Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial cytochrome oxidase (COI) sequence-based identification of pod borer of Thylacoptila sp. AA isolated from Senna alata (L.) Roxb. for the first time in India

Abstract In the present study, two pod borer larvae were found to damage pods of the host plant Senna alata. As pods (seeds) are commercially important, it prompted the investigators to find out the adult of pod borer larvae by molecular sequencing and reported in this article for the first time from S. alata. Successful amplification was achieved for chloroplast DNA isolated from leaves of host plant S. alata and tissue DNA from unknown larvae and sequenced. The sequences were submitted to NCBI domain, and the taxonomic position of host plant of pod borer larvae was confirmed as S. alata (L.) Roxb. Of the two sequences belonging to pod borer larvae, specimen 1 (S1) matched with already available three sequences of Thylacoptila sp. AA. But, specimen 2 (S2) showed significant variation in its genetic distance in Neighborhood Joining tree and maximum likelihood tree; these factors imply that specimen 2 (S2) is distinct from Thylacoptila sp. AA. Therefore, it is reported that specimen 2 may be represented as Thylacoptila sp. BB where in BB indicates variant from other available sequences. Nonetheless, reporting species of Thylacoptila as insect pest in pods of S. alata is an important contribution to the annals of insect–pest–plant interaction more importantly in medicinally important plant species S. alata.
T cell engineered with a novel nanobody‐based chimeric antigen receptor against VEGFR2 as a candidate for tumor immunotherapy

Solid tumors that are responsible for more than 85% of cancer death cases need angiogenesis for their growth and metastasis. Among antiangiogenic therapies, targeting the vascular endothelial growth factor receptor 2 (VEGFR2) that is over‐expressed on tumor vasculatures has been a promising strategy. In this study, we developed a second generation nanobody (VHH)‐based CAR T cell targeting VEGFR2‐expressing tumor cells. The CAR T cell was developed by linking the anti‐VEGFR2 VHH to a spacer, and signaling domains of CD28 and CD3 ζ. The T cells were activated with anti‐CD3 plus rIL‐2 and electroporated with a plasmid encoding the CAR construct. The expression of activation markers, CD69 and CD25, on CAR T cells upon coculturing with VEGFR2‐expressing cells were 41% and 48%, and the IL‐2 and IFN‐γ production were 470 pg/mL and 360 pg/mL, respectively. The expression of degranulation marker, CD107a, was 30% and the cytotoxic activity of the CAR T cells reached to more than 30% with E:T ratio of 9:1. The anti‐VEGFR2 CAR but not mock T cells mediated specific lysis of 293‐KDR cells expressing human VEGFR2 and might be considered as a candidate for adoptive T‐cell immunotherapy of solid tumors. © 2019 IUBMB Life, 71(9):1259–1267, 2019
A framework to measure the wildness of managed large vertebrate populations

As landscapes continue to fall under human influence through habitat loss and fragmentation, fencing is increasingly being used to mitigate anthropogenic threats and enhance the commercial value of wildlife. Subsequent intensification of management potentially erodes wildness by disembodying populations from landscape‐level processes, thereby disconnecting species from natural selection. Tools are needed to measure the degree to which populations of large vertebrate species in formally protected and privately owned wildlife areas are self‐sustaining and free to adapt. We devised a framework to measure such wildness based on 6 attributes relating to the evolutionary and ecological dynamics of vertebrates (space, disease and parasite resistance, exposure to predation, exposure to limitations and fluctuations of food and water supply, and reproduction). For each attribute, we set empirical, species‐specific thresholds between 5 wildness states based on quantifiable management interventions. We analysed data from 205 private wildlife properties with management objectives spanning ecotourism to consumptive utilization to test the framework on 6 herbivore species representing a range of conservation statuses and commercial values. Wildness scores among species differed significantly, and the proportion of populations identified as wild ranged from 12% to 84%, which indicates the tool detected site‐scale differences both among populations of different species and populations of the same species under different management regimes. By quantifying wildness, this framework provides practitioners with standardized measurement units that link biodiversity with the sustainable use of wildlife. Applications include informing species management plans at local scales; standardizing the inclusion of managed populations in red‐list assessments; and providing a platform for certification and regulation of wildlife‐based economies. Applying this framework may help embed wildness as a normative value in policy and mitigate the shifting baseline of what it means to truly conserve a species.
The Grass is Greener on the Other Side: Understanding the Effects of Green Spaces on Twitter User Sentiments

Green spaces are believed to improve the well-being of users in urban areas. While there are urban research exploring the emotional benefits of green spaces, these works are based on user surveys and case studies, which are typically small in scale, intrusive, time-intensive and costly. In contrast to earlier works, we utilize a non-intrusive methodology to understand green space effects at large-scale and in greater detail, via digital traces left by Twitter users. Using this methodology, we perform an empirical study on the effects of green spaces on user sentiments and emotions in Melbourne, Australia and our main findings are: (i) tweets in green spaces evoke more positive and less negative emotions, compared to those in urban areas; (ii) each season affects various emotion types differently; (iii) there are interesting changes in sentiments based on the hour, day and month that a tweet was posted; and (iv) negative sentiments are typically associated with large transport infrastructures such as train interchanges, major road junctions and railway tracks. The novelty of our study is the combination of psychological theory, alongside data collection and analysis techniques on a large-scale Twitter dataset, which overcomes the limitations of traditional methods in urban research.
Psoralen accelerates bone fracture healing by activating both osteoclasts and osteoblasts

Bone fracture healing is a complex, dynamic process that involves various cell types, with osteoclasts and osteoblasts playing indispensable roles. In this study, we found that psoralen, the main active ingredient in Psoralea corylifolia L. fruit extract, enhanced bone fracture healing through activation of osteoclast and osteoblast activity via the ERK signaling pathway. In detail, psoralen promoted receptor activator of nuclear factor‐κB ligand‐induced osteoclastogenesis, mRNA expression of osteoclast‐specific genes, and osteoclastic bone resorption in primary bone marrow‐derived macrophages. Meanwhile, psoralen induced osteogenic differentiation by promoting the mRNA expression of the osteoblast differentiation markers alkaline phosphatase, runt‐related transcription factor 2, osterix, and osteocalcin. At the molecular level, psoralen preferentially activated ERK1/2 but not JNK or p38 MAPKs. Further experiments revealed that psoralen‐induced osteoclast and osteoblast differentiation was abrogated by a specific inhibitor of phosphorylated ERK. In addition, psoralen accelerated bone fracture healing in a rat tibial fracture model, and the numbers of osteoclasts and osteoblasts were increased in psoralen‐treated fracture callus. Taken together, our findings indicate that psoralen accelerates bone fracture healing through activation of osteoclasts and osteoblasts via ERK signaling and has potential as a novel drug in the orthopedic clinic for the treatment of bone fractures. —Zhang, T. , Han, W. , Zhao, K. , Yang, W. , Lu, X. , Jia, Y. , Qin, A. , Qian, Y. Psoralen accelerates bone fracture healing by activating both osteoclasts and osteoblasts. FASEB J. 33, 5399–5410 (2019). www.fasebj. org
Prognostic Significance of the C-Reactive Protein-to-Albumin Ratio in Patients With Metastatic Colorectal Cancer Treated With Trifluridine/Thymidine Phosphorylase Inhibitor as Later-line Chemotherapy

Background/Aim: New drugs for metastatic colorectal cancer (mCRC) have been recently developed for use in later-line chemotherapy and have contributed to further prolongation of the survival of patients. However, in later-line chemotherapy, treatment failure may lead to discontinuation of chemotherapy and the transition to best supportive care. Therefore, a biomarker able to predict the effects of later-line chemotherapy is required. The C-reactive protein-to-albumin ratio (CAR), which is an inflammatory marker, has been reported to correlate with therapeutic outcome in patients with mCRC who underwent first-line chemotherapy. However, the significance of the CAR as a marker for predicting the chemotherapeutic outcome in patients with mCRC treated with later-line chemotherapy is unknown. Patients and Methods: We retrospectively reviewed the medical records of 40 patients with mCRC who were treated with trifluridine/thymidine phosphorylase inhibitor (FTD/TPI) as a later-line chemotherapy. The CAR was calculated from the blood samples obtained within 1 week before the initiation of FTD/TPI by dividing the serum C-reactive protein level by the serum albumin level. Results: According to the receiver operating characteristic curve analysis, we set 0.122 as the CAR cut-off, and patients were classified into groups with high or low CAR. The low-CAR group had a significantly higher disease control rate than the high-CAR group. The progression-free and overall survival rates were significantly better in the low-CAR group than in the high-CAR group. A high-CAR was associated with a greater number of prior regimens, higher serum lactate dehydrogenase level and more organs with metastases, considered to be correlated with the rate of disease progression. However, no significant differences were observed in the incidence of grade 3 or more adverse events, the relative dose intensity, or the rate of discontinuing chemotherapy between the two groups. Conclusion: The CAR may be a useful indicator for predicting the chemotherapeutic outcome in patients with mCRC treated with FTD/TPI as a late-line chemotherapy. The correlation between a high-CAR and poor prognosis was presumed to be due to the rate of cancer growth and increased resistance to chemotherapy rather than an insufficient dose of the drug.
The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

It has been long thought that RNA Polymerase (Pol) II transcriptional regulation does not operate in trypanosomes. However, recent reports have suggested that these organisms could regulate RNA Pol II transcription by epigenetic mechanisms. In this paper, we investigated the role of TbRRM1 in transcriptional regulation of RNA Pol II‐dependent genes by focusing both in genes located in a particular polycistronic transcription unit (PTU) and in the monocistronic units of the SL‐RNA genes. We showed that TbRRM1 is recruited throughout the PTU, with a higher presence on genes than intergenic regions. However, its depletion leads both to the decrease of nascent RNA and to chromatin compaction only of regions located distal to the main transcription start site. These findings suggest that TbRRM1 facilitates the RNA Pol II transcriptional elongation step by collaborating to maintain an open chromatin state in particular regions of the genome. Interestingly, the SL‐RNA genes do not recruit TbRRM1 and, after TbRRM1 knockdown, nascent SL‐RNAs accumulate while the chromatin state of these regions remains unchanged. Although it was previously suggested that TbRRM1 could regulate RNA Pol II‐driven genes, we provide here the first experimental evidence which involves TbRRM1 to transcriptional regulation.
Mutational analysis of a catalytically important loop containing active site and substrate-binding site in Escherichia coli phytase AppA

ABSTRACT A phytase from Escherichia coli, AppA, has been the target of protein engineering to reduce the amount of undigested phosphates from livestock manure by making phosphorous from phytic acid available as a nutrient. To understand the contribution of each amino acid in the active site loop to the AppA activity, alanine and glycine scanning mutagenesis was undertaken. The results of phytase activity assay demonstrated loss of activity by mutations at charged residues within the conserved motif, supporting their importance in catalytic activity. In contrast, both conserved, non-polar residues and non-conserved residues tended to be tolerant to Ala and/or Gly mutations. Correlation analyses of chemical/structural characteristics of each mutation site against mutant activity revealed that the loop residues located closer to the substrate have greater contribution to the activity of AppA. These results may be useful in efficiently engineering AppA to improve its catalytic activity. Abbreviations: AppA: pH 2.5 acid phosphatase; CSU: contacts of structural units; HAPs: histidine acid phosphatases; SASA: solvent accessible surface area; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SSM: site-saturation mutagenesis; WT: wild type Graphical Abstract Alanine and glycine scanning mutagenesis revealed contribution of each amino acid in the active site loop to the activity of E. coli phytase AppA.
PLK1 plays dual roles in centralspindlin regulation during cytokinesis

Cytokinesis starts in anaphase with the formation of an actomyosin-based contractile ring at the equatorial cortex, which is governed by the local activation of the small GTPase RhoA. Here we delineated the contributions of PLK1 and Aurora B to RhoA activation and cytokinesis initiation in human cells. Knock-down of PRC1, which disrupts the spindle midzone, revealed the existence of two pathways that can initiate cleavage furrow ingression. One pathway depends on a well-organized spindle midzone and PLK1, while the other depends on Aurora B activity and centralspindlin oligomerization at the equatorial cortex and can operate independently of PLK1. We further show that PLK1 inhibition sequesters centralspindlin onto the spindle midzone making it unavailable for Aurora B-dependent oligomerization at the equatorial cortex. We propose that PLK1 activity promotes the release of centralspindlin from the spindle midzone through inhibition of PRC1, allowing centralspindlin to function as a regulator of spindle midzone formation and as an activator of RhoA at the equatorial cortex.
Exogenous melatonin improves lead tolerance of bermudagrass through modulation of the antioxidant defense system

Abstract Lead (Pb) is a major anthropogenic contaminant that can be devastating on both animals and plants. It is essential to develop methods to decrease the Pb contaminant in soil by phytoremediation using plants that are tolerance to Pb. In this study, we investigated the tolerance of bermudagrass (Cynodon dactylon (L.) Pers. ) and the role of exogenous application of melatonin for improving its tolerance to Pb. Bermudagrass growing in soil treated with Pb at 1,000 or 2,000 mg kg−1 were assessed with or without melatonin pretreatment at various concentrations. Under Pb stresses, bermudagrass plants showed stunted growth and increased cellular oxidative stress. Pre-treating bermudagrass plants with melatonin at 20 or 100 μM significantly increased the activities of antioxidant enzymes (superoxide dismutase, catalase, peroxidase, ascorbate peroxidase, and glutathione reductase) and the contents of non-enzymatic antioxidants (ascorbic acid and glutathione), and decreased reactive oxygen species (hydrogen peroxide, superoxide), and ultimately reduced membrane lipid peroxidation and permeability. These changes contributed to improvements in the water status, photosynthetic pigment synthesis, and biomass production of bermudagrass under Pb stresses. Our study provides the first evidence that melatonin may be a promising tool for enhancing Pb tolerance and phytoremediation potential of bermudagrass.
Seasonal Variations in the Achievement of Guideline Targets for HbA1c, Blood Pressure, and Cholesterol Among Patients With Type 2 Diabetes: A Nationwide Population-Based Study (ABC Study: JDDM49)

OBJECTIVE Precise monthly achievement rates for reaching guideline targets for HbA1c, blood pressure (BP), and lipid levels remain unknown. We evaluated achievement rates on a monthly basis in persons with type 2 diabetes mellitus (T2DM) and explored related factors. RESEARCH DESIGN AND METHODS This retrospective study initially analyzed data on 104,601 persons with T2DM throughout Japan. Patients whose HbA1c, BP, and LDL cholesterol were measured ≥12 times during a 24-month period were included. We evaluated monthly achievement rates. Achieved targets were defined as HbA1c <7%, BP <130/80 mmHg, and LDL cholesterol <100 mg/dL. Achievement of all targets was expressed as the “all ABC achievement. ” RESULTS A total of 4,678 patients were analyzed. The achievement rates of all ABC, HbA1c, BP, and LDL cholesterol were lowest in winter, with those for systolic BP (SBP) being particularly low (all ABC, summer 15.6%, winter 9.6%; HbA1c, 53.1%, 48.9%; SBP, 56.6%, 40.9%; LDL cholesterol, 50.8%, 47.2%). In winter, age ≥65 years (odds ratio 0.47 [95% CI 0.34–0.63]) was independently related to decreased achievement rates for SBP, BMI ≥25 kg/m2 (BMI 25–30 kg/m2, 0.45 [0.29–0.70]; BMI ≥30 kg/m2, 0.35 [0.22–0.57]), and diabetes duration ≥10 years (0.53 [0.37–0.76]) were independently related to lower achievement rates for HbA1c. Insulin use and sulfonylurea use were independently associated with the decreased all ABC achievement rates in both summer and winter. CONCLUSIONS The all ABC achievement rate for guideline targets changed on a monthly basis. Seasonal variations in the all ABC achievement rate should be considered when managing T2DM in ordinary clinical practices.
Dopaminergic Mechanisms Underlying Normal Variation in Trait Anxiety

Trait anxiety has been associated with altered activity within corticolimbic pathways connecting the amygdala and rostral anterior cingulate cortex (rACC), which receive rich dopaminergic input. Though the popular culture uses the term “chemical imbalance” to describe the pathophysiology of psychiatric conditions such as anxiety disorders, we know little about how individual differences in human dopamine neurochemistry are related to variation in anxiety and activity within corticolimbic circuits. We addressed this issue by examining interindividual variability in dopamine release at rest using [11C]raclopride positron emission tomography (PET), functional connectivity between amygdala and rACC using resting-state functional magnetic resonance imaging (fMRI), and trait anxiety measures in healthy adult male and female humans. To measure endogenous dopamine release, we collected two [11C]raclopride PET scans per participant. We contrasted baseline [11C]raclopride D2/3 receptor binding and D2/3 receptor binding following oral methylphenidate administration. Methylphenidate blocks the dopamine transporter, which increases extracellular dopamine and leads to reduced [11C]raclopride D2/3 receptor binding via competitive displacement. We found that individuals with higher dopamine release in the amygdala and rACC self-reported lower trait anxiety. Lower trait anxiety was also associated with reduced rACC–amygdala functional connectivity at baseline. Further, functional connectivity showed a modest negative relationship with dopamine release such that reduced rACC–amygdala functional connectivity was accompanied by higher levels of dopamine release in these regions. Together, these findings contribute to hypodopaminergic models of anxiety and support the utility of combining fMRI and PET measures of neurochemical function to advance our understanding of basic affective processes in humans. SIGNIFICANCE STATEMENT It is common wisdom that individuals vary in their baseline levels of anxiety. We all have a friend or colleague we know to be more “tightly wound” than others, or, perhaps, we are the ones marveling at others' ability to “just go with the flow. ” Although such observations about individual differences within nonclinical populations are commonplace, the neural mechanisms underlying normal variation in trait anxiety have not been established. Using multimodal brain imaging in humans, this study takes initial steps in linking intrinsic measures of neuromodulator release and functional connectivity within regions implicated in anxiety disorders. Our findings suggest that in healthy adults, higher levels of trait anxiety may arise, at least in part, from reduced dopamine neurotransmission.
A Survey of Techniques for Automatically Sensing the Behavior of a Crowd

Crowd-centric research is receiving increasingly more attention as datasets on crowd behavior are becoming readily available. We have come to a point where many of the models on pedestrian analytics introduced in the last decade, which have mostly not been validated, can now be tested using real-world datasets. In this survey, we concentrate exclusively on automatically gathering such datasets, which we refer to as sensing the behavior of pedestrians. We roughly distinguish two approaches: one that requires users to explicitly use local applications and wearables, and one that scans the presence of handheld devices such as smartphones. We come to the conclusion that despite the numerous reports in popular media, relatively few groups have been looking into practical solutions for sensing pedestrian behavior. Moreover, we find that much work is still needed, in particular when it comes to combining privacy, transparency, scalability, and ease of deployment. We report on over 90 relevant articles and discuss and compare in detail 30 reports on sensing pedestrian behavior.