Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of Immune Infiltration in HNC and Their Clinical Implications: A Gene Expression-Based Study

Background: Immune infiltration of head and neck cancer (HNC) highly correlated with the patient's prognosis. However, previous studies failed to explain the diversity of different cell types that make up the function of the immune response system. The aim of the study was to uncover the differences in immune phenotypes of the tumor microenvironment (TME) between HNC adjacent tumor tissues and tumor tissues using CIBERSORT method and explore their therapeutic implications. Method: In current work, we employed the CIBERSORT method to evaluate the relative proportions of immune cell profiling in 11 paired HNC and adjacent samples, and analyzed the correlation between immune cell infiltration and clinical information. The tumor-infiltrating immune cells of TCGA HNC cohort was analyzed for the first time. The fractions of LM22 immune cells were imputed to determine the correlation between each immune cell subpopulation and survival and response to chemotherapy. Three types of molecular classification were identified via “CancerSubtypes” R-package. The functional enrichment was analyzed in each subtype. Results: The profiles of immune infiltration in TCGA HNC cohort significantly vary between paired cancer and para-cancerous tissue and the variation could reflect the individual difference. Total Macrophage, Macrophages M0 and NK cells resting were elevated in HNC tissues, while total T cells, total B cells, T cells CD8, B cell navie, T cell follicular helper, NK cells activated, Monocyte and Mast cells resting were decreased when compared to paracancerous tissues. Among each cell immune subtype, T cells regulatory Tregs, B cells naïve, T cells follicular helper, and T cells CD4 memory activated was significantly associated with HNC survival. Three clusters were observed via Cancer Subtypes R-package. Each cancer subtype has a specific molecular classification and subtype-specific immune cell characterization. Conclusions: Our data suggest a difference in immune response may be an important driver of HNC progression and response to treatment. The deconvolution algorithm of gene expression microarray data by CIBERSOFT provides useful information about the immune cell composition of HNC patients.
How Does a Walker Pass Between Two People Standing in Different Configurations? Influence of Personal Space on Aperture Passing Methods

Most studies on aperture passability focus on aperture passing involving non-human physical objects. In this study, we examined experimentally how participants pass between two box-shaped frames and between the same frames, each with a human confederate in it, facing various directions. Seven configuration conditions were set up, six of which differed in terms of the human confederates’ sets of directions in the two frames: face-to-face, back-to-back, facing toward or away from the participants, facing leftward or rightward from the participants’ perspective, and the empty frames condition without human confederates. There were seven aperture-width conditions—50, 55, 60, 65, 70, 75, and 80 cm—and participants walked at their normal speed through the apertures. We found that the participants’ shoulder rotation angle in the face-to-face condition was significantly greater than that in the empty frames condition. Further, the participants preferred to rotate their shoulders counterclockwise when our confederates in the aperture faced leftward, and clockwise, when they faced rightward. These results suggest that people change their passing-through methods by considering the social nature of the aperture as well as its width.
Prevalence of enuresis among children and adolescents: A systematic review and meta-analysis

Background: Enuresis is a common dilemma among minors, which is under-documented and under-disclosed. The plight has a negative effect on the quality of life, with an adverse bearing on social and academic development. The recognition of its strains on the family added to the aforementioned necessitated the designation of every last Tuesday of May as annual bedwetting day to create complacent personality among subjects faced with this challenge. Enuresis has worldwide distribution; however, the national prevalence of enuresis is unknown in Nigeria. Objective: The aim of our review is to determine the prevailing prevalence of juvenile enuresis in the country and its regions. Materials and Methods: We used electronic databases to explore reviews and select studies, and then extracted necessary data from the appraisals on prevalence and incidence of enuresis among children and adolescents from Nigerian communities. STATA 12 random effect meta-analysis of observational studies was used to compute the pooled prevalence and other estimates. Results: Twenty-four studies fall within the inclusion criteria. The combined pooled population studied was 15,172 (n = 3567 children and adolescents). The pooled prevalence of enuresis was 28.19% (22.37%–34.00%) (95% confidence interval). Conclusion: This study showed that enuresis is hyperendemic among Nigerian children and adolescents.
Mapping Alterations Induced by Long-Term Axenic Cultivation of Leishmania amazonensis Promastigotes With a Multiplatform Metabolomic Fingerprint Approach

Leishmaniases are widespread neglected diseases with an incidence of 1.6 million new cases and 40 thousand deaths per year. Leishmania parasites may show distinct, species-specific patterns of virulence that lead to different clinical manifestations. It is well known that successive in vitro passages (SIVP) lead to the attenuation of virulence, but neither the metabolism nor the pathways involved in these processes are well understood. Herein, promastigotes of a virulent L. amazonensis strain recently isolated from mice was compared to SIVP derived and attenuated promastigotes, submitted to 10, 40, and 60 axenic passages and named R10, R40, and R60, respectively. In vitro assays and in vivo tests were performed to characterize and confirmed the attenuation profiles. A metabolomic fingerprint comparison of R0, R10, and R60 was performed by means of capillary electrophoresis, liquid and gas chromatography coupled to mass spectrometry. To validate the metabolomic data, qPCR for selected loci, flow cytometry to measure aPS exposure, sensitivity to antimony tartrate and ROS production assays were conducted. The 65 identified metabolites were clustered in biochemical categories and mapped in eight metabolic pathways: ABC transporters; fatty acid biosynthesis; glycine, serine and threonine metabolism; β-alanine metabolism; glutathione metabolism; oxidative phosphorylation; glycerophospholipid metabolism and lysine degradation. The obtained metabolomic data correlated with previous proteomic findings of the SVIP parasites and the gene expression of 13 selected targets. Late SIVP cultures were more sensitive to SbIII produced more ROS and exposed less phosphatidylserine in their surface. The correspondent pathways were connected to build a biochemical map of the most significant alterations involved with the process of attenuation of L. amazonensis. Overall, the reported data pointed out to a very dynamic and continuous metabolic reprogramming process, accompanied by changes in energetic, lipid and redox metabolisms, membrane remodeling and reshaping of parasite-host cells interactions, causing impacts in chemotaxis, host inflammatory responses and infectivity at the early stages of infection.
Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases

The overwhelming majority of participants in current genetic studies are of European ancestry1–3, limiting our genetic understanding of complex disease in non-European populations. To address this, we aimed to elucidate polygenic disease biology in the East Asian population by conducting a genome-wide association study (GWAS) with 212,453 Japanese individuals across 42 diseases. We detected 383 independent signals in 331 loci for 30 diseases, among which 45 loci were novel (P < 5 × 10−8). Compared with known variants, novel variants have lower frequency in European populations but comparable frequency in East Asian populations, suggesting the advantage of this study in discovering these novel variants. Three novel signals were in linkage disequilibrium (r2 > 0.6) with missense variants which are monomorphic in European populations (1000 Genomes Project) including rs11235604(p.R220W of ATG16L2, a autophagy-related gene) associated with coronary artery disease. We further investigated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupancy, andidentified 378 significant enrichments across nine diseases (FDR < 0.05) (e.g. NF-κB for immune-related diseases). This large-scale GWAS in a Japanese population provides insights into the etiology of common complex diseases and highlights the importance of performing GWAS in non-European populations.
The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway

The outer potato periderm layer consists of dead suberized cells. Suberin, a protective biopolymer, is made of a polyaliphatic portion covalently linked to polyaromatic moieties. Evidence accumulates that Streptomyces scabies, the main causal agent of potato common scab, can degrade the suberin aliphatic part but its ability to degrade the aromatic portion has not been documented. This polyaromatic portion is mainly composed of cinnamic acids. In this study, two cinnamates (trans-ferulic or p-coumaric acids) were added to the culture medium of S. scabies strains EF-35 and 87.22. HPLC quantification revealed that both strains efficiently utilized these compounds. A proteomic study coupled with gene expression analysis led to the identification of putative catabolic pathways for cinnamates. Catabolism of both compounds appeared to occur via the β-ketoadipate pathway. Gene SCAB_15301, encoding for a putative vanillate monooxygenase, was partly deleted from S. scabies strain 87.22 genome. The mutant retained its ability to catabolize trans-ferulic acid into vanillate but lost its ability to further degrade the latter compound. When the wild-type mutant and complemented strains were grown in the presence of suberin-enriched potato periderm, accumulation of vanillic acid was observed only in the mutant culture medium. This work presents evidence that S. scabies can degrade not only the aliphatic part of suberin but also the constituents of suberin aromatic portion. This may provide ecological and pathological advantages to S. scabies as a saprophyte and pathogen.
Taming the Unknown Unknowns in Complex Systems: Challenges and Opportunities for Modeling, Analysis and Control of Complex (Biological) Collectives

Despite significant effort on understanding complex biological systems, we lack a unified theory for modeling, inference, analysis, and efficient control of their dynamics in uncertain environments. These problems are made even more challenging when considering that only limited and noisy information is accessible for modeling, which can prove insufficient for explaining, and predicting the behavior of complex systems. For instance, missing information hampers the capabilities of analytical tools to uncover the true degrees of freedom and infer the model structure and parameters of complex biological systems. Toward this end, in this paper, we discuss several important mathematical challenges that could open new theoretical avenues in studying complex systems: (1) By understanding the universal laws characterizing the asymmetric statistics of magnitude increments and the complex space-time interdependency within one process and across many processes, we can develop a class of compact yet accurate mathematical models capable to potentially providing higher degree of predictability, and more efficient control strategies. (2) In order to better predict the onset of disease and their root cause, as well as potentially discover more efficient quality-of-life (QoL)-control strategies, we need to develop mathematical strategies that not only are capable to discover causal interactions and their corresponding mathematical expressions for space and time operators acting on biological processes, but also mathematical and algorithmic techniques to identify the number of unknown unknowns (UUs) and their interdependency with the observed variables. (3) Lastly, to improve the QoL of control strategies when facing intra- and inter-patient variability, the focus should not only be on specific values and ranges for biological processes, but also on optimizing/controlling knob variables that enforce a specific spatiotemporal multifractal behavior that corresponds to an initial healthy (patient specific) behavior. All in all, the modeling, analysis and control of complex biological collective systems requires a deeper understanding of the multifractal properties of high dimensional heterogeneous and noisy data streams and new algorithmic tools that exploit geometric, statistical physics, and information theoretic concepts to deal with these data challenges.
SYSTEMATIC REVIEW: WHAT IS THE BEST AVAILABLE EVIDENCE FOR USING HOMEOPATHY IN PATIENTS WITH INTELLECTUAL DISABILITIES?

Objective: The debate about the effectiveness of homeopathy hits the headlines from time to time. Reported evidences for the role of homeopathy in psychiatric illness relevant to people with intellectual disabilities are patchy and inconsistent. In this review we summarize the best available evidence for the use of homeopathy to treat the psychiatric disorders common in this population. Methods: Systematic literature review was conducted through February 2012 to July 2012 in AMED, CINHAL, BNI, EMBASE, MEDLINE, PSYCHINFO and GOOGLE SCHOLAR. In the next steps thirty eight homeopathic associations were contacted and a top-up literature search was done on Scopus and World of Science databases till March 2014. Twelve relevant clinical trials were identified and included in this study. The quality of each trial was assessed by the Oxford quality scoring system (Known as Jadad score) as well as subjective review by two reviewers independently (good versus poor). Findings: The largest body of evidence pertained to the use of homeopathy in the treatment of attention deficit hyperactivity disorder (ADHD). There is heterogeneity in the quality of trials and also the outcome of studies but overall our findings suggest some potential for using homeopathy in ADHD. Current evidences do not support the use of homeopathy for treatment of speech and language difficulties. There was only one trial concerning the use of homeopathy in Autistic Spectrum Disorder. This was of a poor quality and unable to provide any recommendation. Conclusion: Whilst acknowledging the risk of publication and language bias in our study, the currently available evidences are neither conclusive nor comprehensive enough to give us a clear picture for the use of homeopathy in patients with intellectual disabilities. There are large gaps in the body of evidence concerning the role of homeopathy in the treatment of common disorders in intellectual disability, such as autism, challenging behavior or developmental arrest in childhood. Iranian Journal of Pediatrics, Volume 24 (Number 4), Aug 2014, Pages: 339-244
E2-SR: a novel energy-efficient secure routing scheme to protect MANET-IoT

Integration of mobile ad hoc networks (MANETs) and internet of things (IoT) becomes an emerging paradigm to enable opportunistic communication in IoT. However, the lack of infrastructure in MANET increases involvement of adversaries in IoT environment. Thus security provisioning against severe adversaries is still challenging in MANET-IoT. In this paper, we propose an energy efficient secure routing (E2-SR) scheme to ensure data security and integrity in MANET-IoT. We adapt Certificate based authentication in Hash Chain based Certificate Authentication (HCCA) scheme. Cluster formation is involved with secure verification of IoT devices by elliptic curve group law formulations. For cluster formation, secure dual head clustering with elliptic curve verification (SDHC-EC) algorithm is proposed. Secure routing is enabled by a new Worst Case Particle Swarm Optimization (WC-PSO) algorithm. The WC-PSO algorithm is supported by dual state markov chain model (DS-MCM) for security enhancement. Data security is ensured with data integrity using novel dual XOR-Rivest Cipher6 Encryption with Fuzzy Evaluation (DXOR-RC6 with FE) algorithm. The proposed MANET-IoT network is modeled and tested in ns-3.26 environment. The evaluation shows that E2-SR achieves better results in packet delivery ratio, throughput, residual energy, and routing overhead.
Wireless information and power transfer with optimal transmit antenna selection

A dual hop, half-duplex amplify and forward (AF) relay is considered for a source equipped with multiple transmit antennas. A power splitter is employed at the relay to harvest energy from the signal received from the source. The outage probability (OP) is derived considering optimal antenna selection to maximise the end-to-end signal-to-noise ratio. It is shown that the performance of the proposed energy harvesting based scheme improves with the number of transmit antennas. The effect of the power splitting factor on the OP is studied for different relay locations. Further, the OP is examined for different distances between the source and relay.
Optimizing and Satisficing: The Interplay Between Platform Architecture and Producers' Design Strategies for Platform Performance

Two-sided platforms are gaining increasing attention in practice and as the subject of IS and management research. We explore an assumption of research and practice: that a platform’s architecture needs to be decoupled so that producers can easily mix and match the platform’s design elements (APIs, code libraries, process models, etc.) into apps that perform well competitively, and insulate the platform from skewed outcomes and low market performance. However, in practice, complete decoupling is not just difficult but almost impossible. Based on more than two million runs of an exploratory NK model in which producers use a platform’s design space for the creation of apps, we generate several surprising insights. First, we show that tighter coupling may not necessarily be harmful depending on the producers’ design strategies and the amount of constraints placed on design elements. Second, we observe that if moderate to tightly coupled platforms with optimizing producers focused exclusively on being competitive, platform performance is lower compared to platforms with satisficing producers who put a lower priority of being competitive because of other interests. This is surprising since optimizers are better suited to cope with the inherent uncertainty of coupling. Finally, moderately coupled platforms can outperform platforms with loose coupling when constraints nudge producers into distant design moves while also isolating them from downside uncertainty. These three findings offer implications for multiple streams of literature on platform architectures.
Impacts of spray-drying conditions on the physicochemical properties of soy sauce powders using maltodextrin as auxiliary drying carrier

Naturally brewed soy sauce was spray-dried using a pilot-scale spray-dryer with two-fluid atomization nozzle. Maltodextrin (DE 10) was incorporated into liquid soy sauce as a drying aid, to form a uniform liquid of 40% w/v. The influence of spray-drying parameters including inlet drying air temperature, feed flow rate, and atomization air flow was examined. The product yield, bulk density, cohesiveness and particle size of the spray-dried powders were found to be influenced by the spray-drying conditions. Extremely cohesive soy sauce powders were obtained when the air-drying temperature reached 180°C and above. Moreover, surface NaCl concentration of the soy sauce powders was shown to have insufficient expression in comparison with that in bulk. Surface NaCl content was also found to increase with increasing drying temperature.
Leucocyte Groups and Histocompatibility

A large number of leucocyte antigens have now been defined [30, 40, 411, and duriug the last year the relevance of several of these antigens for histocompatibility has been proven, which means that transplantation antigens in man can a t last be recognized serologically [17,40]. This would seem to be an appropriate time to look back over the long and torturous road which led to the present knowledge.
Complexity and safety in medical computing: a clinician’s musings

Some technologies, like scissors and chopsticks, appear inherently simple. Others, like nuclear reactors or life-support electronics, are inherently complex. By nature, the safety issues associated with complex systems are more involved than those associated with simple systems. There are always added cost requirements in complexity, such as special requirements for ensuring safe operation of the system. The very subsystems added to increase safety, however, necessarily add to complexity and, ironically, enrich the number of possible failure modes in the overall system. Thus there is a concern that the failure of any additional safety system may itself lead to new system failure modes that would not have otherwise occurred [1]. These comments explain why simply adding complexity to a system may not always improve on the system’s performance. The following illustrates some of the concerns that I have developed about the potential misapplication of computers in medical technology. These concerns are based on my clinical experience over the last decade in dealing with high-tech aspects of medical care.
Progressive Non-rigid Registration of Temporal Mesh Sequences

We present an algorithm for progressive mesh registration to provide temporal consistency, simplify temporal texture editing and optimize the data rate of 3D mesh sequences recorded in a volumetric capture studio. The capture pipeline produces a sequence of manifold meshes with varying connectivity. We split the sequence into groups of frames that will share connectivity and chose a keyframe in each group that is progressively deformed to approximate the surface of the adjacent meshes. Our algorithm works with a coarse-to-fine ICP approach, which makes it robust against large deformations in the scene while preserving small details. Applying a deformation graph constrains the transformations to be locally as-rigid-as-possible, while allowing it to work with any natural objects in the scene, not just humans. We show how to robustly track sequences of human actors with varying clothing over hundreds of frames recorded in a volumetric capture studio. We verify our results with a publicly available dataset of more than 40,000 frames. Our mesh registration takes less than five seconds per frame on a single desktop machine and has been successfully integrated into a volumetric capture pipeline for commercial use.