Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunoexpressions of embryonic and nonembryonic stem cell markers (Nanog, Thy-1, c-kit) and cellular connections (connexin 43 and occludin) on testicular tissue in thyrotoxicosis rat model

In this study, possible thyrotoxicosis-related histological changes in testicular tissues of rats with experimentally induced thyrotoxicosis model were evaluated on cellular connections and stem cell markers. Two experimental groups, thyrotoxicosis and control, each consisting of eight animals were used. Rats in the thyrotoxicosis group were injected intraperitoneally with 3,3′,5-triiodo-l-thyronine (50 µg/100 g body weight/day) for 10 days. At the end of the study, animals in both groups were anesthetized, and blood samples were collected for biochemical analyses. Their testes were dissected out and histological procedure was conducted to perform further histochemical, immunohistochemical analyses and tissue expression analysis by real-time polymerase chain reaction. Expression of the stem cell markers such as c-kit and Thy-1 significantly decreased in the testes of the thyrotoxicosis group compared with the control group; however, Nanog expression was not detected in any of the groups. Similarly, connexin 43 and occludin expressions were also found to be significantly lower in the thyrotoxicosis group. These results on cellular connections are supported with the tissue expression analysis. Our findings are indicative of supporting microenvironmental tissue decay rather than parenchyma damage, which has been actually ignored in the literature. In conclusion, experimental thyrotoxicosis model may have adverse effects on the cell junctional complexes, cell–cell interactions, and pluripotency capacity.
Un modelo de intervención desde el servicio de microbiología en la alerta precoz de la sepsis

La sepsis es uno de los mayores desafios de la medicina contemporanea, siendo hoy en dia un importante problema sanitario debido a su alta incidencia, morbilidad y mortalidad. La atencion temprana de la sepsis es un estandar de cuidado en muchas instituciones y el papel de los diferentes especialistas es bien reconocido. Sin embargo, el impacto de una llamada telefonica por parte de un especialista en Microbiologia Clinica al momento de la llegada de los hemocultivos al Servicio de Microbiologia no ha sido evaluado. Los objetivos de esta tesis fueron los siguientes. 1) Valorar el conocimiento de sepsis del personal medico y de enfermeria que atiende a pacientes cuyos hemocultivos acaban de ser enviados al Servicio de Microbiologia; 2) Evaluar si se han llevado a cabo, antes de la llamada telefonica, las medidas diagnostico-terapeuticas adecuadas a juicio de un entrevistador medico del Servicio de Microbiologia; 3) Valorar la necesidad de consejo diagnostico y terapeutico de sepsis por parte del personal medico; 4) Medir el impacto diagnostico de una intervencion precoz de sepsis realizada por un entrevistador medico del Servicio de Microbiologia. Para llevar adelante estos objetivos se realizaron llamadas telefonicas seguidas de una entrevista a los medicos y enfermeras a cargo de los pacientes cuyos hemocultivos habian sido recibidos en el Laboratorio de Microbiologia en el Hospital Gregorio Maranon. Los pacientes fueron clasificados al azar en el grupo A (llamado telefonico realizado) y Grupo B (sin llamado telefonico). Se incluyeron 300 pacientes en el estudio. La sepsis fue reconocida inmediatamente por el 30,3 por ciento de las enfermeras y el 50 por ciento de los medicos. Consejos para optimizar el uso de las pruebas bioquimicas y microbiologicas fueron proporcionados en el 36 por ciento de los casos y para mejorar la terapia antimicrobiana en el 57,6 por ciento. El porcentaje de seguimiento de las recomendaciones fue alto. La mediana de dias de uso de antibioticos en los grupos A y B, respectivamente, fueron 6 dias [IQR: 2-12] frente a 9 dias [IQR: 4-16] p=0,008 y el numero medio de la dosis diaria prescripta de antimicrobianos fue de 6 [IQR: 3-17] en el Grupo A frente a 10 [RIC: 5-22] en el grupo B; p= 0,016. Se encontro una reduccion de 40 euros/paciente/dia solo en el consumo de tratamiento antimicrobiano en el grupo A. A modo de conclusion, una llamada telefonica con el asesoramiento de un medico especialista en Microbiologia Clinica y Enfermedades Infecciosas inmediatamente despues de la llegada de los cultivos de sangre en el Departamento de Microbiologia mejora el uso de los recursos de diagnostico y reduce el consumo de antimicrobianos y gastos en el manejo de los pacientes con sospecha de sepsis.
Mapping of natural anti-factor VIII antibodies in plasma pools from healthy donors: use of rationally designed synthetic peptides.

Inhibitor antibodies of blood coagulation factor VIII (FVIII) impair FVIII replacement therapy, constituting a serious complication in haemophilic patients. anti-FVIII antibodies may also develop in a variety of disease-associated autoimmunity. Mapping of human FVIII inhibitors in haemophilia A or autoantibody origin have delineated three major clusters of B-cell inhibitory epitopes (domain A2, A3 and C2). Inhibitory and non-inhibitory FVIII antibodies have also been described in plasma of healthy donors and pools of immunoglobulins. The purpose of this study was to use synthetic FVIII-peptides to more closely define regions of the molecule targeted by natural anti-FVIII antibodies. Predictive algorithms were used for defining the positions of potential continuous epitopes. To investigate the presence of peptide-reactive antibodies in normal plasma pools of healthy donors, a plasma fraction (Cohn fraction II+III) containing all IgG subclasses was purified by affinity chromatography on peptide-Sepharose columns. The results of ELISAs and Western blotting experiments (with the selected peptides and well-defined recombinant FVIII thrombin fragments) confirmed the reaction specificities of the affinity-purified human antibodies. For each IgG preparation, the isotopic subclass was also determined. In the clotting assay, several IgG preparations showed neutralising activity in a dose-dependent manner. Our observations support the recent hypothesis that FVIII inhibitors in haemophilia A and autoimmune disease may originate from the proliferation of natural FVIII-specific B-cell clones.
Clinical genomic profiling to identify actionable alterations for investigational therapies in patients with diverse sarcomas

Background There are currently no United States Food and Drug Administration approved molecularly matched therapies for sarcomas except gastrointestinal stromal tumors. Complicating this is the extreme diversity, heterogeneity, and rarity of these neoplasms. Few therapeutic options exist for relapsed and refractory sarcomas. In clinical practice many oncologists refer patients for genomic profiling hoping for guidance on treatment options after standard therapy. However, a systematic analysis of actionable mutations has yet to be completed. We analyzed genomic profiling results in patients referred to MD Anderson Cancer Center with advanced sarcomas to elucidate the frequency of potentially actionable genomic alterations in this population. Methods We reviewed charts of patients with advanced sarcoma who were referred to investigational cancer therapeutics department and had CLIA certified comprehensive genomic profiling (CGP) of 236 or 315 cancer genes in at least 50ng of DNA. Actionable alterations were defined as those identifying anti-cancer drugs on the market, in registered clinical trials, or in the Drug-Gene Interaction Database. Results Among the 102 patients analyzed median age was 45.5 years (range 8-76), M: F ratio 48:54. The most common subtypes seen in our study were leiomyosarcoma (18.6%), dedifferentiated liposarcoma (11%), osteosarcoma (11%), well-differentiated liposarcoma (7%), carcinosarcoma (6%), and rhabdomyosarcoma (6%). Ninety-five out of 102 patients (93%) had at least one genomic alteration identified with a mean of six mutations per patient. Of the 95 biopsy samples with identifiable genomic alterations, the most commonly affected genes were TP53 (31.4%), CDK4 (23.5%), MDM2 (21.6%), RB1 (18.6%), and CDKN2A/B (13.7%). Notable co-segregating amplifications included MDM2-CDK4 and FRS2-FGF. Sixteen percent of patients received targeted therapy based on CGP of which 50% had at least stable disease. Conclusions Incorporating CGP into sarcoma management may allow for more precise diagnosis and sub-classification of this diverse and rare disease, as well as personalized matching of patients to targeted therapies such as those available in basket clinical trials.
ToF-SIMS : materials analysis by mass spectrometry

Contents Prologue: ToF-SIMS - An evolving mass spectrometry of materials (John C. Vickerman The history of Static SIMS - A personal perspective (Alfred Benninghoven) Status of cascad theory (Herbert M. Urbassek) Fundamentals of organic SIMS: insights from experiments and models (Arnaud Delcorte) Molecular speciation analysis of inorganic compounds (Luc van Vaeck) Molecular dynamics simulations, the theorectical partner to dynamic cluster SIMS experiments (Barbara J.Garrison and Zbigniew Postawa)) Cationisation (Birgit Hagenhoff) Laser post-ionisation - fundamentals (Andreas Wucher) Time-of-flight mass analysers (Bruno W. Schueler) Analysis beams used in toF-SIMS (Rowland Hill) Cluster and polyatomic primary ion beams (John S. fletcher and Christopher Szakal) Molecular depth profiling (Alex Shard, Ian Gilmore and Andreas Wucher) Role of operating conditions in ToF-SIMS (Ian Gilmore) Laser post-ionisation for elemental and molecular surface analysis (Nicholoas P. Lockyer) Sample handling for ToF-SIMS (Fraser Reich) Qualitative interpretation of spectra (David Briggs and Ian W. Fletcher) Multivariate analysis of SIMS spectra (Alex Henderson) ToF-SIMS image analysis (Bonnie J. Tyler) Characterisation of polymeric materials (Lutao Weng and Chiming Chan) li>Functional modification of surfaces using self-assembled monolayers (Amy Walker) Application of SIMS to study of biological systems (Alain M. Piwowar and Nicholas Winograd) Medical and biological applications of cluster ToF-SIMS (David Touboul, Oliver Laprevote and Alain Brunelle) Depth profiling of inorganic materials (Ewald Niehuis and Thomas Grehl) Depth profiling in organic electronics (Ewald Niehuis) Contamination monitoring and failure analysis (Arwa Ginwalla, Thomas, F. Fister and Ian A. Mowat) Photographic and digital graphic materials (Luc van Vaeck, Yannick Vercammen, Jens Lenaerts, Roel de Mondt, Jaymes van Luppen and Frank Vangaever) Applications of ToF-SIMS in cosmochemistry (Thomas Stephan and Ian C. Lyon) Index
Searching for nitrile hydratase using the Consensus‐Degenerate Hybrid Oligonucleotide Primers strategy

Consensus‐Degenerate Oligonucleotide Hybrid Primers (CODEHOP) were designed by using the WWW‐implemented strategy, based on multiple alignments of nitrile hydratase (NHase) α subunit, available from EMBL database. These primers were successfully tested with known NHase‐producing bacterial strains such as Agrobacterium tumefaciens DSM 9674, Rhodococcus erythropolis DSM 9675, R. erythropolis 9685 and R. erythropolis 11397 and also allowed amplification from organisms not previously referenced (Variovorax sp. DSM 11402 and Agrobacterium sp. DSM 11401). Hybrid primer utilisation was evaluated by analysing the incorporated sequences in cloned PCR fragments. Several primers from the oligonucleotide pool seemed to participate in the amplification of the correct fragment. Common garden soil was used as a source for both acetonitrile culture enrichment screening and direct DNA extraction. A R. erythropolis strain (CCMI 1005) was isolated by culture enrichment and allowed the PCR amplification of a DNA sequence (AJ548493) identical to the NHase coding sequences commonly described for that species, while the direct use of soil DNA as template led to the CODEHOP detection of two putative NHase coding sequences (AJ548498 and AJ548499), which were significantly different from any other known sequence. The phylogenetic relationship between all sequences obtained and the published NHase coding sequences was assessed by neighbour‐joining analysis.
Enhanced TENG Performance by Engineering the Compression Modulus of Triboelectric Layers

A vertical contact-separation mode (CS-mode) triboelectric nanogenerator (TENG) was developed for energy harvesting applications. The TENG was fabricated using polytetrafluoroethylene (PTFE) and Polyimide (kapton) films as negative and positive triboelectric layers, respectively and copper tape was used as top and bottom electrodes. Polydimethylsiloxane (PDMS) was used as a support layer to reduce the compression modulus of kapton and to improve the contact stress between kapton and PTFE, resulting in an enhanced TENG output voltage. The stress, strain, and compression modulus of triboelectric layers at three different conditions: bare kapton as tribo-layer (Case-1), bare PDMS as tribo-layer (Case-2), and PDMS/kapton as tribo-layer (Case-3) were modeled using COMSOL software. The voltage generation performance of TENG (Case 1, 2, and 3) was demonstrated by investigating the open-circuit voltage (OCV) at an applied mechanical force of 5 N. A maximum OCV of 11 Vp-p was measured for TENG with PDMS as support layer and a lower compression modulus of 8 MPa when compared to the TENG without PDMS (OCV of 2 Vp-p).
A Research Overview and Evaluation of Performance Metrics for Self-Organization Algorithms

Self-organization (SO) algorithms are supposed to restructure and reconfigure the system at run-time in order to empower it to fulfill its requirements under uncertain environmental conditions. For this purpose, information about the state of the environment and the system is used in feedback loops to establish a flexible, powerful system. Consequently, the performance of the SO algorithms has a significant effect on the overall performance of the system. Indeed, it is hard to design high-performing SO algorithms, because the environmental conditions the system has to operate in are partially unpredictable at design time. A crucial aid for the development of SO algorithms are tools that enable the evaluation of the algorithms' performance at design time. These tools could also be used to select the best-fitting algorithm and parametrization for a specific application, among others. We show how existing performance metrics can be applied to SO algorithms by evaluating different partition-based algorithms. Based on these results, we discuss the advantages and limitations of the existing metrics and deduce requirements for performance metrics for SO algorithms.
Fog Computing as a Resource-Aware Enhancement for Vicinal Mobile Mesh Social Networking

Mobile Mesh Social Network (MMSN) represents an environment where the mobile device users are capable of performing various virtual social network activities such as sharing information, forming social groups, text messaging when they encounter each other in the physical vicinity within the wireless network range. Moreover, the characteristics of MMSN such as the Internetless activities and Wireless Mesh Network (WMN)-based connectivity provides various potentials including but not limited to business opportunities, scalable crowdsourcing or crowdsensing deployment, edge computing and so on. Although there exist a fair number of software platforms that help developers to implement MMSN, they still cannot fully overcome the limitation derived from the hardware resource constraint nature of the participative mobile devices. In order to enhance the MMSN in terms of cost efficiency, we introduce Fog Social Network (FSN) model, which utilises the computing and networking resources in users' close vicinity to improve the overall efficiency of MMSN. Further, the proposed FSN framework consists of an adaptive resource-aware cost-performance index (CPI) scheme, which performs dynamic approach selection autonomously at runtime to choose the most efficient route for the delivery of the messages for MMSN activities. With this intention, we have implemented and validated a proof-of-concept prototype.
Regulation of Self‐Renewal and Pluripotency by Sox2 in Human Embryonic Stem Cells

Human embryonic stem (hES) cells, derived from blastocysts, are capable of unlimited self‐renewal and differentiation into all cell lineages of the body. Because of their pluripotent nature, hES cells are valuable tools for understanding human development and advancing the field of regenerative medicine. However, one key to harnessing the therapeutic power of hES cells for biomedical applications begins with determining how these cells maintain their pluripotent and undifferentiated state. Studies in mice have implicated three factors in regulating pluripotency in embryonic stem cells, Oct4, Nanog, and Sox2. However, significant differences in growth regulation between mouse embryonic stem and hES cells have been identified, suggesting a need to determine when and how factors work in hES cells. To date, the transcription factors Oct4 and Nanog have been identified as critical regulators of stem cell fate by functional studies in hES cells. To determine the role of Sox2 in maintaining hES cell pluripotency and self‐renewal, we used RNA interference to specifically knock down Sox2 gene expression. Reduction of Sox2 expression in hES cells results in loss of the undifferentiated stem cell state, as indicated by a change in cell morphology, altered stem cell marker expression, and increased expression of trophectoderm markers. In addition, knockdown of Sox2 results in reduced expression of several key stem cell factors, including Oct4 and Nanog, linking these three factors together in a pluripotent regulatory network.
Sequence variability of bovine leukemia virus env gene and its relevance to the structure and antigenicity of the glycoproteins

The nucleotide sequences of the env genes of seven bovine leukemia viruses and the encoded peptide sequence were compared, with the objective of (i) determining the genetic distance separating bovine leukemia virus isolates from different geographical regions, (ii) identifying particular amino acids that contribute to the sequential and conformational epitopes, and (iii) relating such epitopes to their projected position in a three-dimensional model of the structure of the gp51 surface glycoprotein. Two bovine leukemia virus subgroups were clearly identified, a Japanese-American subgroup represented by strains lambda BLV-1, VdM, and FLK-BLV and a European subgroup by strains T15-2, LB285, and LB59. It was possible to identify amino acids that were important in determining three of the epitopes (F, G, and H) recognized by neutralizing monoclonal and polyclonal antibodies. On the model, these epitopes were adjacent and located on the exposed region of the molecule. Amino acid sequences contributing to a fourth cryptic epitope were identified; as predicted by the model, they lay on the opposite side to the neutralizable epitopes in a region involved in glycoprotein subunit association. The fact that this region is not normally exposed on the virion surface provides further evidence for the validity of the model.
Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial‐genetic patterns of connectivity

Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within‐species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population‐level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G”ST) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G”ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species.
Factors Associated with the Uptake of Sodium Dichloroisocyanurate (NADCC) Tablets as Household Water-Treatment Product among Caregivers of Children under Five in Benin, West Africa

Improving access to safe drinking water is a critical step in mitigating diarrheal diseases that affect millions of children under 5 years throughout the developing world each year. While the delivery of safe water is out of the reach of many countries, the utilization of Sodium dichloroisocyanurate (NaDCC) is a proven cost-effective alternative to prevent diarrhea caused by waterborne pathogens. However, its uptake remains low in many developing countries, such as the Republic of Benin. This study examines the trends and the determinants of NaDCC uptake in Benin. Population Services International and its affiliate conducted two multistage household surveys among caregivers of children under five in Benin to examine the practices towards diarrheal disease in children under five and identify the factors associated with the use of NaDCC in this population. 2912 respondents/caregivers of children under five were interviewed in 2009 versus 3196 in 2011. The proportion of caregivers who reported ever treating water with NaDCC increased from 5.8% in 2009 to 11.5% in 2011, p<0.001. The logistic regression model showed that caregivers who knew places that sell NaDCC in the community; those who felt capable of utilizing NADCC correctly to treat drinking water as well as caregivers who reported to be Muslim were more likely than their counterparts to use NaDCC as water treatment product. In order to increase the use of NADCC among caregivers, the Government of Benin and its development partners should focus not only on making NADCC available in the community and informing the community members about the different points of sale, but also in building up the capacity and confidence of caregivers in utilizing it.