Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow Cytometry Sorting to Separate Viable Giant Viruses from Amoeba Co-culture Supernatants

Flow cytometry has contributed to virology but has faced many drawbacks concerning detection limits, due to the small size of viral particles. Nonetheless, giant viruses changed many concepts in the world of viruses, as a result of their size and hence opened up the possibility of using flow cytometry to study them. Recently, we developed a high throughput isolation of viruses using flow cytometry and protozoa co-culture. Consequently, isolating a viral mixture in the same sample became more common. Nevertheless, when one virus multiplies faster than others in the mixture, it is impossible to obtain a pure culture of the minority population. Here, we describe a robust sorting system, which can separate viable giant virus mixtures from supernatants. We tested three flow cytometry sorters by sorting artificial mixtures. Purity control was assessed by electron microscopy and molecular biology. As proof of concept, we applied the sorting system to a co-culture supernatant taken from a sample containing a viral mixture that we couldn't separate using end point dilution. In addition to isolating the quick-growing Mimivirus, we sorted and re-cultured a new, slow-growing virus, which we named “Cedratvirus. ” The sorting assay presented in this paper is a powerful and versatile tool for separating viral populations from amoeba co-cultures and adding value to the new field of flow virometry.
Hybrid language models for out of vocabulary word detection in large vocabulary conversational speech recognition

In this paper, we propose a method for out-of-vocabulary (OOV) word detection and take a step toward open vocabulary automatic speech recognition. The proposed method uses a hybrid language model combining words and subword units such as phones or syllables. We describe a detection algorithm based on the posterior count of the OOV words given the hybrid model, and compare it to using the posterior probability of the best word string given a conventional word only model. Experimental results on the Switchboard corpus are presented for different vocabulary sizes. The new method yields a gain of over 10% in OOV word detection. In addition, a modest number of the OOV word pronunciations are found correctly.
Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This modular structure is likely to play a key role in the response of grassland ecosystems to future changes by limiting the impact of changes in agricultural practices such as intensification to some modules leaving species from other modules poorly impacted. The next step is to understand the importance of this modular structure for the long-term maintenance of grassland ecosystem structure and functions as well as to develop tools to integrate network structure into models to improve their capacity to predict future changes.
Prediction of performace parameters using artificial neural network for 4-stroke C I engine fueled with esterified neem oil and biogas

Experiments on the technical feasibility of the use of esterified neem oil and biogas under dual fuel mode has been carried out in a 3.7 kW diesel engine. Esterified neem oil (ENO) blends and bottled biogas was used for the experimentation. Biogas is directly mixed with the inlet air in the induction manifold and tests were carried out for varying loads and pressures. The performance parameters obtained from test were within the acceptable range for ENO and biogas combination. Mechanical efficiency was improved and ENO consumption was reduced due to higher biogas introduction; however, a distinguishable noise was noticed when further increase in supply of biogas. Artificial neural network (ANN) technique was also applied for prediction of thermal efficiency and BSFC of the engine. The input parameters for ANN method were speed, gas flow rate, temperature, total fuel consumption, and load. It was seen that ANN predicted performance values were close to experimentally obtained data when 90% of data were in training set.
River basin modelling for Shipra River using MIKE BASIN

ABSTRACT In present study, MIKE 11NAM rainfall runoff(R-R) and MIKE BASIN models were used to develop R–R relationship and to analyze the water availability status of the Shipra river basin under changing hydrological conditions. The model was developed using discharge data observed for 9 years at the Ujjain G/d site. The coefficient of determination(R 2) values for NAM R-R model calibration and validation were 0.685 and 0.642, respectively, indicating good agreement between the simulated and observed runoff. As the Shipra River is subjected to a number of hydrological interventions, the MIKE BASIN model was used to develop various scenarios to study the influence of river diversion, on-stream dam, river interlinking on water availability in different time-scale at desired locations. Scenario analysis of MIKEBASIN results indicated that the Khan diversion, which was executed to avoid entry of contaminated Khan river water into Shipra has reduced the water availability in the Shipra river. However, the simulation results indicated that the water availability in Shipra has been improved due to Narmada-Shipra link, a minimum of 1.7 m3/s flow is available at Ujjain even during the low-flow period. Gambhir reservoir was developed to evaluate how demand deficit can be fulfilled through proper reservoir operation during a drought period.
Effects of Intrathecal Fentanyl and Lidocaine on Somatosensory‐Evoked Potentials, the H‐Reflex, and Clinical Responses

Intravenous narcotics increase the latency of somatosensory-evoked potentials (SSEPS), whichare decreased but not abolished by epidural local anesthetics. In addition, intrathecal narcotics decrease spasticity in patients with central nervous system disease. This study of the effectsof intrathecal fentanyl on posterior tibial SSEPS and the monosynaptic H-reflex arc found that intrathecal fentanyl had no effect on the latency of SSEPS, indicating the effects of narcotics on SSEPS are likely to exist at a supraspinal level. H-reflexes were not affected, confirming thelack of effect on this spinal motor reflex. In the same group of patients, intrathecal lidocaineadministered 1 week later completely abolished SSEPS and H-reflexes. Complete suppression of SSEPS corresponded to full motor blockade, but sensation to pain and temperature was already many dermatomes higher than the S1 level. Return of SSEPS occurred with return of motor but not sensory function, indicating the likelihood that SSEPS are carried at least in part by large A-fibers. The study shows that spinal narcotics neither affect the transmission of SSEPS nor decrease the H-reflex, a spinal motor reflex. In addition, changes in SSEPS after intrathecal lidocaine do not correlate with the level of surgical anesthesia.
Large-Scale Analysis of KIT Aberrations in Chinese Patients with Melanoma

Purpose:KIT aberrations were described in acral and mucosal melanomas in largely Caucasian populations. Asian populations are more prone to develop acral and mucosal than cutaneous melanomas, and may harbor a high frequency of KIT aberrations. Experimental Design: Melanoma subtypes (n = 502) were analyzed histologically to determine melanoma subtype. Tissue samples were analyzed for mutations in exons 9, 11, 13, 17, and 18 of KIT gene in genomic DNA by PCR amplification and Sanger sequencing. The copy numbers of the KIT gene were analyzed by quantitative PCR, and protein expression levels of KIT (CD117) were determined by immunohistochemistry. Results: The most common melanoma subtypes were acral (38.4%) and mucosal (33.3%) melanomas in this population. The overall incidence of somatic mutations within the KIT gene was 10.8% (54/502), and all subtypes of melanoma contained KIT mutations. Increases in KIT gene copy numbers were correlated to CD117 overexpression. The genetic mutations of KIT were unrelated to the age, gender, stage, thickness, and ulceration of primary melanomas. Importantly, the overall survival of melanoma patients with KIT mutations (P = 0.001) or with KIT aberrations (mutation plus amplification, P = 0.0002) was significantly shorter than that of patients without such alterations. Conclusion: In China, the prevalent melanomas are acral and mucosal melanomas. KIT mutations are detected in all melanoma subtypes. Our study suggests that increases in KIT gene copy numbers, but not KIT mutations, may be correlated to CD117 overexpression. For the first time, our study suggests that genetic KIT aberration is an adverse prognostic factor for melanoma. Clin Cancer Res; 17(7); 1684–91. ©2011 AACR.
AB124. Co-expression of RAGE and HMGB1 is associated with cancer progression and poor patient outcome of prostate cancer

Objective Receptor for advanced glycation end products (RAGE), along with its ligand high mobility group box 1 (HMGB1), is believed to play an important role in prostate cancer. The aim of this retrospective study was to investigate the expression of RAGE and HMGB1 and their clinical impact on prostate cancer progression and prognosis. Methods The expression of RAGE and HMGB1 were assessed by immunohistochemistry in cancer lesions from 85 confirmed prostate cancer cases. We determined the potential association between the expression level of these two proteins and the clinicopathological features and overall patient survival. Results The RAGE and HMGB1 were expressed in 78.8% (67/85) and 68.2% (58/85) cases of prostate cancers, respectively, and in the majority (54/85) of cases, these two proteins were co-expressed. There was a strong correlation between RAGE and HMGB1 expressions (P<0.001). The expression of RAGE, HMGB1 and their co-expression were all associated with advanced tumor clinical stage (P<0.05 for all). RAGE expression was also associated with the prostate specific antigen (PSA) level (P=0.014). However, neither the individual expression of those genes nor their co-expression was significantly related with age and Gleason score. The co-expression of RAGE and HMGB1 was associated with poor overall survival in patients with stage III and IV prostate cancer (P=0.047). Conclusions These results suggest that the expression of RAGE and HMGB1 is associated with the progression and poor prognosis of prostate cancer. RAGE and HMGB1 could be new prognostic biomarkers for prostate cancer as well as molecular target for novel forms of therapies.
Effects of bovine somatotropin (rbSt) concentration at different moisture levels on the physical stability of sucrose in freeze-dried rbSt/sucrose mixtures.

The inherent instability of many proteins during freeze-drying and storage necessitates the addition of excipients to protect the proteins. It is emphasized in the literature that lyophilized sugar/protein composites should be stored at temperatures below their glass transition temperature (T(g)) to prevent crystallization of excipients. The influence of bovine somatotropin (rbSt) concentration on inhibition of sucrose crystallization at different relative humidities (RH) was of interest. Thermally modulated differential scanning calorimetry (MDSC) was used to measure T(g) and sucrose crystallization temperatures (T(c)) of the composites. Sorption isotherms of the various sucrose/rbSt mixtures were determined gravimetrically with a controlled atmosphere microbalance (CAM) and verified by Karl Fischer analysis of selected samples. The CAM was also used to determine lag times and sucrose crystal growth rates by monitoring weight losses resulting from water liberation upon crystallization of sucrose at 23 degrees C. Results obtained by MDSC indicate that the T(c) increased linearly from approximately 110 degrees C for pure sucrose to approximately 140 degrees C with 20% rbSt at very low water content (<0.1%). Similarly, at 22% RH (4.4% H2O), T(c) increased from approximately 70 degrees C to 120 degrees C. In neither case was T(g) impacted significantly by increasing protein from 0 to 20%. No T(c) could be noted for samples with > or = 30% rbSt in nonisothermal conditions. Plasticization by water decreased both T(g) and T(c) quite similarly but didn't impact the noted effect of protein on T(c). Induction time for sucrose crystallization (i.e. nucleation) at approximately 45% RH (23 degrees C) increased almost 10-fold by addition of 10% rbSt, whereas rates of water loss due to crystallization decreased by no more than 2-3-fold. The overall results strongly indicate that formulations of higher protein concentration will be more resistant to sucrose crystallization and thus more robust when transiently exposed to storage temperatures above their T(g).
Stereotype formation and endorsement: The role of implicit theories.

Five experiments supported the hypothesis that peoples' implicit theories about the fixedness versus malleability of human attributes (entity versus incremental theories) predict differences in degree of social stereotyping. Relative to those holding an incremental theory, people holding an entity theory made more stereotypical trait judgments of ethnic and occupational groups (Experiments 1, 2, and 5 ) and formed more extreme trait judgments of novel groups (Experiment 3 ). Implicit theories also predicted the degree to which people attributed stereotyped traits to inborn group qualities versus environmental forces (Experiment 2). Manipulating implicit theories affected level of stereotyping (Experiment 4), suggesting that implicit theories can play a causal role. Finally, implicit theories predicted unique and substantial variance in stereotype endorsement after controlling for the contributions of other stereotype-relevant individual difference variables (Experiment 5). These results highlight the importance of people's basic assumptions about personality in stereotyping.
WSPred: A Time-Aware Personalized QoS Prediction Framework for Web Services

The exponential growth of Web service makes building high-quality service-oriented applications an urgent and crucial research problem. User-side QoS evaluations of Web services are critical for selecting the optimal Web service from a set of functionally equivalent service candidates. Since QoS performance of Web services is highly related to the service status and network environments which are variable against time, service invocations are required at different instances during a long time interval for making accurate Web service QoS evaluation. However, invoking a huge number of Web services from user-side for quality evaluation purpose is time-consuming, resource-consuming, and sometimes even impractical (e.g., service invocations are charged by service providers). To address this critical challenge, this paper proposes a Web service QoS prediction framework, called WSPred, to provide time-aware personalized QoS value prediction service for different service users. WSPred requires no additional invocation of Web services. Based on the past Web service usage experience from different service users, WSPred builds feature models and employs these models to make personalized QoS prediction for different users. The extensive experimental results show the effectiveness and efficiency of WSPred. Moreover, we publicly release our real-world time-aware Web service QoS dataset for future research, which makes our experiments verifiable and reproducible.
Immune Response to Bifidobacterium bifidum Strains Support Treg/Th17 Plasticity

In this work we analyzed the immune activation properties of different Bifidobacterium strains in order to establish their ability as inductors of specific effector (Th) or regulatory (Treg) responses. First, we determined the cytokine pattern induced by 21 Bifidobacterium strains in peripheral blood mononuclear cells (PBMCs). Results showed that four Bifidobacterium bifidum strains showed the highest production of IL-17 as well as a poor secretion of IFNγ and TNFα, suggesting a Th17 profile whereas other Bifidobacterium strains exhibited a Th1-suggestive profile. Given the key role of Th17 subsets in mucosal defence, strains suggestive of Th17 responses and the putative Th1 Bifidobacterium breve BM12/11 were selected to stimulate dendritic cells (DC) to further determine their capability to induce the differentiation of naïve CD4+ lymphocytes toward different Th or Treg cells. All selected strains were able to induce phenotypic DC maturation, but showed differences in cytokine stimulation, DC treated with the putative Th17 strains displaying high IL-1β/IL-12 and low IL-12/IL-10 index, whereas BM12/11-DC exhibited the highest IL-12/IL-10 ratio. Differentiation of naïve lymphocytes confirmed Th1 polarization by BM12/11. Unexpectedly, any B. bifidum strain showed significant capability for Th17 generation, and they were able to generate functional Treg, thus suggesting differences between in vivo and vitro responses. In fact, activation of memory lymphocytes present in PBMCS with these bacteria, point out the presence in vivo of specific Th17 cells, supporting the plasticity of Treg/Th17 populations and the key role of commensal bacteria in mucosal tolerance and T cell reprogramming when needed.
Polynomial Mixing of the Edge-Flip Markov Chain for Unbiased Dyadic Tilings

We give the first polynomial upper bound on the mixing time of the edge-flip Markov chain for unbiased dyadic tilings, resolving an open problem originally posed by Janson, Randall and Spencer in 2002 [14]. A dyadic tiling of size n is a tiling of the unit square by n non-overlapping dyadic rectangles, each of area 1/n, where a dyadic rectangle is any rectangle that can be written in the form [a2−s, (a + 1)2−s] × [b2−t, (b + 1)2−t] for a, b, s, t ∈ ℤ⩾ 0. The edge-flip Markov chain selects a random edge of the tiling and replaces it with its perpendicular bisector if doing so yields a valid dyadic tiling. Specifically, we show that the relaxation time of the edge-flip Markov chain for dyadic tilings is at most O(n4.09), which implies that the mixing time is at most O(n5.09). We complement this by showing that the relaxation time is at least Ω(n1.38), improving upon the previously best lower bound of Ω(n log n) coming from the diameter of the chain.
Anti‐endomysium and anti‐gliadin antibodies as serological markers for coeliac disease in childhood: a clinical study to develop a practical routine

Anti‐gliadin and anti‐endomysium antibodies were analysed in 174 children with suspected or verified coeliac disease with the aim of developing a practical routine. The biopsy was performed without knowledge of the antibody levels. To screen for coeliac disease is children younger than 2 years, we suggest the use of IgA anti‐gliadin antibodies, giving a sensitivity of 100% and a specificity of 86%. In older children both tests should be used in parallel, i.e. a biopsy should be performed if at least one of the tests is positive, giving a sensitivity of 98% and a specificity of 81%. To avoid unnecessary biopsy before mucosal relapse can be demonstrated during gluten challenge in a child without clinical symptoms, we suggest that the tests are used as serial testing, i.e. a biopsy should be performed if both tests are positive.
Intracorneal inlay complicated by intrastromal epithelial opacification.

OBJECTIVE To report epithelial perilenticular opacity as a new complication of intracorneal inlay implantation for the correction of hyperopia. DESIGN Prospective observational case series. PARTICIPANTS Eleven eyes of 7 patients underwent intracorneal inlay implantation for the correction of hyperopia. METHODS Intracorneal inlays were implanted onto the stromal bed by using a microkeratome cut to create an inferior hinged corneal flap. MAIN OUTCOME MEASURES Postoperative complication occurrence of intracorneal perilenticular opacity, microbiological laboratory analysis, histopathological analysis, and confocal microscopy study. RESULTS Of 11 implanted eyes, 5 showed diffuse perilenticular opacity of varying intensity that was unresponsive to steroid use following intracorneal inlay implantation. All patients had moderate to severe loss of best-corrected visual acuity. The inlays showed deposits at the edge and on the surface. Confocal microscopy in all eyes produced images compatible with the confocal morphologic features of epithelial cells. Explantation of inlays was performed in 5 eyes. The histopathologic study showed the presence of epithelial cells, and microbiological analysis and cultures were negative for bacteria, fungi, and mycobacteria. CONCLUSION Epithelial perilenticular opacity is a new and serious complication in patients with intracorneal inlay implantation for the correction of hyperopia.