jimnoneill/paper-to-field-training huggingface dataset:
Comparative Efficacy of Cemiplimab Versus Other Systemic Treatments for Advanced Cutaneous Squamous Cell Carcinoma

Field: Medicine (Health Sciences)

Aim: To estimate the comparative efficacy of cemiplimab, a programmed cell death protein 1 inhibitor, versus EGFR inhibitors, pembrolizumab and platinum-based chemotherapy in terms of overall survival (OS) and progression-free survival. Patients & methods: We performed an indirect treatment comparison of cemiplimab and other available systemic therapies for patients with advanced cutaneous squamous cell carcinoma. Results: Cemiplimab was associated with benefits in OS (hazard ratios range: 0.07-0.52) and progression-free survival (hazard ratios range: 0.30-0.67) versus EGFR inhibitors and pembrolizumab (data from KEYNOTE-629). Cemiplimab was more efficacious versus platinum-based chemotherapy in terms of OS. Conclusion: Cemiplimab may offer improvements in survival for advanced cutaneous squamous cell carcinoma patients compared with existing systemic therapies.
The Contribution of roots: the division of labor between grammar and the lexicon in meaning composition

Field: Arts and Humanities (Social Sciences)

This dissertation explores the division of labor between grammar and the lexicon from the viewpoint of event structural theories which take verb meanings to decompose into event templates and roots. Event templates define the temporal and causal structure of the event, while roots fill in real-world details. On this view, the semantics of the whole syntactic structure and the grammatical properties of the verbs are solely determined by the event templates, and never by roots. In this dissertation, I argue against this strong division of labor by showing that roots play a bigger role in grammar and meaning composition. I argue in favor of an event structural theory of verb meaning in which the contributions of event templates and roots are not mutually exclusive, but complement each other with grammatical consequences. Namely, root-specific entailments are shown to be grammatically relevant insofar as they restrict the syntactic structure and in turn determine the grammatical properties of verbs. I argue thus in favor of an event structural approach which needs to be sensitive to the semantic contribution of roots insofar as roots impose restrictions on their syntactic contexts.
Diagnostics of cyst nematodes: use of the polymerase chain reaction to determine species and estimate population levels

Field: Agricultural and Biological Sciences (Life Sciences)

Summary The effective management of cyst nematodes requires accurate assessments of the species composition and size of field populations. Compared to traditional diagnostics the polymerase chain reaction offers high specificity, sensitivity and a more rapid means of identifying large numbers of cyst nematode samples. PCRRFLP of the ITS I ribosomal DNA region from Heterodera and Globodera species produced diagnostic profiles that allowed identification of six pest species. Quantitative PCR was assessed as a means of determining the population sizes of cyst nematode species. A positive correlation was demonstrated between numbers of viable juveniles in cysts and the amount of DNA that could be extracted from them. An internal control template was subsequently used in competitive PCR reactions with G. rostochiensis DNA and was shown to co-amplify with the nematode template. The resulting PCR product ratio allowed assessments of the levels of G. rostochiensis DNA extracted from cyst samples.
Effect of Clofibrate on the Metabolism of Bilirubin, Bromosulphophthalein and Indocyanine Green and on the Biliary Lipid Composition in Gilbert's Syndrome

Field: Medicine (Health Sciences)

1. Clofibrate (20 mg day−1 kg−1 body weight) given orally for 2 weeks to 18 subjects with Gilbert's syndrome reduced the total serum bilirubin concentration from 44.4 (22.1–71.7) μmol/l (median, range) to 15.0 (7.9–28.9) μmol/l, mainly by decreasing the ‘indirect’ fraction to 34.5% of pretreatment values. 2. In contrast to treatment with phenobarbitone, clofibrate did not change the ratio of bilirubin mono- to di-conjugates in bile. 3. The initial plasma disappearance rate of indocyanine green and of bromosulphophthalein did not show consistent changes during clofibrate treatment but the ‘apparent’ maximal biliary secretion capacity of bromosulphophthalein (Tm) decreased in most of the patients studied, whereas the relative storage capacity (S) tended to increase. 4. As expected, the cholesterol saturation of bile increased in all subjects. 5. These results suggest that clofibrate increases mainly the glucuronidation of bilirubin, promoting as such the overall hepatic transport in Gilbert's syndrome. However, it decreases the maximal biliary secretion of bromosulphophthalein, possibly by an increased hepatic retention. These phenomena might be linked to the augmented content of Z protein in the liver.
COSMONAUT: A COmpact spectrometer for measurements of neutrons at the ASDEX upgrade tokamak

Field: Physics and Astronomy (Physical Sciences)

A COmpact Spectrometer for Measurements Of Neutrons at the ASDEX Upgrade Tokamak (COSMONAUT) has been developed for spectroscopy measurements of the 2.45 MeV neutron emission from deuterium plasmas at the ASDEX Upgrade. The instrument is based on a CLYC-7 inorganic scintillator, whereby the detection of fusion neutrons occurs via their interaction with 35Cl nuclei in the detector crystal, leading to a peak in the detector response function and providing excellent neutron/gamma-ray discrimination capabilities. The diagnostics is installed along a radial line of sight and makes use of a digital system to record time resolved data for the whole duration of the discharge. Measurements in ASDEX Upgrade plasmas with neutral beam injection have been carried out and are successfully interpreted using state-of-the-art modeling codes. Next step applications of the diagnostics are in experiments aimed at generating energetic particles by ion cyclotron resonance heating schemes. In these scenarios, COSMONAUT will provide unique information on the acceleration of deuterons beyond the beam injection energy and on their confinement, for comparison with modeling.
A new protein (J1-31 antigen, 30 kD) is expressed by astrocytes, Müller glia and ependyma

Field: Neuroscience (Life Sciences)

Monoclonal antibody (MAb) J1–31 raised using human brain homogenate as immunogen in mice can be used as a cell type marker for certain types of CNS macroglia, namely astrocytes, Müller cells and tanycytes as well as ciliated ependymal cells. Except for the ciliated ependymal cells, these types of macroglia express glial fibrillary acidic protein (GFAP). J1–31 antigen is an intracellular protein which has a MW of 30 kD under reducing conditions for gel electrophoresis (Singh et al., 1986). This protein is distinct from GFAP (MW 50 kD) and vimentin (MW 55 kD), the two core proteins of 10 nm IFs known to be expressed in the above types ofmacroglia. This conclusion is based on several criteria including temporal differences in the onset of expression of GFAP and J1–31 antigen during development of the rat cerebellum. Also, there is no detectable (by immunofluorescence microscopy) expression of J1–31 antigen in the prenatal CNS or outside the CNS where vimentin has been reported to be abundant. The most direct evidence that J 1–31 antigen and GFAP are distinct proteins comes from studies on the mature ciliated ependymal cells which do not express GFAP and yet show intense immunostaining for J1–31 antigen.
Extraction of Aromatic Hydrocarbons from Lube Oil Using Different Co-Solvent

Field: Chemical Engineering (Physical Sciences)

An investigation was conducted effect of addition co- solvent on solvent extraction process for two types of a lubricating oil fraction (spindle) and (SAE-30) obtained from vacuum distillation unit of lube oil plant of Daura Refinery. In this study two types of co-solvents ( formamide and N-methyl, 2, pyrrolidone) were blended with furfural to extract aromatic hydrocarbons which are the undesirable materials in raw lubricating oil, in order to improve the viscosity index, viscosity and yield of produced lubricating oil. The studied operating condition are extraction temperature range from 70 to 110 °C for formamide and 80 to 120 °C for N-methyl, 2, pyrrolidone, solvent to oil ratio range from 1:1 to 2:1 (wt./wt.) for furfural with formamide extraction and 1:1 to 3:1 (wt./wt.) for furfural with NMP extraction. The results of the investigation show that the viscosity index of lubricating oil fraction increases while viscosity and percentage yield of raffinate decreases with increasing extraction temperature, the solvent to oil ratio and co-solvent to furfural ratio. For formamide the best temperature were 90 °C, furfural to co-solvent ratio (60:40) and solvent to lube oil ratio (1.5:1) to get best value of viscosity index 102, viscosity 3.01 cst and 69.23 % yield. While for NMP co-solvent 110 °C extraction temperature, (2:1) solvent to lube oil ratio and (60:40) furfural to co-solvent ratio, to produce lube oil with 96 viscosity index, 9.10 cst viscosity and 68.50 yield.
Structure, Control, and Communication of Collective Animal Behavior in Dynamic Environments

Field: Agricultural and Biological Sciences (Life Sciences)

Collective behavior in animal aggregations is highly complex and spans multiple spatial scales, across a wide range of environmental conditions. In socially active fish, aggregation into schools is a widespread adaptation that confers a variety of safety benefits. The emergent patterns exhibited by collectively behaving fish schools may be influenced by biotic (i.e. predation) or abiotic (i.e. habitat complexity, turbidity) factors in the local environment. Our knowledge of the ways and extent to which environment variability affects schooling behavior at the collective level is currently limited. In this dissertation, I investigated whether environmental factors influenced the collective behavior of fish schools. I focused on three main questions: (1) does habitat context modulate the collective state of fish schools? (2) does the simultaneous presence of habitat structure and high predation risk influence the collective state of fish schools? (3) do environmental constraints on visual sensory perception affect collective responses to predation? Using advanced field methods to observe schooling behavior in restrictive environmental contexts, question one demonstrated that habitat context, not predation, drives change in the collective state of fish schools, suggesting that the local environment plays a larger role than predation risk in structuring collective behavior. Using the same field method at an anthropogenic structure containing both habitat complexity and increased predation risk, question two shows that collective behavior is influenced by the coupling of the two conditions, in a different manner than with habitat complexity alone. Finally, using a behavioral arena that creates three dimensional virtual environments, question three showed that mechanosensory information becomes prioritized when visual perception is compromised, and that multiple sensory systems can control schooling behavior in conditions where information about the environment is unreliable. As a collective itself, the results of these questions advance our understanding of the role the environment plays on influencing collective animal behavior, and offers insights into this understanding from both a mechanistic and process based perspective.
Zika Virus Public Health Crisis and the Perpetuation of Gender Inequality in Brazil

Field: Social Sciences (Social Sciences)

Abstract

Background: In 2015-2017, the Americas experienced a highly consequencial epidemics for pregnancy and childbearing. Mainly transmitted by the mosquito Aedes aegypti, but also through sexual intercourse, the Zika virus poses the risk of congenital Zika syndrome to fetus, which includes microcephaly and other child development complications. When a public health crisis taps directly into reproductive health, typically a feminine realm, gender systems may reproduce deeply-rooted gender norms, especially those linked to cultural beliefs and expectations. This paper investigated the role of gender in two relational contexts: public health messaging to prevent Zika infections and women’s Zika and pregnancy prevention negotiation with their sexual partners during the Zika outbreak. Methods: We conducted a systematic content analysis of 94 unique pieces, governmental agencies mass-produced public health communication campaigns promoting Zika awareness. Print and online materials were collected for one year (May 2016-May 2017), such as TV ads, Internet Pop-ups, and pamphlets. We also analyzed transcripts from 16 focus groups we conducted with reproductive-aged women (18-40) in Belo Horizonte and Recife, two large cities differently affected by the Zika outbreak. Women answered open-ended questions related to personal knowledge of and experiences with the Zika virus, the related experiences of their friends and acquaintances, their primary information sources, and their perceptions of public health efforts and women’s contraceptive use.Results: Campaign pieces handling pregnancy and microcephaly demonstrated robust gendering, drastically targeting women, placing on their shoulders the responsibility for protecting a potential fetus from the disease. Campaigns neglected male´s participation on Zika prevention and contraceptive management, and failed to address Brazil´s large proportion of unplanned pregnancies. Women were placed in a double bind by being expected to prevent pregnancy and Zika amidst a relationship power dynamic that included unprotected sexual intercourse and gender norms regarding division of labor. Conclusion: Government and individual responses to the epidemics reinforced gender roles, situating pregnant women as responsible for averting mosquito bites and microcephaly, emphasizing prevention of both disease and vector among women while excluding men. Since low-socioeconomic status women possessed fewer resources to preclude infection, we also find that beyond the gender divide, this subgroup faced more pronounced Zika prevention challenges.
Formal Reminiscence Space and Memory in Sufjan Stevens’s Storytelling

Field: Arts and Humanities (Social Sciences)

Storytelling can be a vehicle for bonding and closeness, particularly between the narrator and their rapt audience, whether in traditional spoken storytelling or musical narrative. One of the ways a listener is drawn into a musical story is by triggering their memory, and, in his sung narratives, Sufjan Stevens creates a specific formal space for enacting moments of remembering with his audience. Through recurring thematic cues and a deliberate formal space I call the “reminiscence space,” Stevens creates a musical window during which the audience can remember events of the story with him. The reminiscence space promotes a participatory act of remembering between artist and audience, which psychological literature demonstrates can increase feelings of connectedness, intimacy, and community. Three songs by Stevens are analyzed as a case study for the way in which remembering together is used to create intimacy between the audience and Stevens.
MEDiDEN: Automatic Medicine Identification Using a Deep Convolutional Neural Network

Field: Computer Science (Physical Sciences)

This paper presents MEDiDEN: a smart phone application for automatic medicine identification and medication reminders. The main features of MEDiDEN include the classification of medicine packages, a reminder function that can be set in details and integrates with the mobile OS's notification system, and news feeds for medication-related articles. The most innovative function of the application is medicine classification, which was implemented using the Inception deep-learning architecture. For medicine package classification, the researchers compared the performance of Inception-V3and Inception- V4 with the data in this work. The two models could identify medicine with 92.75% and 94.85% accuracy, respectively. Even though Inception-V4 provided slightly better results, the researchers selected Inception-V3as the model for deployment due to its smaller size, which has the ability to speed up inference run time. The server consists of a Python backend used to run the neural network model. The client application is available on the Android platform. Actual use testing showed that the application could correctly and consistently identify the medicine in the training data.
RNA Sequencing Reveals Transcription Factors and Genes in Phenylpropanoid Biosynthesis That Positively Regulate Size and Weight of Oak Tree Seeds

Field: Agricultural and Biological Sciences (Life Sciences)

Acorn size is of great importance, both ecologically and economically. However, the long lifespan is an obstacle to improvement in breeding. Keumsura1ho is a recently bred cultivar of oak (Quercus acutissima Carruth) selected after eight years of selection due to its larger acorns and higher weight compared to the control. In the present study, we investigated the transcriptional mechanisms underlying the outstanding morphological characteristics of Keumsura1ho. For this purpose, one- and two-year-old acorns from the control and Keumsura1ho groups were used for comparative transcriptome analyses of their seeds. Among morphological characteristics, the Keumsura1ho seeds were 18.3% longer than those of the control. Seed width and depth were 33.9% greater than those of the control. In the transcriptome analysis, genes related to seed size were further enriched, with biennial Keumsura1ho showing higher enrichment in comparison to control genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the upregulated genes of the two-year-old Keumsura1ho seeds showed higher enrichment in phenylpropanoid metabolism compared to the control, with OMT1 and PRXs exhibiting high expression levels. This pathway has a significant impact on seed coat lignification and size in Keumsura1ho. The results of this study will benefit the development of breeding techniques by identifying marker genes for seed size.
MINERALOGY OF STREAM SEDIMENTS IN THE GABAL KAB-AMIRI AREA, CENTRAL EASTERN DESERT, EGYPT

Field: Earth and Planetary Sciences (Physical Sciences)

This study provides an information about the heavy mineral composition of stream sediments of Wadi Kab -Amiri, Wadi Kab Um El Abas and Wadi El Saqia in the central Eastern Desert of Egypt.Geological and mineralogical investigations reveal the significant potential of the stream sediments in all the wadis for radioactive anomalies.Mineralogy of the heavy mineral separates includs variable contents of rare metal-, Th-and U-bearing minerals.Monazite, thorite and allanite are recorded in addition to several Nb-Ta-bearing phasess.Electron microprobe and EDX analyses constrain on the variable contents of Th and U in most heavy minerals under investigation.Considering the proximal radiometric anomalies and similar mineralogical composition of the KabAmiriintrusion and the more significant episyenitemass, it is concluded that the investigated stream sediments are endogenic sediments with inherited radiogenic and mineral budget.
FIGURE 1. Garra dulongensis, CMK 27239, 104.6 in Laogarra heokheei, a new genus and species of 'garra' from north-eastern Laos (Teleostei: Cyprinidae)

Field: Agricultural and Biological Sciences (Life Sciences)

FIGURE 1. Garra dulongensis, CMK 27239, 104.6 mm SL; ventral view of head, showing external oral and gular morphology. From Kottelat, 2020: 158.
Intravascular Lymphoma in Patient With Celiac Disease With Multi Glandular Involvement

Field: Medicine (Health Sciences)

Abstract Case Presentation: The patient is a 60 year old male with a past medical history of celiac disease, paroxysmal Afib, iron deficiency, and CAD who presented with lightheadedness, dizziness, and fatigue. Notable workup revealed that the patient had Afib with RVR, a TSH of 0.189, Free t4 0.51an LDH of 2726, hemoglobin of 8.7, AST of 155, ALT of 19, WBC of 4.5, and serum iron of 20. The patient’s cardizem dose was adjusted and repeat transthoracic echocardiogram was unremarkable compared to history. The patient presented again with complaints of abdominal distension, postural dizziness, occasional night sweats, and fevers. Repeat workups revealed pancytopenia, proteinuria, hypotension, and anasarca most pronounced in the lower extremity and scrotum. Ultimately, a kidney biopsy revealed an intravascular B cell non-Hodgkin lymphoma (IVBCL). Notable repeat labs include a CRP of 44 and a failed ACTH stimulation test. A brain MRI revealed a 6mm pituitary microadenoma. The patient placed on an R-CHOP regiment and is scheduled for repeat MRI to rule out pituitary involvement. Discussion: IVBCL’s are a rare form of diffuse B cell lymphoma and remain a diagnostic challenge due to the variety of involved systems including skin, CNS, and endocrine. IVBCL is also known to not produce a mass or lymphadenopathy. Celiac disease is a known risk factor for non-Hodgkin’s lymphoma. A literature search reveals a few case reports with common themes of increased LDH and inflammatory markers, anemia, and hepatic and renal dysfunction. Postural hypotension can also be a presenting symptom due to IVBCL’s ability to infiltrate neurovascular tissue to cause autonomic neuropathy. However, in this case, the patient’s history of primary adrenal insufficiency makes this unlikely. Hypothyroidism secondary to pituitary and thyroid involvement was suspected due to TSH level suppressed enough for central hypothyroidism. Repeated MRI showed resolution of Pituitary Microadenoma post Chemo therapy. Sylvain Raoul Simeni Njonnou, Bruno Couturier, Yannick Gombeir, Sylvain Verbanck, France Devuyst, Georges El Hachem, Ivan Theate, Anne-Laure Trepant, Virginie De Wilde, Frédéric-Alain Vandergheynst, “Pituitary Gland and Neurological Involvement in a Case of Hemophagocytic Syndrome Revealing an Intravascular Large B-Cell Lymphoma”, Case Reports in Hematology, vol. 2019, 6 pages, 2019. https://doi.org/10.1155/2019/9625075 Catassi C, Fabiani E, Corrao G, et al. Risk of Non-Hodgkin Lymphoma in Celiac Disease. JAMA. 2002;287(11):1413 Khan MS, McCubbin M, Nand S. Intravascular Large B-Cell Lymphoma: A Difficult Diagnostic Challenge. J Investig Med High Impact Case Rep. 2014 Mar 6;2(1):2324709614526702. Pearce C, Hope S, Butchart J. Intravascular lymphoma presenting with postural hypotension. BMJ Case Rep. Published 2018 Jan 29.
YAP/TAZ Signaling Enhances Angiogenesis of Retinal Microvascular Endothelial Cells in a High-Glucose Environment

Field: Medicine (Health Sciences)

Purpose Diabetic retinopathy (DR) is a major cause of irreversible blindness in the working-age population. Neovascularization is an important hallmark of advanced DR. There is evidence that Yes-associated protein (YAP)/transcriptional co-activator with a PDZ binding domain (TAZ) plays an important role in angiogenesis and that its activity is regulated by vascular endothelial growth factor (VEGF). Therefore, the aim of this study was to investigate the effect of YAP/TAZ-VEGF crosstalk on the angiogenic capacity of human retinal microvascular endothelial cells (hRECs) in a high-glucose environment.