en abril de 2011 y el cercano a finales de 2014. Se dispone de 489.51 dias de datos tomados solo con el detector lejano entre abril de 2011 y enero de 2013. A partir de estos datos se ha analizado el fenomeno de oscilacion, encontrando un valor de θ13 distinto de 0. Este analisis es el descrito en la tesis. Desde 2015 se han estado tomando datos con los dos detectores. En la presente tesis se muestra el analisis preliminar de los primeros 200 dias de datos con los dos detectores.