jimnoneill/paper-to-field-training huggingface dataset:
Mechanistic and Evolutionary Analyses of the Sialic Acid Synthase Family

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Sialic acids are prevalent in many organisms and facilitate a range of cellular processes in both bacteria and mammals. Whilst a variety of sialic acids are present in nature, N-Acetylneuraminic acid (NANA) is the most common and plays a key role in the pathogenesis of a select number of neuroinvasive bacteria such as Neisseria meningitidis. These pathogens coat themselves with polysialic acids, mimicking the exterior surface of mammalian cells and consequentially concealing the bacteria from the host’s immune system. NANA is synthesised in prokaryotes via a condensation reaction between phosphoenolpyruvate and N-acetylmannosamine. This reaction is catalysed by the domain swapped, homodimeric enzyme, N-acetylneuraminic acid synthase (NANAS). Each NANAS monomer is comprised of two distinct domains; a catalytic domain linked to an antifreeze protein-like (AFPL) domain. This thesis outlines research into the role of the AFPL domain using a range of structural and kinetic analyses to compare variant enzymes to the natural, NmeNANAS enzyme. An investigation was also made into the evolutionary relationships between NANAS and other bacterial sialic acid synthases such as Legionaminic acid synthase and Pseudaminic acid synthase.
Angular dependence of stimulated Brillouin scattering in homogeneous plasma

Field: Physics and Astronomy (Physical Sciences)

The angular dependence of stimulated Brillouin scattering (SBS) in a finite homogeneous plasma is studied. For parameters typical of inertial confinement fusion experiments, the initial evolution of SBS is well approximated by a one-dimensional model. In the context of this linear model, the threshold intensity of the absolute instability and the steady-state spatial growth rate of the convective instability are both independent of the scattering angle. However, the saturation time of the convective instability exhibits a strong inverse dependence on the scattering angle: Forward SBS always occurs in the transient regime and the intensity of the scattered light is less than that predicted by a steady-state analysis. In particular, no light is emitted in the propagation direction of the incident wave.
Quantitative sputum culture as a means of excluding false positive reports in the routine microbiology laboratory

Field: Medicine (Health Sciences)

A relatively simple technique for sputum homogenization and dilution is described. Results show that this technique is reliable for isolation and quantitative culture of organisms from cases of chest infection. The technique has resulted in significant reduction in false positive reports, particularly when a system of interpretative reporting is utilized based on 10 7 organisms per millilitre of sputum being accepted as evidence of significant infection.
Contagion and the feminist transnational re-turn

Field: Social Sciences (Social Sciences)

The Covid-19 pandemic has upended life globally and turned the spotlight on the inadequacies of political systems and their infrastructural capacities to deal with the social fallout. Flaunting borders and checkpoints, the virus has been described as the great equalizer. However, the toll has been borne disproportionately by people of color, immigrants and the poor. The pandemic has exposed the fault lines of societies, exacerbated inequalities and gendered injustices are being reproduced in new registers and configurations. For feminist scholars committed to a politics of decoloniality, the critical task of unravelling a radically altered global environment requires a recalibrated re-turn to the framework of the transnational.
A survey of clinical trials with fenbufen.

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

To date, the efficacy and safety of gamma-oxo(1,1'-biphenyl)-4-butanoic acid (fenbufen) have been evaluated in over 200 clinical trials involving several thousand patients. The program of clinical investigation consisted of open dose ranging studies in patients; short-term, double-blind controlled studies of both cross-over and parallel group design to evaluate efficacy and safety compared to placebo and active reference drugs; long-term, double-blind controlled studies of parallel group design versus an active reference agent; open studies to evaluate the long-term efficacy and safety of fenbufen; and special studies to investigate possible effects on eyes, ears and heart. The overall experience with fenbufen in 60 US and 37 foreign clinical trials is summarized in this report with respect to the following: therapeutic efficacy and safety in rheumatoid arthritis, osteoarthritis, ankylosing spondylitis, analgesia and gout. The age range covered in these studies was 13 to 87 years, and included 206 patients over the age of 70. 3457 patients received fenbufen in all phases of these clinical trials, including short-term and long-term studies. The patient total includes: 1462 patients (664 US, 798 foreign) with rheumatoid arthritis, 1225 (420 US, 805 foreign) with osteoarthritis, 55 (19 US, 36 foreign) with ankylosing spondylitis, 39 (foreign) with gout, and 676 patients (103 US, 573 (foreign) who participated in analgesia studies. The worldwide clinical studies have demonstrated very good clinical efficacy of fenbufen in comparison to other non-steroidal antirheumatic (nsa) drugs. The tolerance was much better in many cases compared with tolerance levels of other nsa-drugs. The good results were confirmed by new papers presented during IX International Congress of Rheumatology, Wiesbaden/FR Germany, September 1979. Fenbufen is currently marketed in Brazil, Columbia, Costa Rica, Dominican Republic, Ecuador, El Salvador, Great Britain, Greece, Guatemala, Honduras, Ireland, Italy, Japan, South Korea, Mexico, Nicaragua, Panama, Peru, Philippines, Rhodesia, Spain, South Africa, Switzerland, Trinidad and FR Germany.
Reviewer #1 (Public Review): Automated cell annotation in multi-cell images using an improved CRF_ID algorithm

Field: Computer Science (Physical Sciences)

Cell identification is an important yet difficult process in data analysis of biological images. Previously, we developed an automated cell identification method called CRF_ID and demonstrated its high performance in C. elegans whole-brain images (). However, because the method was optimized for whole-brain imaging, comparable performance could not be guaranteed for application in commonly used C. elegans multi-cell images that display a subpopulation of cells. Here, we present an advance CRF_ID 2.0 that expands the generalizability of the method to multi-cell imaging beyond whole-brain imaging. To illustrate the application of the advance, we show the characterization of CRF_ID 2.0 in multi-cell imaging and cell-specific gene expression analysis in C. elegans. This work demonstrates that high accuracy automated cell annotation in multi-cell imaging can expedite cell identification and reduce its subjectivity in C. elegans and potentially other biological images of various origins.
Essential Oil of Majoram (Origanum majoranaL.) Grown in Cuba

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Water-distilled volatiles of marjoram (Origanum majorana L.) grown in Cuba were analyzed by GC/MS. Among the 41 compounds identified, terpinen-4-ol (17.67%), linalool (16.41%) and thymol (11.55%) were the major constituents. Key Word Index: Origanum majorana Labiataemarjoramessential oil compositionterpinen-4-ollinaloolthymol
Exploring the Third-Order Non-linear Optical Responses and Optical Limiting Properties of p-Nitroaniline Picrate: A Theoretical and Experimental Study

Field: Chemistry (Physical Sciences)

The current study investigates the nonlinear optical behaviour of p-nitroaniline picrate, which has been synthesized and characterized. Its third-order non-linear optical properties were investigated via Z-scan studies. p-Nitroaniline picrate demonstrates a reverse saturable absorption, as indicated by a positive absorption coefficient (b), which is of the order 10–12 m/W. Closed aperture data indicate a positive refractive non-linearity due to self-focusing, with non-linear refractive index (n2), third-order susceptibility (χ(3)) and second-order hyperpolarizability (g) in order of 10–19 m2/W, 10–13 esu and 10–34 esu, respectively. Theoretical calculations corroborated the experimental findings, emphasizing the significant third-order non-linearities of p-nitroaniline picrate. An optical limiting property is demonstrated with a threshold of 16.32 J/cm2. Low HOMO-LUMO energy gaps, intermolecular hydrogen bonding and intramolecular charge transfer interactions are the properties that are related to these qualities according to DFT research. Therefore, p-nitroaniline picrate is highly recommended for the optical limiting applications.
DESIGNING MACHINE PARTS FOR STRENGTH. VOLUME 2,

Field: Engineering (Physical Sciences)

Contents: Design of metal structures and of their welded joints; Tension and compression in bars; Flexible strings; Bending of bars; Torsion of bars; Design of frames; Strength of rings; Stability of bars; Vibration of elastic systems; Critical speeds of rotating shafts; Strength of plates; Strength of cylindrical shells; Stability of plates and shells; and Statistical methods of strength and reliability control.
Supplementary Figure 2 from NOTCH3 Signaling Pathway Plays Crucial Roles in the Proliferation of ErbB2-Negative Human Breast Cancer Cells

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Supplementary Figure 2 from NOTCH3 Signaling Pathway Plays Crucial Roles in the Proliferation of ErbB2-Negative Human Breast Cancer Cells
Positive Spillovers and Free Riding in Advertising of Prescription Pharmaceuticals: The Case of Antidepressants

Field: Economics, Econometrics and Finance (Social Sciences)

Exploiting the discontinuity in advertising along the borders of television markets, I estimate that television advertising of prescription antidepressants exhibits significant positive spillovers on rivals' demand. I apply this identification in a demand model, where estimated parameters indicate significant and persistent spillovers driven by market expansion. Using the demand estimates to calibrate a stylized supply model, I explore the consequences of the positive spillovers on firm advertising choice. Compared with a competitive benchmark in which firms optimally free ride, simulations suggest that a category-wide advertising cooperative would produce a significant increase in total advertising.
Figure S4 from Circulating Tumor Cell Genomic Evolution and Hormone Therapy Outcomes in Men with Metastatic Castration-Resistant Prostate Cancer

Field: Medicine (Health Sciences)

<p>Genomic-wide CNAs analysis in CTCs in the radium-223 trial. Top genomic gain (A) and loss (B) detected in the PROPHECY trial were independently validated in the radium-223 trial CTCs DNA (N=14 patients) study. Before radium-223 treatment, these patients were priorly treated with enza/abi.</p>
Exploring novel Compound Specific Stable Isotopes (CSSIs) tracers with conventional fingerprinting properties for sediment source apportionment in an arable lowland catchment in Central Germany

Field: Environmental Science (Physical Sciences)

&lt;p&gt;Soil erosion and associated sediment transport can cause severe water quality and ecosystems health deterioration. The fingerprinting approach has widely been applied for sediment source apportionment using a variety of sediment tracers. This study evaluates the applicability of the Compound Specific Stable Isotope (CSSI) fingerprinting technique of fatty acids to identify crop-specific soil loss and the importance of upland erosion compared to river bank erosion. We tested this new technique with fallout radionuclides, geochemical and spectral tracers in a small agricultural loess soil catchment (Geesgraben, 75 km&amp;#178;) within the lowland Bode river catchment in Central Germany. The CSSI tracer was combined with a linear multivariate mixing model to discriminate soil loss from areas with specific crop types (e.g., C3 vegetation/wheat and C4 vegetation/maize) and identify the share of river bank sediment source on total sediment loss. We compared the CSSI technique with fallout radionuclides, geochemical and spectral fingerprinting properties for tracing subsurface sediment sources. We found that the CSSI fingerprinting technique of fatty acids allowed to decipher surface sediments from wheat and maize fields. The CSSI &amp;#948;&amp;#185;&amp;#179;C-fatty acids were also used to disentangle arable and river bank sediment sources. The crop-specific soil loss from wheat and maize was 40% and 11%, respectively. Relative sediment contribution from river banks was up to 49%. The outcomes using the CSSI tracer were consistent and similar to those using fallout radionuclides, geochemical and spectral fingerprinting properties for arable land and river bank sediment sources, which indicated a mean sediment source contribution of 46% from river bank and 54% from surface sources, respectively. Our results showed that the stable isotope composition of fatty acids could discriminate C3 and C4 vegetation sources, and such information is of prime importance for decision making. Furthermore, the relatively high proportion of sediment losses from river banks has clear implications for management measures to reduce sediment losses in these agricultural loess areas.&amp;#160;&lt;/p&gt;&lt;p&gt;Keywords: sediment fingerprinting, CSSI, fatty acids, C3 and C4 vegetation sources, sediment sources.&lt;/p&gt;
Investigation of The Association of The Fear of Missing Out with Attention Deficit and Impulsivity in Terms of Age, Gender, and Tobacco Dependence

Field: Psychology (Social Sciences)

Objective: The study aimed to examine the association of the fear of missing out (FoMO) on the symptoms of attention deficit-hyperactivity and impulsivity in terms of gender, age, and tobacco dependence. Materials and Methods: The study sample consisted of a total of 732 individuals. Of the participants, 425 were females and 307 were males. There were 258 smokers and 474 non-smokers in the study sample. Participants were administered a Socio-demographic Questionnaire, The Adult Attention Deficit Hyperactivity Disorder Self-Report Scale (ASRS), The Barratt Impulsiveness Scale (BIS-11), and Üsküdar FoMO Scale to collect data. The Mann Whitney U test was used to test the differences in terms of gender, age, and smoking status. Spearman correlation analysis and a linear regression analysis were performed to examine the correlation between the scales. Results: The intensity of the FoMO was not variable in regard to gender or smoking status. There was a significant difference in terms of the age variable. The model in the regression analysis, which evaluated the features of age, gender, smoking status, attention deficit, and impulsivity was found out to be statistically significant. Conclusions: The analysis of the data revealed that severity of the FoMO was increased with ASRS scores and decreased with age.
Bioinformatic study of the spectrum of mutations for hereditary dentin defects

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Various bioinformatics software programs(PolyPhen-2,SignalP 3.0 and SplicePort) were used to analyze the spectrum of mutations in DSPP gene for hereditary dentin defects.40 mutations within DSPP for the hereditary dentin defects have been identified in 60 independent families.The 19 missense or nonsense mutations were located within the DSP domain,and 21 mutations located in the DPP domain cause frameshift mutations.In DSP domain,a mutation may change the cleavage site for the signal peptide;four mutations may affect signal peptide cleavage;ten mutations may affect normal pre-mRNA splicing;a mutation can create a stop codon;three mutatuons may directly affect the biological function of DSP by changing its normal space conformation.Unfortunately,bioinformatic analysis was unavailable for the frameshift mutations within the DPP domain.
Adrenal Hormone and Metabolic Biomarker Responses to 30 min of Intermittent Cycling Exercise in Breast Cancer Survivors

Field: Medicine (Health Sciences)

The aim of this study was to explore the effect of one bout of aerobic exercise on epinephrine, norepinephrine, cortisol, glucose, lactate, and free fatty acid (FFA) responses in breast cancer survivors and healthy controls. 9 female breast cancer survivors and 9 women without a history of cancer completed 30 min of cycle ergometry exercise at 60 % of VO2peak. Blood samples were taken pre-exercise, immediately post-exercise, and 2 h post-exercise from which plasma concentrations of study variables were measured. Immediately and 2 h post-exercise, increases were observed in epinephrine (control group only) norepinephrine (both groups), lactate (both groups), and FFA (both groups immediately post-exercise; breast cancer survivor group only at 2 h post-exercise) (p < 0.05). Cortisol decreased immediately and 2 h post-exercise in the control group while glucose decreased immediately post-exercise in the breast cancer survivor group (p < 0.05). In conclusion, breast cancer survivors appeared to display attenuated epinephrine, cortisol, and lactate responses while displaying larger magnitude changes in glucose and FFA responses compared to controls. These preliminary findings may have implications for the regulation of metabolism during exercise in breast cancer survivors.
Follow the money: Does the financial sector intermediate natural resources windfalls?

Field: Economics, Econometrics and Finance (Social Sciences)

The need to absorb windfalls gains and manage them appropriately has been discussed extensively by academics and policy makers alike. We explore the role of the financial sector in intermediating these windfalls. Controlling for the level of financial development, inflation, GDP growth and country fixed-effects, we find a relative decline in financial sector deposits in countries that experience an unexpected natural resource windfall as measured by shocks to exogenous world prices. Moreover, we find a similar relative decline in lending, which is mostly due to the decrease in deposits. The smaller role for the financial sector in intermediating resource booms is accompanied by a stronger role of governments in channeling resources into the economy, mostly through higher government consumption.
In Response

Field: Medicine (Health Sciences)

Although we are aware that Staphylococcus enterocolitis (SEC) can occur after antibiotic use and that it is an easily overlooked cause of nosocomial enterocolitis and sepsis, we disagree with Drs. Naughton and Mannion's opinion that our case is more likely caused by SEC than due to foreign body–associated infection.1 Most cases associated with SEC present with large volume, “cholera-like” diarrhea associated with patchy necrotizing segmental gangrene and bowel wall thickening.2 The exploratory laparotomy findings included normal-appearing large colon with stool in the descending and sigmoid colon with no evidence of ischemic colitis, perforation, or diverticulosis, and the small bowel appeared normal except for an isolated 2-inch transmural focal area of ischemia in the jejunum associated with hemorrhagic rugose mucosa per surgical pathology report. Furthermore, SEC associated with antibiotic use is typically due to flouroquinolones, with the median duration of antimicrobial therapy being 7 days. The fact that this patient received 3 doses of cefazolin makes this scenario less likely.3 Clinically, our patient was in septic shock, had positive blood cultures for Staphylococcus aureus, positive cultures for staphylococcus from the neck abscess, and isolated small intestinal perforation associated with ischemia. The indigo scan showed no signs of infection at the surgical site. Although we would rather attribute this patient's postoperative complication to a source such as SEC, we reiterate our conclusion that a more likely cause of the bacteremia was infection at the interscalene catheter site.4 Steven R. Clendenen, MD Christopher B. Robards, MD Department of Anesthesiology Mayo Clinic Florida Jacksonville, Florida [email protected]
Disseminated fusariosis presenting as panniculitis-like lesions on the legs of a neutropenic girl with acute lymphoblastic leukemia

Field: Medicine (Health Sciences)

Fusarium is a filamentous fungus found naturally in the soil and as a contaminant of plumbing systems. In immunocompetent patients, Fusarium causes localized infection, most commonly onychomycosis. Fusarium tends to be resistant to commonly used antifungal medications. In immunocompromised patients, this antifungal resistance is of particular concern because localized infection quickly becomes disseminated disease with high mortality rates. Disseminated fusariosis presents with skin lesions more often than any other systemic fungal infection. We present a case of fusariosis in an 11-year-old neutropenic patient with acute lymphoblastic leukemia whose only symptom of the fungal infection consisted of painful, indurated nodules and plaques on her legs. The diagnosis and treatment of this invasive fungal infection is also discussed.
[Quadrilateral space syndrome: a case report].

Field: Medicine (Health Sciences)

Quadrilateral space syndrome is a rare entity caused by isolated compression of the axillary nerve in the quadrilateral space. A twenty-seven-year-old male patient presented with a poorly localized shoulder pain and point tenderness on the posterior aspect of the shoulder. Magnetic resonance imaging showed a fibrous band causing quadrilateral space syndrome. Surgical excision of the fibrous band was performed and the axillary nerve was released. The patient became symptom-free after surgical decompression.
Heterobifunctional Multivalent Inhibitor-Adaptor Mediates Specific Aggregation between Shiga Toxin and a Pentraxin

Field: Chemistry (Physical Sciences)

[reaction: see text] The first example of a multivalent heterofunctional inhibitor-adaptor, called "BAIT", is described. This multivalent inhibitor-adaptor is able to capture a "target" receptor (Shiga toxin) through its recognition of one ligand of a heterobivalent headgroup while the other ligand binds to an endogenous "trap" protein (serum amyloid P component, SAP). BAIT showed markedly enhanced inhibition of toxin activity. An efficient synthesis of this multivalent cluster containing heterobifunctional ligands was accomplished by chemical and chemoenzymatic approaches.
Target cell lysis by cytotoxic T lymphocytes redirected by antibody-coated polystyrene beads.

Field: Immunology and Microbiology (Life Sciences)

Abstract Cytotoxic T lymphocytes were found to mediate rapid lysis of target cells not normally recognized in the presence of small polystyrene beads coated with a combination of anti-T3 and antitarget cell antibodies. Lysis was not seen with beads bearing one of these antibodies alone, nor with a mixture of two types of beads each coated with a single antibody. The effector cells mediating this lysis include long term allospecific human CTL, and both human and mouse CTL clones recognizing mouse class I MHC Kb Ag. TNP-modified mouse tumor cells, a human lymphoblastoid line, and human red cells were found to be good targets for this cytotoxicity. Polystyrene beads with diameters of 3 to 15 mu caused target lysis, with a dose-response curve which typically went through a maximum and declined at high bead numbers. Maximal bead-redirected lysis by CTL was less efficient than that mediated by soluble antibody heteroconjugates of the same two antibodies. Bead-redirected target lysis was calcium dependent. These results are interpreted as a form of bystander lysis induced by the beads, since the target cell membrane is not directly crosslinked to the region of CTL activation. These observations thus favor a mechanism of lysis involving the polarized secretion of a locally acting lytic agent by CTL.