Miracle-dz/UniFAR-FTUs huggingface dataset:
A new record of plant parasitic green algae, Cephaleuros diffusus (Trentepohliaceae, Chlorophyta), on Acacia auriculiformis hosts in Thailand

Sunpapao A, Pitaloka MK. 2015. A new record of plant parasitic green algae, Cephaleuros diffusus (Trentepohliaceae, Chlorophyta), on Acacia auriculiformis hosts in Thailand. Biodiversitas 16: 116-120. Cephaleuros diffusus algae were found to cause leaf spot disease of the host Acacia auriculiformis. The identification was based on morphological and molecular properties. The observed morphology identified the algae as C. diffusus. Transverse sections of the host leaves were used to quantify the disease severity of the host in terms of a four-point necrosis index. The hostâ€™s lesions were subcuticular and subepidermal on the upper leaf surfaces. The identification of the algae was confirmed from molecular analysis, and a phylogenetic tree distinguished our samples from other Cephaleuros species. This is the first report of C. diffusus on Acacia auriculiformis in Thailand.Key words: Cephaleuros, disease severity, morphology, necrosis, phylogenetic analysis
Micro‐morpho‐anatomical mechanisms involve in epiphytic adaptation of micropropagated plants of Vanda tessellata (Roxb.) Hook. ex G. Don

Vanda tessellata (Roxb.) Hook. ex G. Don. (grey orchid, family Orchidaceae) is an epiphytic orchid of horticultural importance and currently under threat due to overharvesting and habitat destruction. Micropropagation protocols were developed for the production of grey orchid but the survival success of in vitro regenerated plantlets is uncertain due to lack of understanding about the adaptation mechanism during hardening. The present study describes the structural adaptation mechanism of V. tessellata when the in vitro regenerated plantlets were acclimatized under the greenhouse conditions. Light microscopy has been implicated to identify the adaptational alterations during in vitro to ex vitro transition of micropropagated plantlets. The in vitro induced morpho‐anatomical anomalies were more prominently observed in the density of stomata, veins (architecture) and raphides, leaf, and root structural parameters such as water cells and velamen tissues. The results indicated that remarkable reconciliation occurred in structural developments of mechanical and vascular tissues upon epiphytic adaptations of V. tessellata. The study could help in understanding the adaptation mechanism of in vitro regenerated plantlets (especially velamen tissues of epiphytic roots) when transferred to the greenhouse for acclimatization.
Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.
Immunomodulatory Dual-Sized Microparticle System Conditions Human Antigen Presenting Cells Into a Tolerogenic Phenotype In Vitro and Inhibits Type 1 Diabetes-Specific Autoreactive T Cell Responses

Current monotherapeutic agents fail to restore tolerance to self-antigens in autoimmune individuals without systemic immunosuppression. We hypothesized that a combinatorial drug formulation delivered by a poly-lactic-co-glycolic acid (PLGA) dual-sized microparticle (dMP) system would facilitate tunable drug delivery to elicit immune tolerance. Specifically, we utilized 30 µm MPs to provide local sustained release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor β1 (TGF-β1) along with 1 µm MPs to facilitate phagocytic uptake of encapsulated antigen and 1α,25(OH)2 Vitamin D3 (VD3) followed by tolerogenic antigen presentation. We previously demonstrated the dMP system ameliorated type 1 diabetes (T1D) and experimental autoimmune encephalomyelitis (EAE) in murine models. Here, we investigated the system’s capacity to impact human cell activity in vitro to advance clinical translation. dMP treatment directly reduced T cell proliferation and inflammatory cytokine production. dMP delivery to monocytes and monocyte-derived dendritic cells (DCs) increased their expression of surface and intracellular anti-inflammatory mediators. In co-culture, dMP-treated DCs (dMP-DCs) reduced allogeneic T cell receptor (TCR) signaling and proliferation, while increasing PD-1 expression, IL-10 production, and regulatory T cell (Treg) frequency. To model antigen-specific activation and downstream function, we co-cultured TCR-engineered autoreactive T cell “avatars,” with dMP-DCs or control DCs followed by β-cell line (ßlox5) target cells. For G6PC2-specific CD8+ avatars (clone 32), dMP-DC exposure reduced Granzyme B and dampened cytotoxicity. GAD65-reactive CD4+ avatars (clone 4.13) exhibited an anergic/exhausted phenotype with dMP-DC presence. Collectively, these data suggest this dMP formulation conditions human antigen presenting cells toward a tolerogenic phenotype, inducing regulatory and suppressive T cell responses.
The Divergent Roles of Symptom and Performance Validity in the Assessment of ADHD

Objective: This study examined concordance between symptom and performance validity among clinically-referred patients undergoing neuropsychological evaluation for Attention-Deficit/Hyperactivity Disorder (ADHD). Method: Data from 203 patients who completed the WAIS-IV Working Memory Index, the Clinical Assessment of Attention Deficit-Adult (CAT-A), and ≥4 criterion performance validity tests (PVTs) were analyzed. Results: Symptom and performance validity were concordant in 76% of cases, with the majority being valid performance. Of the remaining 24% of cases with divergent validity findings, patients were more likely to exhibit symptom invalidity (15%) than performance invalidity (9%). Patients demonstrating symptom invalidity endorsed significantly more ADHD symptoms than those with credible symptom reporting (ηp2 = .06–.15), but comparable working memory test performance, whereas patients with performance invalidity had significantly worse working memory performance than those with valid PVT performance (ηp2 = .18). Conclusion: Symptom and performance invalidity represent dissociable constructs in patients undergoing neuropsychological evaluation of ADHD and should be evaluated independently.
WIFROWAN: Wrapped Imbalanced Fuzzy-Rough Ordered Weighted Average Nearest Neighbor Classification

In this paper we propose an ensemble method based on IFROWANN (Imbalanced Fuzzy-Rough Ordered Weighted Average Nearest Neighbor) algorithm to classify problems with imbalanced data. The ensemble generates many classifiers with different weight strategy and indiscernibility fuzzy relations. Classification is carried out selecting one of three strategies: I- to classify the new instance with the algorithm with best AUC in training. II- to average the memberships of the instance to the fuzzy-rough lower and upper approximation of each class given by the classifiers with best AUC. III- to average the memberships of the instance to the fuzzy-rough lower and upper approximation of each class of the all classifiers. Our method is validated by an extensive experimental study, showing statistically better results than 14 other state-of-the-art methods.
Multimorbidity among incident Finnish systemic lupus erythematosus patients during 2000–2017

The objective of the study was to examine the risk of other morbidities among patients with systemic lupus erythematosus (SLE). A total of 1006 adult new-onset SLE patients were identified during 1.1. 2000- 31.12. 2014 from the register of Social Insurance Institution. For each case three general population controls matched according to age, sex and place of residence at the index day were sampled from the population register. Both groups were followed up from the index date until the end of 2017 or until death. The national register on specialized care was explored to gather broadly their 12 organ-specific morbidities, which were found among 91.2% of SLE patients and 66.7% of comparators. The rate ratio (RR) was elevated in almost all disease groups. Musculoskeletal, cardiovascular and genitourinary conditions were the most common comorbidities with RRs of 1.82 (1.68 to 1.97), 1.91 (1.76 to 2.08) and 1.91 (1.73 to 2.09), respectively. Men with SLE had a significantly higher risk for diseases of the genitourinary system and endocrine, nutritional and metabolic diseases compared to women with SLE. The risk of concurrent morbidities is essential to note in the care of SLE patients.
Knowledge Management, Supply Chain Marketing Implementation and Marketing Capabilities and Tourism Industry Performance in Indonesia

The current study purpose is to conduct the relationship between the knowledge management (KNW), customer orientation (CUO) and tourism industry performance (TIP) of Indonesia with the moderating effect of supply chain marketing planning capabilities (SCMPC) and supply chain marketing implementations capabilities (SCMIC). For this purpose, the data was collected from the 400 professional managers by using a convenient sampling technique which yield a 80 percent response rate. The Structural Equation Modelling (SEM) analysis has shown that knowledge management (KNW) has directly significant and positive association with the tourism industry performance (TIP) but customer orientation (CUO) has an insignificant relationship with the TIP. On the other hand, the indirect effect of the study has shown that both moderating indicators namely SCMPC and SCMIC have a significant moderating effect in the relationship of both of the exogenous and endogenous variable. Therefore, this moderating effect contribution is considered to be an important contribution of the study which fill the previous studies gaps. The research limitations and future directions at the end of the study were also discussed.
Topological Similarity Search in Large Combinatorial Fragment Spaces

In similarity-driven virtual screening, molecular fingerprints are widely used to assess the similarity of all compounds contained in a chemical library to a query compound of interest. This similarity analysis is traditionally done for each member of the library individually. When encoding chemical spaces that surpass billions of compounds in size, it becomes impractical to enumerate all their products, let alone assess their similarity, deeming this approach impossible without investing a substantial amount of resources. In this work, we present a novel search algorithm named SpaceLight for topological fingerprint similarity searching in large, practically non-enumerable combinatorial fragment spaces. In contrast to existing methods, SpaceLight is able to utilize the combinatorial character of these chemical spaces for efficiency while maintaining a high correlation of the description of molecular similarity to well-known molecular fingerprints like ECFP. The resulting software is able to search prominent spaces like EnamineREAL with more than 10 billion compounds in seconds on a standard desktop computer.
Draft Genome Sequence of Salinivibrio sp. Strain EAGSL, a Biotechnologically Relevant Halophilic Microorganism

The halophilic bacterium Salinivibrio sp. strain EAGSL was isolated from the Great Salt Lake (Utah) for use in microbial electrochemical technologies experiencing fluctuating salt concentrations. Genome sequencing was performed with Ion Torrent technology, and the assembled genome reported here is 3,234,770 bp, with a GC content of 49.41%. ABSTRACT The halophilic bacterium Salinivibrio sp. strain EAGSL was isolated from the Great Salt Lake (Utah) for use in microbial electrochemical technologies experiencing fluctuating salt concentrations. Genome sequencing was performed with Ion Torrent technology, and the assembled genome reported here is 3,234,770 bp with a GC content of 49.41%.
The evolution of SMEs clusters: some insight from Italy

Clusters that emerged in the past have changed over time, so that today the research challenge in economic geography is on their evolution over time. If the attention moves from patterns of clustering to the evolution of spatial concentration, than the “Porter diamond” and the vast literature focused on the advantage of clustering cannot be helpful. Since late ‘90’s many evolutionary studies on cluster have been based on the idea of cluster life cycle and, a minority, on the adaptive cycle model. The aim of this paper is to update on the evolutionary path of SMEs Italian clusters, which faced with the economic crisis are undergoing a process of vertical integration into business groups, usually shaped around a leading firms, able to connect local resources (and firms) to global markets and eventually even to other clusters. We argue that SMEs clusters, leaded by one or more global business groups located inside it are more resilient, and that others firms in the cluster may coevolve with those leading firms over time. To empirically verify these hypotheses both qualitative and quantitative analysis will be carried out. JEL codes: L22, L67, R11, R12.
Privacy s Dead – Solutions for Privacy-Enabled Collections and Use of Personal Health Information in Digital Era

Today’s digital information systems and applications collect every day a huge amount of personal health information (PHI) from sensor and surveillance systems, and every time we use personal computers or mobile phones. Collected data is processed in clouds, platforms and ecosystems by digital algorithms and machine learning. Pervasive technology, insufficient and ineffective privacy legislation, strong ICT industry and low political will to protect data subject’s privacy have together made it almost impossible for a user to know what PHI is collected, how it is used and to whom it is disclosed. Service providers’ and organizations’ privacy policy documents are cumbersome and they do not guarantee that PHI is not misused. Instead, service users are expected to blindly trust in privacy promises made. In spite of that, majority of individuals are concerned of their privacy, and governments’ assurance that they meet the responsibility to protect citizens in real life privacy is actually dead. Because PHI is probably the most sensitive data we have, and the authors claim it cannot be a commodity or public good, they have studied novel privacy approaches to find a way out from the current unsatisfactory situation. Based on findings got, the authors have developed a promising solution for privacy-enabled use of PHI. It is a combination of the concept of information fiduciary duty, Privacy as Trust approach, and privacy by smart contract. This approach shifts the onus of privacy protection onto data collectors and service providers. A specific information fiduciary duty law is needed to harmonize privacy requirements and force the acceptance of proposed solutions. Furthermore, the authors have studied strengths and weaknesses of existing or emerging solutions.
Heterologous Rhamnolipid Biosynthesis: Advantages, Challenges, and the Opportunity to Produce Tailor-Made Rhamnolipids

The first heterologous expression of genes responsible for the production of rhamnolipids was already implemented in the mid-1990s during the functional identification of the rhlAB operon. This was the starting shot for multiple approaches to establish the rhamnolipid biosynthesis in different host organisms. Since most of the native rhamnolipid producing organisms are human or plant pathogens, the intention for these ventures was the establishment of non-pathogenic organisms as heterologous host for the production of rhamnolipids. The pathogenicity of producing organisms is one of the bottlenecks for applications of rhamnolipids in many industrial products especially foods and cosmetics. The further advantage of heterologous rhamnolipid production is the circumvention of the complex regulatory network, which regulates the rhamnolipid biosynthesis in wild type production strains. Furthermore, a suitable host with an optimal genetic background to provide sufficient amounts of educts allows the production of tailor-made rhamnolipids each with its specific physico-chemical properties depending on the contained numbers of rhamnose sugar residues and the numbers, chain length and saturation degree of 3-hydroxyfatty acids. The heterologous expression of rhl genes can also enable the utilization of unusual carbon sources for the production of rhamnolipids depending on the host organism.
Soft-Jig-Driven Assembly Operations

To design a general-purpose assembly robot system that can handle objects of various shapes, we propose a soft jig that fits to the shapes of assembly parts. The functionality of the soft jig is based on a jamming gripper developed in the field of soft robotics. The soft jig has a bag covered with a malleable silicone membrane, which has high friction, elongation, and contraction rates for keeping parts fixed. The bag is filled with glass beads to achieve a jamming transition. We propose a method to configure parts-fixing on the soft jig based on contact relations, reachable directions, and the center of gravity of the parts that are fixed on the jig. The usability of the soft jig was evaluated in terms of the fixing performance and versatility for various shapes and postures of parts.
Complete chloroplast genome of Pluchea indica (L.) Less. (Asteraceae) and its phylogenetic analysis

Abstract This study presents the chloroplast genome of Pluchea indica(L.) Less, Asteraceae, one wide distributed species of mangrove associates plant in China, which was assembled and analyzed by de novo assembly using whole-genome sequencing data. The accessing NC_015621 was used as a reference sequence in this study. The size of the complete chloroplast genome was found to be 152,298 bp in length, comprising a large single copy region (LSC) of 84,127bp, a small single copy region (SSC) 18,068 bp, and inverted repeat regions (IRS) of 25,051bp. A total of 128 genes, including 84 protein-coding genes, 36 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 17 genes occur in IRS, containing six protein-coding genes, seven tRNA genes and four rRNA genes. The GC content of P. indica is 37.49%. The phylogenetic analysis with four Asterids species and five other species revealed that P. indica was clusted with Ageratina adenophora.
Viral Related Tools against SARS-CoV-2

At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.
Morphological Characterization, Evaluation and Selection of Hibiscus ( Hibiscus rosa-sinensis L) Hybrids

Fifty-seven hibiscus hybrid progenies from different crosses were characterized and evaluated for morphological traits to select hybrids with unique color and form. A total of 14 progenies with the following pedigrees were selected: 22xDT-9, (LLxEFA)xGC-2, (LLxEFA)xGC-8, DSxGC-7, 20xGC-5, (GCxBGB)xHP-4, GCxDS-4, ABAxMDM-1, ABAxMDM-3, 23xGC-2, CVxNB-1, CVxNB-2, CVxMP-4 and CVxNB-6. Phenotypic data were analyzed for principal component analysis (PCA) and agglomerative cluster analysis. Correlation using PCA revealed signif icant positive association between flower size and leaf size, and between petiole length and leaf size. PCA depicted three major PCs with eigenvalue >1 contributing 78% of the total cumulative variability among different hybrids. The PC-I showed positive factor loadings for all the traits. The contribution of flower size, leaf size and style length was highest in PC-I. Cluster analysis grouped the 57 hybrids into f ive clusters. Cluster-I had the highest number of members (16), consisting of yellow-orange and purple flowers with a mean size of 131.09 mm. Cluster-II had 15 members, possessing white and red-purple hybrids with a mean size of 140.54 mm. Cluster-III was composed of f ive yellow members with a mean size of 131.12 mm. Cluster-IV had 13 members, comprising yellow and yellow-orange hybrids whose flowers are small and have a mean size of 115.20 mm. Cluster- V consists of eight red- and red-purple-colored hybrids with mean size of 130.21 mm. The study revealed that hybrids with large flowers and longer petioles tend to have wider leaves, and these results were in agreement with the dendrogram groupings of the 57 hybrids. Keywords: Agglomerate cluster analysis, Hibiscus rosa-sinensis L. , hybrids, principal component analysis
Identifying Novel Molecular Biomarkers and Therapeutic Targets for Prostate Cancer

Author(s): Shenoy, Tanushree | Advisor(s): Wu, Hong; Witte, Owen | Abstract: Prostate cancer is the most common malignancy in males, and the third leading cause of male cancer-related death in the Western world. Although most prostate cancers are diagnosed at an early and treatable stages, predicting the outcome of prostate cancer progression and treatment has proven to be challenging because of the heterogeneous nature of the disease. Recent cancer genome studies have identified novel alterations as well as the potential actionable targets. Among these novel alterations is chromodomain helicase DNA-binding protein 1 (CHD1). CHD1 deletion occurs in as many as 20% of prostate cancers and may be associated with genomic instability. To validate the function of CHD1 in prostate cancer in vivo, we created the Pb-Cre+;Chd1L/L mouse model, whereby Chd1 is deleted in mouse prostate epithelial cells, and engineered CHD1-deleted prostate cancer cell lines. We found that while Chd1 deletion alone does not induce prostate cancer in vivo, it confers DNA damage sensitivity and homologous recombination impairment, making CHD1-deficient cells sensitive to PARP inhibitors and Platinum-based drugs. A metastatic castrate-resistant prostate cancer patient whose tumors had CHD1 deletion was responsive to carboplatin, suggesting that CHD1 status may be a biomarker for PARP inhibitor and platinum treatment responsiveness.