Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of Tumor-Reactive Cytotoxic CD4+ T-cell Responses after Ipilimumab Treatment in Four Advanced Melanoma Patients

Using archived blood samples from 4 NY-ESO-1-seropositive patients with advanced melanoma who were treated with the CTLA-4-blocking monoclonal antibody ipilimumab, Kitano and colleagues analyzed changes in antigen-specific CD4+ T cells during cancer immunotherapy. They characterized a novel consequence of the CTLA-4 blockade, the induction or expansion of tumorreactive cytotoxic CD4+ T cells after ipilimumab treatment. CD4+ T cells provide help to enhance and sustain cytotoxic CD8+ T-cell responses. A direct lytic role for this cell population in mouse models further supports the use of tumor-reactive CD4+ T cells for cancer immunotherapy. CTLA-4 blockade has been shown to expand antigen-specific cytotoxic CD4+ T cells in mouse models. We took advantage of spontaneous immunity to the NY-ESO-1 cancer-testis antigen to investigate quantitative and qualitative changes in antigen-specific CD4+ T-cell responses after ipilimumab (anti-CTLA-4 monoclonal antibody) treatment in patients with advanced melanoma. Four patients with NY-ESO-1 seropositive melanoma were chosen upon the availability of suitable blood specimens for characterizing the functions of NY-ESO-1 antigen-specific CD4+ T-cell response by enzyme-linked immunospot (ELISPOT), intracellular cytokine staining (ICS), and cytotoxicity assays. Multiple NY-ESO-1 antigen-specific CD4+ T-cell responses with TH1 dominance were induced or enhanced after ipilimumab treatment in peripheral blood in all four patients. NY-ESO-1 antigen–specific CD4+ T-cell lines established from all four patients after ipilimumab treatment recognized naturally processed NY-ESO-1 protein in antigen-presenting cells, expressed master transcription factor Eomesodermin (Eomes), and secreted perforin and Granzyme B. Finally, we showed that these NY-ESO-1 antigen-specific CD4+ T-cell lines directly lysed autologous melanoma cell lines expressing NY-ESO-1 in an MHC class II restricted manner. Our results show that antigen-specific cytotoxic CD4+ T-cell responses are induced after ipilimumab therapy in human cancer patients. Ipilimumab may induce the expression of lytic granules on antigen-specific cytotoxic CD4+ T cells via Eomes, revealing a novel consequence of immunologic checkpoint blockade. Cancer Immunol Res; 1(4); 235–44. ©2013 AACR.
Processes driving freshwater plant production and diversity in upland streams

Upland headwater streams are important sources of freshwater in mountainous temperate to sub-arctic latitude European countries like Scotland. Yet much less is known about the ecology of small, characteristically oligotrophic, mountain streams supporting periphyton and aquatic bryophyte dominated vegetation, and their potential bioindicator capacity of environmental water quality, than lowland rivers impacted by anthropogenic disturbance, in this context. This scarcity of knowledge has significant implications for the success of the recently implemented Water Framework Directive (WFD: 2000/60/EC). The WFD is a major piece of environmental legislation for water policy and sustainable water management in Europe. New contributions are fundamental to environment agencies, such as the Scottish Environment Protection Agency (SEPA), tasked with the responsibility of enforcing WFD statutory requirements and developing effective biomonitoring tools for assessing water quality status in Scotland. A major aim of the WFD is to achieve at least ‘good’ ecological status of inland waterbodies by 2015. Further, in doing so, to ascertain ecological benchmark communities of near-pristine (or minimally-impacted) reference conditions as indicators of high water quality status. The objective is to improve understanding of the environmental processes driving the production and diversity of freshwater plant species-assemblages in upland streams. Such information can be used for assessing perturbations threatening the ecological integrity of rivers impacted by anthropogenic disturbances (human pressure). This enables environment agencies such as SEPA, to respond appropriately by implementing corrective measures and sustainable management strategies. This project monitored a range of near-pristine headwater streams of contrasting underlying geology in the Scottish Highlands. The approach adopted was compatible with current WFD river characterisation and biomonitoring strategies. These were used to investigate the structural and functional response of freshwater plant communities (chiefly diatoms and other algal groups; aquatic bryophyte and vascular submerged macrophyte vegetation) to environmental drivers (e.g. flow, substrate morphology, nutrient inputs, water chemistry, underwater light availability). The work was carried out with the aim of contributing to future development of baseline monitoring tools for assessing upland stream habitat quality in Scotland.
The Challenge of Scaling Genome Big Data Analysis Software on TH-2 Supercomputer

Whole genome re-sequencing plays a crucial role in biomedical studies. The emergence of genomic big data calls for an enormous amount of computing power. However, current computational methods are inefficient in utilizing available computational resources. In this paper, we address this challenge by optimizing the utilization of the fastest supercomputer in the world - TH-2 supercomputer. TH-2 is featured by its neo-heterogeneous architecture, in which each compute node is equipped with 2 Intel Xeon CPUs and 3 Intel Xeon Phi coprocessors. The heterogeneity and the massive amount of data to be processed pose great challenges for the deployment of the genome analysis software pipeline on TH-2. Runtime profiling shows that SOAP3-dp and SOAPsnp are the most time-consuming components (up to 70% of total runtime) in a typical genome-analyzing pipeline. To optimize the whole pipeline, we first devise a number of parallel and optimization strategies for SOAP3-dp and SOAPsnp, respectively targeting each node to fully utilize all sorts of hardware resources provided both by CPU and MIC. We also employ a few scaling methods to reduce communication between different nodes. We then scaled up our method on TH-2. With 8192 nodes, the whole analyzing procedure took 8.37 hours to finish the analysis of a 300 TB dataset of whole genome sequences from 2,000 human beings, which can take as long as 8 months on a commodity server. The speedup is about 700x.
Transcriptomic Analysis of Fiber Strength in Upland Cotton Chromosome Introgression Lines Carrying Different Gossypium barbadense Chromosomal Segments

Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes), glycolysis/gluconeogenesis (122 genes), phenylpropanoid biosynthesis (101 genes), and oxidative phosphorylation (87 genes), etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.
A case report of Schatzker type VI tibial plateau fracture treated with double reverse traction closed reduction combined with minimally invasive percutaneous plate osteosynthesis technique

Rationale: The knee joint is an important weight-bearing joint, tibial plateau fractures affect knee function and stability. High-energy intra-articular fractures involving the tibial plateau can cause management-related problems such as wound dehiscence; severe comminution leading to malalignment; and delayed complications such as varus collapse, implant failure, and arthritis of the knee joint. The treatment of severe or complex tibial plateau fractures can be quite difficult. Traditional methods of open reduction and plating require extensive exposures, which may further compromise soft tissue and devascularize bone fragments, leading to infection. In this case, a novel device, double reverse traction combined with MIPPO technique, was used and provided the possibility of minimally invasive and personalized orthopedic surgery to treat severe comminuted Schatzker type VI tibial plateau fracture and tibial shaft fracture and got satisfactory results. Patient concerns: A previously healthy 56-year-old man presented to the emergency room after a fall from a height, who lost the movement of the left knee with pain and swelling. Diagnoses: X-rays showed a tibial plateau comminuted fracture, Schatzker type VI, and tibial shaft fracture. Interventions: Applying less extensile exposure and the indirect reduction technique of double reverse traction and closed reduction combined with minimally invasive percutaneous plate osteosynthesis (MIPPO) technique, we got satisfactory recovery of the severe comminuted Schatzker type VI tibial plateau fracture and tibial shaft fracture. Outcomes: This severe comminuted fracture and tibial shaft fracture were successfully reduced and got satisfactory recovery of knee joint function. Lessons: Double reverse traction combined with MIPPO technique can reduce the risk of surgical complications, such as bleeding, oozing, and wound infection. It can be applied in patients with comorbidities such as cardiac disease, hypertension, and heart failure who may otherwise not be candidates for surgery. The cost burden is lower than that of the traditional traction table.
Formation Tracking Control of Multiagents in Constrained Space

In this paper, formation tracking control based on potential field is studied. The objective is to control a group of agents to track a desired trajectory while maintaining a given formation in nonomniscient constrained space. Aiming at this purpose, the average of all agents' positions is viewed as the virtual leader, and the task is translated into that controlling the virtual leader to track the center of the desired formation. The situation where agents may not have global environmental information will lead to that they may have to avoid collisions with unexpected spatial constraints. By introducing the concepts of line source and surface source, two main types of spatial constraints: 1) borders and 2) obstacles are defined mathematically and unified into a common expression in an artificial potential function. In this way, the tasks of formation tracking and obstacle avoidance in a bounded environment can be solved by the control law proposed in this paper. Furthermore, concerning the situation of multiple spatial constraints, a Dirac delta function is introduced. Meanwhile, a formation optimal algorithm is proposed to minimize the formation generation time cost. Following that, a controller is designed, and the conditions for asymptotic stability of multiagent systems are proved based on the Lyapunov function. The maximum duration that the conditions cannot be satisfied is elaborated to indicate whether the tracking task should be given up. Meanwhile, the impulsive influence from spatial constraints is analyzed. Finally, the simulation results are presented to illustrate the performance of proposed approaches.
Is Self Myofascial Release an Effective Preexercise and Recovery Strategy? A Literature Review

The use of self myofascial release (SMR) via a foam roller or roller massager is becoming increasingly popular both to aid recovery from exercise and prevent injury. Our objective was to review the literature on SMR and its use for preexercise, recovery, or maintenance. PUBMED, EBSCO (MEDLINE), EMBASE, and CINAHL were searched for variations and synonyms of “self myofascial release” and “foam rolling. ” Data from nine studies were examined, and overall quality varied based on study protocol, muscle group targeted, and outcomes measured. Despite the heterogeneity of these studies, SMR appears to have a positive effect on range of motion and soreness/fatigue following exercise, but further study is needed to define optimal parameters (timing and duration of use) to aid performance and recovery.
Monitoring a large surveillance space through distributed face matching

Large space with many cameras require huge storage and computational power to process these data for surveillance applications. In this paper we propose a distributed camera and processing based face detection and recognition system which can generate information for finding spatiotemporal movement pattern of individuals over a large monitored space. The system is built upon Hadoop Distributed File System using map reduce programming model. A novel key generation scheme using distance based hashing technique has been used for distribution of the face matching task. Experimental results have established effectiveness of the technique.
Towards Multilevel Human Body Modeling and Tracking in 3D: Investigation in Laplacian Eigenspace (LE) Based Initialization and Kinematically Constrained Gaussian Mixture Modeling (KC-GMM)

Vision-based automatic human body pose estimation has many potential applications and it is also a challenging task. Together, these two factors have made vision-based human body pose estimation an attractive research area with closely related research areas including body pose, hand pose, and head pose estimation. Up to now, these research works however only deal with each task of estimating body pose, hand pose or head pose separately. In this paper, we bring out the issue of multilevel human body pose estimation and focus on model based methods for articulated human body pose estimation using volumetric data (voxel data). Important steps in this kind of methods will be described and several recent techniques will be analyzed and compared. Based on this analysis, we propose a fairly general method combining the discovered properties of LE transformation in [23] and KC-GMM method [3] for automatic initialization and tracking of both body model and hand model using voxel data. We also propose a framework for human body pose estimation at multilevel (i.e. body pose, hand pose, head pose) in an integrated way. The proposed method and framework will be presented along with experimental support and other possible avenues for future work in the area will be discussed.
Paleoenvironment and Human Occupation in the Maya Lowlands of the Usumacinta River, Southern Mexico

Paleosol sequences along the lowest terraces of the Usumacinta River in southern Mexico were used to reconstruct Holocene environmental changes and examine human–environmental interactions. Study sections were correlated through paleosol morphology, radiocarbon dating, and artifact seriation of Formative, Classic, and Postclassic ceramics. The oldest paleosols have gleyic features. Although they contain hard carbonate concretions dating to 5450–5380 cal. yr B.P., these Gleysols formed in the Late Pleistocene to Early Holocene. Carbonates were deposited later. The uppermost paleosols lack gleyic features, the oldest of which contains vertic features, dating to 2000–2700 cal. yr B.P., and contains abundant Formative period ceramics. The upper two paleosols are morphologically less developed and are strongly affected by human activities; radiocarbon ages and ceramic assemblages indicate that they belong to the Maya Classic and Postclassic periods. Stable carbon isotope values from the decalcified organic matter vary among paleosols of different ages and sites. δ13C values are highest (−16 to −20‰) in the Formative period paleosol. Although it is possible that maize cultivation could contribute to the isotopic signatures, we believe that the δ13C values indicate the dominance of drought‐resistant C4 and CAM vegetation due to their association with vertic soils. The Classic period paleosol has a slightly lower isotopic value (−20 to −22‰), while the Postclassic paleosol shows the lowest values (−22 to −23‰), suggesting reforestation of the floodplain. These results indicate that the Early Holocene paleosols formed in a humid climate similar to that of today, which transitions toward dryer conditions around 5500 cal. yr B.P. In the Late Holocene (approximately 3000 B.P.) an increase in seasonality occurs. This condition favored the formation of Vertisols, suitable for agriculture.
Tissue proteomics of splenic marginal zone lymphoma

Splenic marginal zone lymphoma (SMZL) is a rare chronic B lymphoproliferative disease, whose molecular pathogenesis has still not been well established. For the first time, a proteomic approach was undertaken to analyse the protein profiles of SMZL tissue. 1D and 2D Western blot, immunohistochemical analysis, and functional data mining were also performed in order to validate results, investigate protein species specific regulation, classify proteins, and explore their potential relationships. We demonstrated that SMZL is characterized by modulation of protein species related to energetic metabolism and apoptosis pathways. We also reported specific protein species (such as biliverdin reductase A, manganese superoxide dismutase, beta‐2 microglobulin, growth factor receptor‐bound protein 2, acidic leucine‐rich nuclear phosphoprotein 32 family member A, and Set nuclear oncogene) directly involved in NF‐kB and BCR pathways, as well as in chromatin remodelling and cytoskeleton. Our findings shed new light on SMZL pathogenesis and provide a basis for the future development of novel biomarkers. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD001124.
Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein

The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton) expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests) to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC) marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC) transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the detailed mode-of-action of the two Bt Cry toxins.
Initial observations of the simultaneous multithreading Pentium 4 processor

We analyze an Intel Pentium 4 hyper-threading processor. The focus is to understand its performance and the underlying reasons behind that performance. Particular attention is paid to putting the processor in context with prior published research in simultaneous multithreading-validating and reevaluating, where appropriate, how this processor performs relative to expectations. Results include multiprogrammed speedup, parallel speedup, as well as synchronization and communication throughput. The processor is also evaluated in the context of prior work on the interaction of multithreading with the operating system and compilation.
Banana (Musa spp.) domestication in the Asia-Pacific Region: linguistic and archaeobotanical perspectives

An examination of linguistic terms for ‘banana’ within Island Southeast Asia and Melanesia sheds light on the history of Musa spp. domestication. Linguistic investigations suggest a westward dispersal of banana from New Guinea, mixing with a Philippine variety (or at least sphere of cultural usage), then westward again to mainland Southeast Asia, and (as far as can be linguistically inferred) onward to the western edge of South Asia. The linguistically-derived interpretation accords generally with the archaeobotanical evidence and botanical models for the dispersal of banana cultivars.
Modulation of Histone Acetyltransferase Activity through Interaction of Epstein-Barr Nuclear Antigen 3C with Prothymosin Alpha

ABSTRACT The Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA3C) is essential for EBV-dependent immortalization of human primary B lymphocytes. Genetic analysis indicated that amino acids 365 to 992 are important for EBV-mediated immortalization of B lymphocytes. We demonstrate that this region of EBNA3C critical for immortalization interacts with prothymosin alpha (ProTα), a cellular protein previously identified to be important for cell division and proliferation. This interaction maps to a region downstream of amino acid 365 known to be involved in transcription regulation and critical for EBV-mediated transformation of primary B lymphocytes. Additionally, we show that EBNA3C also interacts with p300, a cellular acetyltransferase. This interaction suggests a possible role in regulation of histone acetylation and chromatin remodeling. An increase in histone acetylation was observed in EBV-transformed lymphoblastoid cell lines, which is consistent with increased cellular gene expression. These cells express the entire repertoire of latent nuclear antigens, including EBNA3C. Expression of EBNA3C in cells with increased acetyltransferase activity mediated by the EBV transactivator EBNA2 results in down-modulation of this activity in a dose-responsive manner. The interactions of EBNA3C with ProTα and p300 provide new evidence implicating this essential EBV protein EBNA3C in modulating the acetylation of cellular factors, including histones. Hence, EBNA3C plays a critical role in balancing cellular transcriptional events by linking the biological property of mediating inhibition of EBNA2 transcription activation and the observed histone acetyltransferase activity, thereby orchestrating immortalization of EBV-infected cells.