Miracle-dz/UniFAR-FTUs huggingface dataset:
LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins

The adaptive immune system includes populations of B and T cells capable of binding foreign epitopes via antigen specific receptors, called immunoglobulin (IG) for B cells and the T cell receptor (TCR) for T cells. In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we present LymAnalzyer, a software package that significantly improves the completeness and accuracy of TCR/IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available. Implemented in Java, it includes both a command line version and a graphical user interface and is freely available at https://sourceforge.net/projects/lymanalyzer/.
EspJ effector in enterohemorrhagic E. coli translocates into host mitochondria via an atypical mitochondrial targeting signal

EHEC is a bacterial pathogen causing diarrhea and hemorrhagic colitis in humans. To exert virulence, EHEC exploits a subset of effectors that are translocated into host cells via the type III secretion system. EspJ, which was recently identified as a type III secreted effector, is conserved in related pathogens such as EPEC and Citrobacter rodentium. However, the exact function of EspJ remains unclear. In the present study, we found that EspJ was unstable in host cells, which might be attributable to the N‐terminal part beginning from amino acid number 59. Using stable forms of EspJ derivatives, we demonstrated for the first time that EspJ has the ability to translocate into mitochondria via an atypical mitochondrial targeting signal at the N terminus (1–36 a.a.) of EspJ. It has been reported that a mitochondrial targeting effector, EspF, disrupts the mitochondrial membrane potential, resulting in an induction of host cell death. To further investigate EspJ function in mitochondria, HeLa cells were infected with wild‐type EPEC, an isogenic EspJ‐mutant or an EspJ‐overexpressing strain. The result of LDH release assay using an EspJ‐mutant showed that the EspJ effector appears not to be involved in cytotoxicity.
Streptococcus suis outbreak investigation using multiple‐locus variable tandem repeat number analysis

Two outbreaks of Streptococcus suis ST7 occurred in humans in 1998 and 2005 in China. PFGE of chromosome restriction fragments found all ST7 isolates to be indistinguishable. Due to the genetic homogeneity of ST7 isolates, development of a rapid sub‐typing method with high discriminatory power for ST7 isolates is required. In this study, a novel method, MLVA, was developed to type S. suis serotype 2 strains. Further, this method was used to analyze outbreak‐associated ST7 strains in China. A total of 144 ST7 S. suis isolates were sub‐typed into 34 MLVA types. Among these, eight isolates from the 1998 outbreak were sub‐typed into five MLVA types, of which four MLVA types were also detected in Sichuan in 2005. These data indicate that the pathogens responsible for the two outbreaks had the same origin. In addition, some observations also provided molecular evidence for the transmission route, possibly indicating that the MLVA method has usefulness in epidemiology. The developed MLVA scheme for S. suis has greater discriminative power than PFGE. The method described here may be useful for identifying the source of S. suis infection and monitoring its spread.
Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms

DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collectively termed microhomology-mediated end-joining (MMEJ), relies on short homologies for the end-joining process. Here, we constructed GFP reporter assays to characterize and distinguish MMEJ variant pathways, namely the simple MMEJ and the DNA synthesis-dependent (SD)-MMEJ mechanisms. Transfection of these assay vectors in Chinese hamster ovary (CHO) cells and characterization of the repaired DNA sequences indicated that while simple MMEJ is able to mediate relatively efficient DSB repair if longer microhomologies are present, the majority of DSBs were repaired using the highly error-prone SD-MMEJ pathway. To validate the involvement of DNA synthesis in the repair process, siRNA knock-down of different genes proposed to play a role in MMEJ were performed, revealing that the knock-down of DNA polymerase θ inhibited DNA end resection and repair through simple MMEJ, thus favoring the other repair pathway. Overall, we conclude that this approach provides a convenient assay to study MMEJ-related DNA repair pathways.
Three‐Dimensional Microfluidic Tissue‐Engineering Scaffolds Using a Flexible Biodegradable Polymer

Organ loss and failure is one of the most critical issues facing the healthcare industry in developed nations. The shortage of available organ donors has driven the growth and expansion of the field of tissue engineering as a means of developing replacement tissues and organs[1,2] including the liver. [3] Microfabrication and bio-microelectromechanical system (bio-MEMS) technology is an attractive tool for developing tissue-engineering systems because of the improved spatial resolutions over traditional scaffold fabrication techniques such as casting and porogen leaching,[4] gas foaming,[5] and three-dimensional printing. [6] Polymer scaffolds replica-molded on micromachined silicon substrates can achieve feature resolutions of less than 10 µm,[7] the same lengthscale of mammalian cells. Microfluidic bioreactors have been both fabricated and seeded with a variety of cell types, including endothelial cells[7–10] and hepatocytes. [10–12] However, one limiting factor in previous studies of microfluidic scaffolds has been the choice of material. Microfabricated silicon and replica-molded poly(dimethylsiloxane) (PDMS), although ubiquitous and inexpensive, are not biodegradable and have limited biocompatibility, and therefore are not suitable biomaterials for a tissue-engineering scaffold. Microfluidic scaffolds fabricated from poly(L-lactic-co-glycolic acid) (PLGA),[13] while biodegradable, exhibit suboptimal properties for an implant material, such as rigid mechanical properties,[14] undesirable bulk degradation kinetics,[15] and limited biocompatibility in some cases. [16] High concentrations of PLGA byproducts has also been shown to be cytotoxic,[17] which is a major limitation in the prospect of fabricating large, organ-size scaffolds.
Remarkable similarity in genome nucleotide sequences between the Schwarz FF‐8 and AIK‐C measles virus vaccine strains and apparent nucleotide differences in the phosphoprotein gene

The Schwarz FF‐8 (FF‐8) and AIK‐C measles virus vaccine strains are currently used for vaccination in Japan. Here, the complete genome nucleotide sequence of the FF‐8 strain has been determined and its genome sequence found to be remarkably similar to that of the AIK‐C strain. These two strains are differentiated only by two nucleotide differences in the phosphoprotein gene. Since the FF‐8 strain does not possess the amino acid substitutions in the phospho‐ and fusion proteins which are responsible for the temperature‐sensitivity and small syncytium formation phenotypes of the AIK‐C strain, respectively, other unidentified common mechanisms likely attenuate both the FF‐8 and AIK‐C strains.
Enhancement of In Vitro Capillary Tube Formation by Substrate Nanotopography

Vascular engineering remains a key thrust in advancing the field of tissue engineering of highly vascularized, complex, metabolic organs. A wide variety of strategies have been employed to control the formation of organized vascular structures in vitro and in vivo. Some of these methods include, but are not limited to, controlled growth factor delivery,[1] filamentous scaffold geometry,[2] protein micropatterning,[3] and enhanced scaffold biomaterials. [4] Many of these approaches are motivated by biomimicry of the in vivo microenvironment. Extracellular matrix (ECM) proteins, both in vitro and in vivo, provide mammalian cells with biophysical cues including specific surface chemistry and rich three-dimensional surface topography[5] with features on the nanometer length scale. [6] ECM substrates provide chemical and physical external cues that dictate a variety of cell responses. Therefore, it is not only the milieu of soluble, diffusible factors, but also the adhesive, mechanical interactions with scaffolding materials, both natural and synthetic, that control select cell functions including cell attachment, migration, proliferation, differentiation, and regulation of genes. [7–9] We hypothesized that physical features on nanofabricated substrates could promote the organization of endothelial cell lineages into well-defined vascular structures in vitro by inducing the contact guidance phenomenon, which is known to affect the morphology of endothelial cells. [10–12]We found that endothelial progenitor cells (EPCs) responded to ridge-groove grating of 1200 nm in period and 600 nm in depth through alignment, elongation, reduced proliferation, and enhanced migration. Although endothelial- specific markers were not significantly altered, EPCs cultured on substrate nanotopography formed supercellular band structures after 6 d. Furthermore, an in vitro Matrigel assay led to enhanced capillary tube formation and organization.
Working Paper 29. Extra Classes and Learning Outcomes of Eight-year-old Children in Vietnam.

Although primary school enrolment in Vietnam is high (91 per cent), most primary school students receive little more than half the annual teaching time defined by international norms. The Vietnamese school year is very short by international standards, covering only 33 weeks. In addition, only around 20 per cent of children in Vietnam receive a full-day of schooling, 5 or 6 hours according to international standards. Extra classes, outside of the normal school system, have proliferated in all regions of Vietnam. These classes fall into two categories. Legal classes, organised by schools themselves, include those provided for low-score performers or for outstandingly talented children. Illegal classes are taught by teachers who deliberately reduce the duration and content of their school-based classes to encourage students to take private tuition. The Vietnamese government is committed to providing full shifts of primary education by 2015 and has banned extra classes provided outside the normal school system. Nonetheless, the availability of and enrolment in illegal extra classes continue to increase. Young Lives research examined the extent and effects of extra classes for eight-year-old children in Vietnam. It tested for association between extra classes and numeracy, reading and writing skills. The paper presents statistical data on the amount of time and money spent on extra classes. The authors argue that such classes should be restricted because of the financial pressure that they place on poor households –without improving the attainment of children who take them.
Precision Polymers: Monodisperse, Monomer‐Sequence‐Defined Segments to Target Future Demands of Polymers in Medicine

The established technology platforms of solid‐phase‐supported oligopeptide and oligonucleotide synthesis can be expanded to access fully synthetic macromolecules, preserving both the monodisperse character and the defined monomer sequence. Precision polymers are sequentially assembled from a library of functional building blocks, enabling one to program interaction capabilities or generate functions by sequence‐specific positioning of functionalities. Examples are provided, showing that these monodisperse macromolecules can be conjugated to oligonucleotides, oligopeptides, or poly(ethylene glycol)s. The resulting model systems can contribute to the understanding of complex biomedical‐related processes. Due to the absence of chemical and molecular‐weight distributions in these multifunctional segments, exact correlation of the monomer sequence and (bio)properties is attainable. This is demonstrated by the design of carrier systems that exhibit fine‐tuned interactions with plasmid DNA, actively controlling important steps in DNA delivery and transfection, such as polyplex formation, DNA compression, and release of the cargo.
Rad61/Wpl1 (Wapl), a cohesin regulator, controls chromosome compaction during meiosis

Meiosis-specific cohesin, required for the linking of the sister chromatids, plays a critical role in various chromosomal events during meiotic prophase I, such as chromosome morphogenesis and dynamics, as well as recombination. Rad61/Wpl1 (Wapl in other organisms) negatively regulates cohesin functions. In this study, we show that meiotic chromosome axes are shortened in the budding yeast rad61/wpl1 mutant, suggesting that Rad61/Wpl1 negatively regulates chromosome axis compaction. Rad61/Wpl1 is required for efficient resolution of telomere clustering during meiosis I, indicating a positive effect of Rad61/Wpl1 on the cohesin function required for telomere dynamics. Additionally, we demonstrate distinct activities of Rad61/Wpl1 during the meiotic recombination, including its effects on the efficient processing of intermediates. Thus, Rad61/Wpl1 both positively and negatively regulates various cohesin-mediated chromosomal processes during meiosis.
RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery

DNA-based antisense oligonucleotides (ASOs) elicit cleavage of the targeted RNA by the endoribonuclease RNase H1, whereas siRNAs mediate cleavage through the RNAi pathway. To determine the fates of the cleaved RNA in cells, we lowered the levels of the factors involved in RNA surveillance prior to treating cells with ASOs or siRNA and analyzed cleavage products by RACE. The cytoplasmic 5′ to 3′ exoribonuclease XRN1 was responsible for the degradation of the downstream cleavage products generated by ASOs or siRNA targeting mRNAs. In contrast, downstream cleavage products generated by ASOs targeting nuclear long non-coding RNA Malat 1 and pre-mRNA were degraded by nuclear XRN2. The downstream cleavage products did not appear to be degraded in the 3′ to 5′ direction as the majority of these products contained intact poly(A) tails and were bound by the poly(A) binding protein. The upstream cleavage products of Malat1 were degraded in the 3′ to 5′ direction by the exosome complex containing the nuclear exoribonuclease Dis3. The exosome complex containing Dis3 or cytoplasmic Dis3L1 degraded mRNA upstream cleavage products, which were not bound by the 5′-cap binding complex and, consequently, were susceptible to degradation in the 5′ to 3′ direction by the XRN exoribonucleases.
Aberrant splicing and protease involvement in mesothelin release from epithelioid mesothelioma cells

Elevated amounts of soluble mesothelin‐related proteins (SMRP) have already been reported in sera and pleural effusions from mesothelioma patients, providing a useful diagnostic marker for malignant pleural mesothelioma (MPM). However, the origin of SMRP is not yet understood. Production of SMRP could be related to abnormal splicing events leading to synthesis of a secreted protein (release) or to an enzymatic cleavage from membrane‐bound mesothelin (ectodomain shedding). To test these hypotheses, we used a panel of mesothelioma cells established in culture from pleural effusions of MPM patients. Our in vitro results confirmed specific mesothelin expression and SMRP production in supernatants from epithelioid MPM cell lines, thus providing a relevant cellular model to study soluble mesothelin production mechanisms. The expression of mesothelin‐encoding RNA variants was screened by reverse transcription–polymerase chain reaction experiments. Protease involvement in mesothelin cleavage from the cellular surface was investigated by treatment of MPM cells with GM6001, a broad‐spectrum MMP‐ and ADAM‐family inhibitor. GM6001 treatment significantly impaired SMRP production by MPM cell lines, in favor of an enzymatic‐mediated shedding process. In addition, a splice variant transcript of mesothelin (variant 3) was detected in these MPM cell lines, in accordance with the release of a secreted part of the protein. Our results indicate that both mechanisms could be implicated in soluble mesothelin production by epithelioid mesothelioma cells. (Cancer Sci 2008; 99: 590–594)
iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications

Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.
The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection

Mutations acquired during development and aging lead to inter- and intra-tissue genetic variations. Evidence linking such mutations to complex traits and diseases is rising. We detected somatic mutations in protein-coding regions in 140 benign tissue samples representing nine tissue-types (bladder, breast, liver, lung, prostate, stomach, thyroid, head and neck) and paired blood from 70 donors. A total of 80% of the samples had 2–39 mutations detectable at tissue-level resolution. Factors such as age and smoking were associated with increased burden of detectable mutations, and tissues carried signatures of distinct mutagenic processes such as oxidative DNA damage and transcription-coupled repair. Using mutational signatures, we predicted that majority of the mutations in blood originated in hematopoietic stem and early progenitor cells. Missense to silent mutations ratio and the persistence of potentially damaging mutations in expressed genes carried signatures of relaxed purifying selection. Our findings have relevance for etiology, diagnosis and treatment of diseases including cancer.
The Role of Matra Basti with Bala taila in Sandhigata Vata w.s.r to ability to Climbing stairs in patients of osteoarthritis - Knee Joint

Aims and Objectives: Aim to investigate whether the procedure of Matra Basti with Bala Taila has any effect on the symptom of difficulty in climbing up-stairs and down-stairs in the patients of Osteoarthritis of Knee Joints. Materials and Methods: A total of 20 patients having Osteoarthritis of knee joints were included in the present study. Patients were administered with “Matra Basti using Bala Taila” after giving snehan and svedana to them. The time of administration of Basti, time of expulsion and samyaka anuvasita lakshanas were noted on each day. The readings for climbing up-stairs and climbing down-stairs were noted before treatment and after treatment of 7 days. Observation: Twenty patients of osteoarthritis of knee joint of age group 40 to 70 years irrespective of sex, religion and socioeconomic status were included for the study. Patients having systemic disorders, which might interfere with the treatment and those having traumatic conditions were not part of study. Results: The study showed significant improvement in Ability to climbing up-stairs and down-stairs scores after administration of Matra Basti with Bala Taila. Conclusion: The administration Matra Basti of Bala Taila has significant results in the management of the symptom of difficulty in climbing up-stairs and down-stairs in the patients of Osteoarthritis of Knee Joints
The SWISS-MODEL Repository—new features and functionality

SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline. It currently holds >400 000 high quality models covering almost 20% of Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update of features and functionalities which have been implemented recently. We address improvements in target coverage, model quality estimates, functional annotations and improved in-page visualization. We also introduce a new update concept which includes regular updates of an expanded set of core organism models and UniProtKB-based targets, complemented by user-driven on-demand update of individual models. With the new release of the modeling pipeline, SMR has implemented a REST-API and adopted an open licencing model for accessing model coordinates, thus enabling bulk download for groups of targets fostering re-use of models in other contexts. SMR can be accessed at https://swissmodel.expasy. org/repository.
siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2

Efﬁcient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5 (cid:2) - phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5 (cid:2) - phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5 (cid:2) -(E)-vinylphosphonate (5 (cid:2) -E-VP) guide RNA at 2.5- ˚A resolution. The structure demonstrates how the 5 (cid:2) binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5 (cid:2) -nucleotide binding pocket to compensate for the change introduced by the modiﬁed nucleotide. This observation also explains improved binding afﬁnity of the 5 (cid:2) -E-VP -modiﬁed siRNA to human Argonaute-2
Patterning and Templating for Nanoelectronics

The semiconductor industry will soon be launching 32 nm complementary metal oxide semiconductor (CMOS) technology node using 193 nm lithography patterning technology to fabricate microprocessors with more than 2 billion transistors. To ensure the survival of Moore's law, alternative patterning techniques that offer advantages beyond conventional top‐down patterning are aggressively being explored. It is evident that most alternative patterning techniques may not offer compelling advantages to succeed conventional top‐down lithography for silicon integrated circuits, but alternative approaches may well indeed offer functional advantages in realising next‐generation information processing nanoarchitectures such as those based on cellular, bioinsipired, magnetic dot logic, and crossbar schemes. This paper highlights and evaluates some patterning methods from the Center on Functional Engineered Nano Architectonics in Los Angeles and discusses key benchmarking criteria with respect to CMOS scaling.