jimnoneill/paper-to-field-training huggingface dataset:
Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Abstract Background Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. Results The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. Conclusions On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research.

Topic: Leptospirosis research and findings
Subfield: Parasitology
Field: Immunology and Microbiology
Domain: Life Sciences
Fully 3D time-dependent simulation of free electron laser within an overmoded rectangular waveguide

Numerical simulation codes are basic tools for designing Free Electron Lasers\n(FELs). This paper describes a numerical method for the time-dependent,\nthree-dimensional simulation of the free electron laser (FEL) using a\nrectangular waveguide within overmoded configuration when the radiation\nwavelength is much shorter than the waveguide cut-off wavelength. Instead of\ndeveloping a new code, the GENESIS simulation code is modified for our purpose.\nThis method presented here can be used for extending the capacity of GENESIS to\ncover this special configuration. The major modification is to apply the metal\nboundary conditions on the field equations in a limited rectangular region and\nthe full Cartesian mesh using the Alternating Direction Implicit (ADI)\nintegration scheme to solve the field equation remains adopted.\n

Topic: Particle Accelerators and Free-Electron Lasers
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Rotationally resolved depletion spectroscopy of ultracold KRb molecules

We report on the use of depletion spectroscopy to detect ultracold ground-state KRb molecules with rotational resolution. The population of a specific ground-state vibrational level ${v}^{\ensuremath{''}}$, produced by photoassociation of ultracold atoms, is monitored by one-color two-photon pulsed-laser ionization. When a cw laser is resonant with a rovibrational transition to an excited state, the ground-state population, and hence the ion signal, is depleted. This narrow-band spectroscopic technique allows the individual rotational levels in both ground and excited states to be resolved, and thus the population of a single ground-state rovibrational level to be monitored. These resolved transitions are a necessary first step in transferring population from high vibrational levels of the ground state, such as produced by photoassociation, to the absolute molecular ground state $X\phantom{\rule{0.2em}{0ex}}^{1}\ensuremath{\Sigma}^{+}$ (${v}^{\ensuremath{''}}=0$, ${J}^{\ensuremath{''}}=0$). This technique can also be used to determine binding energies of high-${v}^{\ensuremath{''}}$ molecules. Combining our binding energy measurement with the results of previous spectroscopy yields an improved dissociation energy of the $X$ state: ${D}_{e}=4217.822\ifmmode\pm\else\textpm\fi{}0.003\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$. We also report on the two-color pulsed-laser ionization used to locate the depletion transitions.

Topic: Cold Atom Physics and Bose-Einstein Condensates
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Environmental management in shipping

This chapter presents a comprehensive review of findings in the literature on energy-efficient ship operation in the shipping markets. It illustrates an empirical case study on the tanker spot market. The chapter discusses the managerial implications of the findings in the literature. It presents a study on the VLCC spot market and considers the vessel's load factor, defined as the ratio between the reported cargo size and a vessel's DWT. The chapter addresses the question: whether charterers are willing to pay a premium freight rate for more energy-efficient tonnage under a voyage charter. It reviews the theory and practice of environmental management in ship operations. Improving availability of ship position and speed data from the automated identification system for the tracking of vessels has allowed empirical studies to evaluate whether the classical speed-optimization theory can explain observed vessel speeds, both for entire voyages and when vessels are switching between different regulatory regimes.

Topic: Maritime Transport Emissions and Efficiency
Subfield: Environmental Engineering
Field: Environmental Science
Domain: Physical Sciences
Method for the Automated Measurement of Fine Particle Nitrate in the Atmosphere

An integrated collection and vaporization cell has been developed to provide automated, 10-min resolution monitoring of fine particle nitrate in the atmosphere. Particles are collected by a humidified impaction process and analyzed in place by flash vaporization and chemiluminescent detection of the evolved nitrogen oxides. Particle collection efficiency was measured between 95% and 100% for particles above 0.1 μm. Evaporative losses for ammonium nitrate were 2 ± 4%. Average nitrate values from the automated system were compared to traditional denuder filter measurements in three cities, with correlation coefficients of greater than 0.97 and regression slopes ranging from 0.96 to 1.06. The detection limit is governed by the field blank, which for the Los Angeles area was 0.4 μg/m3. The system operated unattended for days at a time, with data recovery of 97%.

Topic: Atmospheric chemistry and aerosols
Subfield: Atmospheric Science
Field: Earth and Planetary Sciences
Domain: Physical Sciences
[Functional phlebodebitometry in assessing the venous outflow disorders in varicose disease of the lower extremities].

The functional correlation of the venous system components was studied in 71 patients with different stages of the varicose disease of lower extremities. The complex of diagnostic measures included radioindication, functional phlebotonometry, vertical functional phlebography developed by the authors, functional phlebodebitometry. The essence of the developed method is as follows: the more impeded main venous outflow, the more pronounced the additional exfusion expense. A comparative evaluation of the results of the diagnostic measures employed has confirmed advantages of functional phlebodebitometry for the diagnosis of functional disorders of the main venous outflow in patients with the varicose disease.

Topic: Systemic Sclerosis and Related Diseases
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Spatial Distribution of Employment in

While the suburbanisation process has been well documented in some large cities of several developed countries, much less attention has been devoted to the case of small and middle-sized cities in developing countries. This article focuses on an exploratory spatial data analysis to investigate the location of the central business district (CBD) and other employment centres in Hermosillo, Mexico. The results reveal the signifi-cant presence of spatial dependence and spatial heterogeneity, although their extent varies with the sector under study. These spatial effects take the form of a persistent cluster of high values of employment around the historical district of the city shaping a huge CBD, although a sub-centre of high values emerges to the south and to the north-west of the CBD in 2004. Overall, Hermosillo is still characterised by a tradi-tional monocentric model, but the role of its CBD has changed. 1.

Topic: Regional Economics and Spatial Analysis
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Primary hematological malignancy of the uterine cervix: A case report

The present case report investigated the clinical characteristics of primary hematological malignancy of the uterine cervixin five patients. Among the five patients, three patients were diagnosed with non-Hodgkin's lymphoma (NHL) and two patients with myeloid sarcoma (MS) of the uterine cervix. Biopsies of the uterine cervices demonstrated the involvement of lymphoid cells or myeloid blasts cells. Immunohistochemical staining demonstrated the expression of B-lymphoid and myeloid lineage markers. The associated lysozyme, myeloperoxidase and mast/stem cell growth factor receptor (CD117) markers were specific for the diagnosis of MS. The three patients with NHL survived, and one of the patients survived for 82 months with no evidence of disease; however, was eventually lost to follow-up. The two patients with MS succumbed to the cancer as a result of progressive disease and leukemia. Therefore, pathological examination may be important for the timely diagnosis and appropriate therapeutic regimen for primary hematological malignancy of the uterine cervix.

Topic: Lymphoma Diagnosis and Treatment
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Vulnerability And Adaptations Of Nigeria's Niger Delta Coast Settlements To Sea Level Rise

The Niger delta Coastal settlements, which are already under stress of demographic pressure and unsustainable oil exploitation, are equally under the threat of sea level rise. Global projections of sea level rise put the area under future inundation of up to 100km in land. The implications are the loss of valuable Biodiversity, land, property, economic activities and livelihoods. Though the impact is not expected to be uniform across board, the flora and fauna already enlisted as threatened will be more vulnerable. The poor, marginalized and economically week would be worst affected. The impact would not be spontaneous and as such economic activities and facilities will gradually be relocated and human population will migrate, creating environmental refugees. The burden, which will be more social than economic will be heavy on the government, the community and other stakeholders. In addition increasing scarcity of land will accelerate the stress on available resources and conflict could ensue. Many adaptation measures are in place to contend the negative impact of sea level rise. These have there financial and environmental cost implications. Because of the prohibitive cost of protection, many developing countries such as Nigeria may not be able to afford such measures. This is more so that there are many issues the nation have to tackle. The most probable and affordable approach is through resilience building and vulnerability reduction. This can be achieved with the collaboration of all the stakeholders in a participatory (bottomtop) rather than by imposition (top-bottom) approach.

Topic: Tropical and Extratropical Cyclones Research
Subfield: Atmospheric Science
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Bile Acid Binding Protein STARD5 Suppresses Doxorubicin‐mediated Apoptosis in H1792 Lung Adenocarcinoma Cells

The bile acid chenodeoxycholic acid (CDCA) is a FXR ligand that has anti‐proliferative and pro‐apoptotic actions in gastrointestinal cancer cells. The cytotoxic actions of CDCA appear to be both FXR‐dependent and independent and cell‐type specific. Although FXR is expressed in lung and bile acid biosynthesis is associated with lung inflammation, the role of FXR in lung cancer is unknown. Herein, we have used non‐small cell carcinoma (NSCLC) cancer cell lines to test the effect of the bile acid binding protein, STARD5, on doxorubicin‐mediated apoptosis. Western blot analysis detected high levels of STARD5 protein in 5 lung adenocarcinoma cell lines compared to non‐detectable levels in normal human bronchial epithelial cells (HBEC). These lung adenocarcinoma cells have greater resistance to doxorubicin‐induced apoptosis, measured by caspase activation, compared to HBECs. Notably siRNA silencing of STARD5 in H1792 lung adenocarcinoma cells decreased cell viability and increased sensitivity to doxorubicin‐induced apoptosis. To address possible anti‐apoptotic mechanisms, we measured the mitochondrial function of H1792 cells after siRNA knockdown or transient overexpression of STARD5. Using the Seahorse XF24 analyzer we found that STARD5 knockdown had no effect on mitochondria function while STARD5 overexpression resulted in a 40% decrease in both the ATP‐linked oxygen consumption rate (OCR) and glycolytic reserve. The proton leak was unchanged, suggesting no change in the mitochondria permeability transition pore, an early marker of apoptosis. A decrease in ATP‐linked OCR mediated by STARD5, in the absence of proton leak, may reflect increased mitochondrial ROS production. Decreased mitochondria function and increased mitochondrial ROS would be consistent with suppressed FXR action. To test whether STARD5 affects FXR activity, we measured FXR‐luciferase reporter gene activity in siRNA‐STARD5 knockdown cells. STARD5 knockdown resulted in increased FXR activity, suggesting that STARD5 sequesters FXR ligands (CDCA) which contribute to FXR's pro‐apoptotic activity. Future studies will test the model that FXR signaling in NSCLC sensitizes cells to doxorubicin‐mediated apoptosis and that increased STARD5 in NSCLC mediates suppression of FXR signaling and contributes to acquired chemoresistance. Support or Funding Information This study was supported by a U of L SOM Collaborative Matching Grant to BJC and KY Lung Cancer Research Program to CMK.

Topic: Drug Transport and Resistance Mechanisms
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
P079: Natural history of antenatally-detected pyelectasis in unselected Korean population

The aim of this study was to determine natural history of antenatally-detected pyelectasis by ultrasound examination in unselected Korean population. This was retrospective analysis involving 142 infants with at least one adequate postnatal ultrasound between January 2001 and March 2003. Inclusion criteria used were an anteroposterior diameter of renal pelvis =4 mm before 33 weeks or =7 mm after 33 weeks. At least one adequate postnatal ultrasound was required for inclusion into the study group. Strong male predilection was found with a male/female ratio of 41. Bilateral lesions were present in 83 (58%) of the 142 fetuses. Among unilateral lesions, left kidney was more commonly involved (75%). Borderline ventriculomegaly was associated in 3 cases with all male fetuses and these three cases proved to be normal in postnatal ultrasound. Polyhydramnios was associated in 3 cases with all male fetuses. Among the total 142 cases, 30 cases of pyelectasis were diagnosed at third trimester. Among the 112 cases of second trimester-onset pyelectasis, after exclusion of 30 cases with only one prenatal record of ultrasound was available, 70% (57/82) had progression of lesion and the remained 30% (25/82) of cases had in utero regression or no significant interval change throughout pregnancy. Of the 57 cases of in utero progression of pyelectasis, only 16% (9/57) had progression of pyelectasis in postnatal period. Bilaterality, sex, onset of pyelectasis, mean birth weight makes no difference between progression and nonprogression group. Overall, 11% (16/142) of antenatally-detected pyelectasis had progression of lesion in postnatal period. Most of antenatally-detected pyelectasis (89%) had in utero or postnatal regression in unselected population. pyelectasis; prenatal ultrasound; unselected population.

Topic: Pediatric Urology and Nephrology Studies
Subfield: Pediatrics, Perinatology and Child Health
Field: Medicine
Domain: Health Sciences
The common prophylactic therapy for bowel surgery is ineffective for clearing Bacteroidetes, the primary inducers of systemic inflammation, and causes faster death in response to intestinal barrier damage in mice

Introduction and objective The role of secreted gut microbial components in the initiation of systemic inflammation and consequences of antibiotic therapies on this inflammatory process are poorly elucidated. We investigate whether peripheral innate cells mount an inflammatory response to gut microbial components, the immune cells that are the primary drivers of systemic inflammation, the bacterial populations that are predominantly responsible, and whether perioperative antibiotics affect these processes. Method and experimental design Conditioned supernatants from gut microbes were used to stimulate murine innate cell types in vitro and in vivo , and proinflammatory responses were characterised. Effects of antibiotic therapies on these responses were investigated using a model of experimental intestinal barrier damage induced by dextran sodium sulfate. Results Proinflammatory responses in the periphery are generated by components of anaerobes from the Bacteroidetes phylotype and these responses are primarily produced by myeloid dendritic cells. We found that the common prophylactic therapy for sepsis (oral neomycin and metronidazole administered to patients the day prior to surgery) is ineffective for clearing Bacteroidetes from the murine intestine. A point of critical consequence of this result is the increased systemic inflammation and premature death observed in treated mice, and these outcomes appear to be independent of gut bacterial spread in the initial phase of intestinal barrier damage. Importantly, spillage of gut microbial products, rather than dissemination of gut microbes, may underlay the initiation of systemic inflammation leading to death. Conclusions Our data further affirm the importance of a balanced gut microflora biodiversity in host immune homeostasis and reinforce the notion that inadequate antibiotic therapy can have detrimental effects on overall immune system.

Topic: Gut microbiota and health
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Uniform positive recursion frequency of any minimal dynamical system on a compact space

Using Gottschalk's notion\,---\,weakly locally almost periodic point, we show in this paper that if $f\colon X\rightarrow X$ is a minimal continuous transformation of a compact Hausdorff space $X$ to itself, then for all entourage $\varepsilon$ of $X$, \begin{equation*} \inf_{x\in X}\left\{\liminf_{N-M\to\infty}\frac{1}{N-M}\sum_{n=M}^{N-1}1_{\varepsilon[x]}(f^nx)\right\}&gt;0. \end{equation*} An analogous assertion also holds for each minimal $C^0$-semiflow $π\colon \mathbb{R}_+\times X\rightarrow X$ and for any minimal transformation group with discrete amenable phase group.

Topic: Mathematical Dynamics and Fractals
Subfield: Mathematical Physics
Field: Mathematics
Domain: Physical Sciences
Anomalous Cyclization in an Attempted Synthesis of the '7-Thiomorphinan', System

The acid catalyzed cyclization of 8-benzyl-3,4,5,6,7,8-hexahydro-1 H-thiopyrano[3,4-c]pyridine hydrochloride (10) did not furnish the expected the «7-thiomorphinan» (11) but 4-(2-mercaptoethyl)-1,2,3,5,10,10a-hexahydrobenzo[g]quinoline (12) instead. The synthesis of 10 and the mechanism of formation of 12 are described

Topic: Synthesis of Organic Compounds
Subfield: Pharmacology
Field: Medicine
Domain: Health Sciences
The Mediating Effect of Perceived Social Acknowledgment on the Relationship Between Patient Assaults and Posttraumatic Stress Reactions in Emergency Nurses

This study explored whether posttraumatic stress symptoms resulted from workplace assaults were mediated by the perception of social acknowledgment by the victim. A sample of 444 emergency room nurses in China completed questionnaires measuring the frequency and types of patient assaults, the severity of physical injury, the perception of social acknowledgment, and the posttraumatic stress symptoms. Cross-sectional design, multiregression, and bootstrapping mediation analyses were used to test the hypotheses. Results showed that general disapproval and family disapproval mediated the relationship between the frequency of patient assaults and the severity of posttraumatic stress symptoms. These two factors also mediated the links between the injury severity of patient assaults and the development of posttraumatic stress symptoms. Implications for clinical practice and future research were discussed.

Topic: Posttraumatic Stress Disorder Research
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
Three-dimensional Vision-based Nail-fold Morphological and Hemodynamic Analysis

In this paper, a Three-dimensional Vision-based Nail-fold Morphological and Hemodynamic Analysis (TVNMHA) is proposed to automatically extract morphological/hemodynamic features from an image sequence, reconstruct the corresponding three-dimensional vacular tubular models, and visualize the dynamic blood flow in the model constructed. The morphological features extracted include number, density, width/height, width of the curved segment, arteriolar limb caliber, curved segment caliber, venular limb caliber, blood color and tortuosity of capillaries. The corresponding pathological information derived has a spatial precision accurate up to 1.6μm. TVNMHA also employs optical flow method (OFM) to measure the velocity of the flowing plasma gaps between two consecutive frames with an error ≈10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-32</sup> μm/sec [1]. The laser Doppler velocimetry is a common tool employed in measuring capillary with larger diameter (is about ≈500μm). The average velocity of an area measured comes with an error around ≈100μm/sec [2], much higher than that of TVNMHA. TVNMHA can separately derive velocities for each capillaries within the whole microscopic range and obtain diversified morphological/hemodynamic features of capillaries with a low-cost equipment setup.

Topic: Retinal Imaging and Analysis
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences