jimnoneill/paper-to-field-training huggingface dataset:
How tissue damage MET metabolism: Regulation of the systemic damage response

Living organisms experience tissue damage from both, the surrounding environment and from inside their bodies. Tissue repair/regeneration is triggered by local tissue injury to restore an injured, or lost, part of the body. Tissue damage results in a series of responses, not only locally but also systemically in distant tissues. In our recent publication, we established a "dual system" that induces spatiotemporal tissue damage simultaneously with gene manipulation in surrounding tissues. With this system, we demonstrated that appropriate regulation of methionine metabolism in the fat body is required for tissue repair in Drosophila wing discs, thus highlighting the importance of systemic damage response (SDR) in tissue repair. This "Extra View" aims to discuss our recent reports that propose methionine metabolism to be an essential part of SDR, together with related topics in several model organisms.

Topic: Neurobiology and Insect Physiology Research
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
SuperDARN data in netCDF format (2007-Sep)

2007-Sep SuperDARN radar data in netCDF format. These files were produced using versions 2.5 and 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.The RST is available here: https://github.com/SuperDARN/rstThe research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation. Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications. A brief statement on how to acknowledge use of SuperDARN data is provided below.Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication. A listing of radars and PIs with contact information can be found here: (SuperDARN Radar Overview)<strong>Recommended form of acknowledgement for the use of SuperDARN data:</strong>'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'

Topic: Medical Imaging Techniques and Applications
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
Briefing package for the Yucca Flat pre-emptive review, including overview, UZ model, SZ volcanics model and summary and conclusions sections

Much progress has been made in the last several years in modeling radionuclide transport from tests conducted both in the unsaturated zone and saturated volcanic rocks of Yucca Flat, Nevada. The presentations to the DOE NNSA pre-emptive review panel contained herein document the progress to date, and discuss preliminary conclusions regarding the present and future extents of contamination resulting from past nuclear tests. The presentations also discuss possible strategies for addressing uncertainty in the model results.

Topic: Radioactive contamination and transfer
Subfield: Global and Planetary Change
Field: Environmental Science
Domain: Physical Sciences
ON THE BIOLOGICAL SIGNIFICANCE OF PHOSPHATE ANALYSIS; COMPARISON OF STANDARD AND NEW METHODS WITH A BIOASSAY1

The phosphate concentration of 13 waters was measured by several chemical procedures including a new six‐second method and a solvent extraction procedure. Results were compared with estimates from an algal bioassay procedure to determine which method most accurately measured biologically available phosphorus. Where estimates obtained by these methods differed appreciably, arsenate interference rather than hydrolysis of organic phosphate compounds accounted for the discrepancies. The new extraction method proved less sensitive to arsenate interference than that of Stephens and gave results in agreement with the bioassay.

Topic: Soil and Water Nutrient Dynamics
Subfield: Environmental Chemistry
Field: Environmental Science
Domain: Physical Sciences
[Camptothecin and derivatives: a new class of antitumor agents].

Camptothecin (CPT), an alkaloid isolated from the stem wood and bark of Camptotheca acuminata native to China, was discovered in the early 60's after a systematic screening of natural products by the National Cancer Institute (NCI). This new anticancer agent displays an unique mechanism of action as it inhibits intranuclear enzyme topoisomerase 1, involved in DNA replication. CPT is poorly water soluble and causes severe and unpredictable toxicities such as haemorrhagic cystitis and diarrhea; for therefore reason, a number of analogues have been synthetized in a attempt to define the features of the molecule that are essential for cytotoxicity and to produce derivatives with increased solubility. Clinical trials of several soluble molecules are in progress in the different countries: irinotecan, topotecan, 9-AC. Encouraging results are observed against solid tumors. Irinotecan was recently commercialized in France. It is a prodrug; the active metabolite SN-38 showed a good activity in metastatic colorectal adenocarcinoma; the limiting toxicities are myelotoxicity and essentially late diarrhea. However, new studies are needed for state precisely the optimal schedule of administration and association with other chemotherapeutic agents.

Topic: Cancer therapeutics and mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Review of: "Estimating the Fish Stocks of Six Commercial Species in the Middle Madeira River, Southwest Amazon"

Potential competing interests: No potential competing interests to declare.The study discusses the stock assessment of six commercial species in the Madeira River, Southwest Amazon.The topic could be interesting, but the way the authors present their experiment is not sufficient.Although seasonal data in stock assessment gives us a clear picture of stock and is also crucial for fisheries management, I suggested that the authors could make some improvements in their MS by adding recent citations, study background, sampling method, fishing method, fishing gear, environmental characteristics, and seasonal differences (noted during sampling).However, in the discussion section, authors should address their work with the past, present, and future fish stock.

Topic: Fish Biology and Ecology Studies
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Literary Exchanges between Latin America and Spain during the Spanish Civil War

This essay addresses the intellectual and literary relationship between Latin America and Spain during the Spanish Civil War. It is written within the context of translatlantic studies and explores a body of texts which includes press excerpts, chronicles, poems, articles, and other texts that were never published in books by their respective authors. Among them are names like Federico García Lorca, Jorge Luis Borges, Nicolás Guillén, Pablo Neruda, Pablo de la Torriente Brau, Vicente Huidobro, Alejo Carpentier, Alberto Romero, and César Vallejo. Additionally, this essay studies an essential event in the intellectual history of this time: the Congress of Anti-Fascist Writers. The examination of these texts and episodes demonstrates the importance of the Spanish Civil War within the international intellectual community at the time and provides a fuller understanding of the literary output of Latin America between 1936 and 1939. This analysis demonstrates the need to rethink Latin America's literary and cultural boundaries, which extend beyond the geographical borders of countries.

Topic: Comparative Literary Analysis and Criticism
Subfield: Literature and Literary Theory
Field: Arts and Humanities
Domain: Social Sciences
The interplay between media-for-monitoring and media-for-searching: How news media trigger searches and edits in <i>Wikipedia</i>

This study investigates how traditional news media and Internet services have become entangled in recipients’ habits of gathering information on current topics. Push media enable citizens to scan the issue environment while pull media enable them to seek out in-depth information if information needs have been elicited. Furthermore, content quality in many pull media may increase when more users generate content, removing flaws and adding information. We expected that TV and newspaper coverage of an issue will lead to increases in (a) searches for and (b) user edits in related articles in the online encyclopedia Wikipedia. Our findings reliably support the hypotheses, but the extent to which the count of page views increases is highly dependent on the topic at hand and how the search keyword relates to the issue. This matches the predictions of information-seeking theories and the dynamic transactional model of media effects.

Topic: Wikis in Education and Collaboration
Subfield: Communication
Field: Social Sciences
Domain: Social Sciences
The natural history of eosinophilic oesophagitis in the transition from childhood to adulthood

Summary Background Eosinophilic oesophagitis ( EoE ) is a chronic inflammatory condition affecting both children and adults. Little is known about the natural history of EoE in the transition from childhood into adulthood. Aim To determine the prevalence of EoE symptoms and impact of EoE on quality of life among adults diagnosed with EoE during childhood. Methods This is a cross‐sectional study of EoE patients from the Children's Hospital of Philadelphia EoE registry. Patients ≥18 years diagnosed with EoE during childhood were administered validated dysphagia [Mayo Dysphagia Questionnaire ( MDQ )‐30] and Quality of Life ( PAGI ‐ QOL ) questionnaires. Ongoing EoE treatments were ascertained. Results A total of 140 EoE patients ≥18 years were identified; 53 completed all questions. Only 6 (11%) subjects had positive ( n = 2) or indeterminate ( n = 4) dysphagia scores. However, of 47 patients with negative scores, 18 (37%) reported ongoing difficulty swallowing. The mean PAGI ‐ QOL score was 4.58/5. The dietary dimension score was 3.73/5. Current pharmacological EoE treatments were topical steroids (3/53) and interleukin‐5 antagonists (3/53). Additionally, 26/53 (49%) were on PPI therapy and 40/53 (76%) were following allergy directed diets. Conclusions The majority of young adults diagnosed with EoE during childhood continue to require pharmacological treatment and/or dietary modification for EoE . A substantial proportion of this population experiences ongoing swallowing difficulties that a standard dysphagia questionnaire fails to capture. Dietary quality of life, but not total quality of life, appears to be adversely affected. These data suggest that EoE diagnosed during childhood remains a significant medical issue during early adulthood, and that better EoE symptom measurement instruments are needed.

Topic: Eosinophilic Esophagitis
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
On-chip test vector generation and downsampling for testing RSFQ circuits

Abstract An on-chip high-frequency testing method for rapid single flux quantum circuits is proposed. This method employs test vectors based on pseudo-random sequences created by an on-chip high-frequency clock generator (CG) and a linear feedback shift register with parallel outputs (LSPO). Downsamplers (DSMs) at the outputs of a circuit under test (CUT) decimate the CUT output data so that high-frequency testing can be performed at sufficiently low data rates between the CUT and room-temperature electronics. The proposed testing can continuously test the circuit at high frequency with low-cost instruments. All of the critical subsystems, including LSPO, CG, and DSM, were designed, fabricated, and successfully tested. We validated proper operation at up to 40 GHz, confirming the concept and execution.

Topic: Quantum and electron transport phenomena
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
The Miracle of Microfinance? Evidence from a Randomized Evaluation

This paper reports results from the randomized evaluation of a group-lending microcredit program in Hyderabad, India. A lender worked in 52 randomly selected neighborhoods, leading to an 8.4 percentage point increase in takeup of microcredit. Small business investment and profits of preexisting businesses increased, but consumption did not significantly increase. Durable goods expenditure increased, while “temptation goods” expenditure declined. We found no significant changes in health, education, or women's empowerment. Two years later, after control areas had gained access to microcredit but households in treatment area had borrowed for longer and in larger amounts, very few significant differences persist. (JEL G21, G31, O16, O12, L25, I38)

Topic: Microfinance and Financial Inclusion
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Exercise Training Reduces Neointimal Growth and Stabilizes Vascular Lesions Developing After Injury in Apolipoprotein E–Deficient Mice

Background— Population-based studies have shown that exercise reduces cardiovascular morbidity and mortality. However, it is unknown whether these effects are solely a result of risk factor modification or whether exercise directly affects the homeostasis of the vessel wall. Methods and Results— We subjected 19-week-old apolipoprotein E (apoE)–knockout mice (apoE −/− ; n=25) to a 6-week training program on a motorized treadmill. The control group consisted of 17 sedentary mice. After 3 weeks in the program, training and sedentary mice underwent carotid artery injury with ferric chloride. Training was then resumed for another 3 weeks. Exercise did not change body weight or lipid levels in apoE −/− mice but resulted in upregulated expression of nitric oxide synthase in the endothelium. Physical training did not significantly affect the thrombotic response to injury. However, morphometric analysis of vessels harvested 3 weeks after injury showed that neointima formation was reduced in the exercising group. This resulted in a lower intima/media ratio (0.29±0.03 versus 0.41±0.03 in sedentary mice; P =0.008) and less luminal stenosis (21±2.7% versus 33±2.3%; P =0.003). Importantly, exercise reduced the number of Mac-3–positive, oxidized LDL-containing macrophages in the vessel wall while increasing the content in collagen fibers (14.1±0.9% versus 4.8±0.8%; P &lt;0.001). Plasminogen activator inhibitor-1, tissue factor, and fibrinogen were all significantly reduced in the lesions of trained mice. Conclusions— In the apoE −/− mouse, exercise training reduces neointimal growth and stabilizes vascular lesions after injury. These effects appear to be at least partly independent of changes in lipid levels or the initial thrombotic response to injury.

Topic: Cardiovascular Health and Disease Prevention
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
The Regulation and Function of the L-Type Amino Acid Transporter 1 (LAT1) in Cancer

The progression of cancer is associated with increases in amino acid uptake by cancer cells. Upon their entry into cells through specific transporters, exogenous amino acids are used to synthesize proteins, nucleic acids and lipids and to generate ATP. The essential amino acid leucine is also important for maintaining cancer-associated signaling pathways. By upregulating amino acid transporters, cancer cells gain greater access to exogenous amino acids to support chronic proliferation, maintain metabolic pathways, and to enhance certain signal transduction pathways. Suppressing cancer growth by targeting amino acid transporters will require an in-depth understanding of how cancer cells acquire amino acids, in particular, the transporters involved and which cancer pathways are most sensitive to amino acid deprivation. L-Type Amino Acid Transporter 1 (LAT1) mediates the uptake of essential amino acids and its expression is upregulated during the progression of several cancers. We will review the upstream regulators of LAT1 and the downstream effects caused by the overexpression of LAT1 in cancer cells.

Topic: Amino Acid Enzymes and Metabolism
Subfield: Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Case Report: Pancytopenia as an indicator for lysosomal storage disease (Gaucher's Disease)

<ns3:p><ns3:bold>Introduction: </ns3:bold>Lysosomal storage disorders are a rare group of diseases with genetic origin in which Gaucher Disease (GD) stands out as the most frequent. GD type 1 is the most common form of this condition, and patients with this pathology present with unexplained cytopenias, in addition to hepatosplenomegaly, bone involvement, and in other cases neurological disorders. A case of a patient is presented, whose results showed thrombocytopenia and leukopenia in addition to hepatosplenomegaly. In Latin America, there are very few reported cases of this clinical entity, and information on this disease is very limited.</ns3:p><ns3:p> <ns3:bold>Case</ns3:bold>: We present a case of a patient diagnosed with GD, who presented with thrombocytopenia and leukopenia in addition to hepatosplenomegaly, with the aim of emphasizing the importance of early recognition of this pathology, especially in patients with unexplained cytopenia’s or hepatosplenomegaly’s. In suspicion of GD, enzymatic quantification of β-glucocerebrosidase was performed, showing its deficit in addition to alteration in the <ns3:italic>GBA</ns3:italic> gene. Unfortunately, enzymatic replacement could not be done because the Cerazyme (imiglucerase for injection) is not available in Ecuador. Nevertheless, the patient was treated with analgesic (1g of paracetamol generally three times a day) and vitamin supplements (Dayamineral). Currently the patient is waiting for transfer to a foreign institution; she continues with bicytopenia and hepatosplenomegaly, her conditions are expected to be remit once the enzymatic treatment has been administered. </ns3:p><ns3:p> <ns3:bold>Conclusion</ns3:bold>: We believe that the timely recognition of this disease will allow the initiation of enzymatic replacement therapy in an effective manner, in order to reduce morbidity and improve the clinical aspects of the patient.</ns3:p>

Topic: Lysosomal Storage Disorders Research
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Diazoxide induces delayed preconditioning against transient focal cerebral ischemia in Rats

Diazoxide is the prototypical opener of mitochondrial ATP‐sensitive potassium channels (mitoK ATP ) and protects neurons in vivo and in vitro against chemical and anoxic stresses. While we have previously shown that diazoxide administration induces delayed protection of the blood‐brain barrier against ischemic damage in rats ( Brain Res. 2005; 1051 :–80), we did not examine whether diazoxide limits infarct volume in stroke. The purpose of this study was to determine whether diazoxide promotes delayed preconditioning against experimental strokes. We tested the delayed effect of Diazoxide on 90 min middle cerebral artery occlusion (MCAO) in male Wistar rats. Diazoxide (10mg/kg) was injected 24 hours before MCAO intraperitonealy. Infarct volumes were measured 72 hr after reperfusion. Treatment with diazoxide 24 hr before the onset of ischemia exhibited a 28 % reduction (235.2±7.1 vs. 169.2± 22.5mm 3 ) and a 32 % reduction (179.6±2.0 vs.122.0±18.0mm 3 ) in infarct volumes for total brain and cortex, respectively. These findings are consistent with the assumption that delayed preconditioning is produced by the activation of mitoK ATP in the rat brain. Supported by NIH grants (HL‐30260, HL‐46558, HL‐50587, DK‐62372) for D. W. Busija.

Topic: Cardiac Ischemia and Reperfusion
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
TOMOMAN: Streamlining Cryo-electron Tomography and Subtomogram Averaging Workflows Using TOMOgram MANager

Cryo-electron tomography coupled with subtomogram averaging is becoming the preferred tool for investigating cellular and macromolecular structures in their native or near-native environments.Despite this, the process of resolving these structures, starting from the stage of data acquisition to structure determination, is becoming progressively more complex with an increasing number of packages for each step.These packages are developed independently with different design philosophies and input types, making it complicated to interface with one another to form a cohesive pipeline.Tomogram Manager (TOMOMAN) is a MATLAB-based modular package developed to reduce this complexity and streamline the process of resolving structures by subtomogram averaging (Figure 1).TOMOMAN achieves this by maintaining the essential metadata in a MATLAB structure format for all tilt-series in the dataset.The core of TOMOMAN package comprises wrapper scripts for each step of preprocessing from the raw tilt series data to reconstructed tomographic volumes.For motion correction of frames from direct detection devices, TOMOMAN offers wrappers for MotionCor2 and a modified version of RELION's implementation of MotionCor.Resulting tilt stacks are then cleaned in a supervised fashion to eliminate any obvious outliers (contamination, run-away defocus, etc.).For CTF estimation, TOMOMAN offers a choice of CTFFIND4, gCTF, and our own implementation of CTF estimation for tilted data, tiltCTF.For subsequent alignment of these stacks and tomogram reconstruction, TOMOMAN offers a multitude of options to a user.While there are wrappers to streamline the tilt series-alignment using IMOD, we have also implemented wrapper scripts for recently developed AreTomo package for automated tilt series alignment.Reconstruction of uncorrected or CTF corrected tomogram can be performed using wrapper scripts for IMOD or NovaCTF.resulting tomograms and associated metadata are readily exportable for template matching, subtomogram averaging, and classification in STOPGAP.Although, TOMOMAN was initially developed in conjunction with STOPGAP, TOMOMAN projects can also be directly exported to WARP/RELION3/M workflow as well as newly developed RELION4 tomography workflow for subtomogram averaging.Furthermore, there are scripts to import particles from RELION to STOPGAP, facilitating the interoperability.In addition, TOMOMAN also offers a set of wrapper scripts to refine the initial tilt series alignment using either IMOD's local alignments or TomoAlign's motion aware reconstruction by tracking subvolume fiducials in STOPGAP_refine.

Topic: Advanced Electron Microscopy Techniques and Applications
Subfield: Structural Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Proton-transporting Heliorhodopsin from Coccolithovirus

私たちは円石藻に感染する巨大ウイルスの持つヘリオロドプシンが光でプロトンを輸送するイオンチャネルであることを世界で初めて明らかにした.本稿ではヘリオロドプシンの発見から機能の解明,さらにイオン透過のメカニズムについて紹介する.円石藻ウイルスは光とヘリオロドプシンを利用してブルーム(白潮)の消失に関与している可能性も考えられ,ヘリオロドプシンの研究は地球環境の観点からも注目されている.

Topic: Photoreceptor and optogenetics research
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
Bruce Reichenbach. Is Man the Phoenix? A study of Immortality. Pp. 190. (University Press of America1983.) $9.50 - Stanley Krippner (ed.). Advances in Parapsychological Research, vol. 3. Pp. 338. (Plenum Publishing Corporation.) $32.50

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Topic: Paranormal Experiences and Beliefs
Subfield: Social Psychology
Field: Psychology
Domain: Social Sciences