jimnoneill/paper-to-field-training huggingface dataset:
Measurement of human tissue protein synthesis: an optimal approach

Field: Medicine (Health Sciences)

This paper reviews the evidence for and against the adoption of methods for the measurement of human tissue protein synthesis based upon the incorporation of stable isotopically labeled amino acids administered either as a continuous infusion or as a flooding dose. The practical advantages of the flooding dose method are the relative ease of application of the tracer and the ability to make a repeat measurement within approximately 2 h. For the method depending upon continuous infusion of labeled amino acid, the advantages include the use of labeled amino acids at true tracer doses (i.e., with no disturbance of metabolism) and the ability to make simultaneous measurements of whole body turnover and limb or organ turnover (given appropriate sampling techniques). The crucial question concerning the accuracy of the two methods (e.g., the 2-fold difference in the rate of skeletal muscle protein synthesis) remains unresolved, but in our opinion more evidence exists in favor of the values obtained from the continuous infusion method. Furthermore, as techniques for measurement of stable isotopically labelled amino acids improve, the length of time necessary for tracer infusion will fall, and the practical advantages of the flooding dose protocol will lessen in comparison.
Do cover crops give short term benefits for soil health

Field: Agricultural and Biological Sciences (Life Sciences)

Cover crop use in the UK is increasing with establishment often before spring cereal crops. Therefore trials were implemented to assess two different cover crop mixtures for i) their ability to remediate soil compaction, ii) aid water management and iii) increase earthworm numbers. Two cover crop mixtures; frost sensitive (black oats, oil radish and mustard) and winter hardy (forage rye, oil radish and berseem clover) were compared to control plots. This replicated trial was based at G’s Growers on an organo-mineral soil with a cover crop sown between wheat harvested in August 2016 and maize sown in May 2017. The results suggest that in the short term there are small differences in soil physical characteristics. Notably at a depth of 10–20 cm there is a reduction in soil strength as measured by the penetrologger and shear vane following the frost sensitive cover crop mix. Juvenile earthworm population was significantly greater in the control treatment compared to the frost sensitive cover crop treatment. In May 2017 maize was established across all plots.
Perioperative Outcomes in Robotic-Assisted Versus Conventional Laparoscopic Treatment of Endometrial Cancer

Field: Medicine (Health Sciences)

Objective: To compare perioperative outcomes of robotic-assisted (RALS) versus conventional laparoscopic surgery (CLS) in endometrial cancer. Methods: This is a retrospective analysis of a prospectively maintained database of procedures performed from January 2009 to January 2014 by a single surgeon experienced in both minimally invasive techniques. One hundred and five patients underwent surgical staging of endometrial cancer via either conventional or robotic-assisted laparoscopy. Characteristics such as age, body mass index (BMI), prior abdominal surgery, number of comorbidities, stage of disease, and extent of surgery were compared. Outcomes, including estimated blood loss (EBL), operating room time (ORT), length of stay (LOS), number of lymph nodes resected, conversion rates, and intra-operative and postoperative complications were analyzed. Results: Fifty-seven patients received RALS; 48 had CLS. RALS patients had a higher mean BMI (38.1 ± 11.8 vs. 30.1 ± 7.5 kg/m2; p=0.0003) and more comorbidities. Median ORT was longer for RALS patients [277 (135-660) vs. 223.5 (120-547) minutes; p=0.0012]. RALS ORT remained significantly longer for BMI ≥ 25 to <30, and appeared near significance in the BMI<25 and BMI>35 groups. Only in the BMI ≥ 30 to <35 group there was no apparent difference in the ORT. Among patients with endometrioid adenocarcinoma histology, ORT was longer in the RALS group [273 (135-660) vs. 222 (120-420) minutes; p=0.0018]. There was no difference in EBL or LOS between the two surgical approaches. Conclusions: In our experience, perioperative outcomes of endometrial cancer staging are comparable between RALS and CL. Furthermore, the overall ORT is significantly longer in the RALS group. Further studies of patients stratified by BMI are needed.
High-Affinity Factor IXa Receptors Induced by Factor Vil Are Deficient on Platelets in Scott Syndrome

Field: Medicine (Health Sciences)

We have studied factor IXa binding and factor X activation with normal platelets and with platelets obtained from a patient with a bleeding disorder and an isolated deficiency of platelet procoagulant activity termed Scott syndrome. In the absence of factor VIIIa and factor X, normal, thrombin-treated platelets exposed 560±35 sites for factor IXa with a Kd of 2.75±0.27 mM, compared with 461±60 sites per patient platelet with Kd of 3.2±0.33 nM. The addition of factor VIIIa and factorX resulted in a decrease in the Kd for normal platelets to 0.68 nM but had no effect on the Kd for patient platelets. The concentrations of factor IXa required for half-maximal rates of factor X activation for normal (0.52 nM) and patient platelets (2.5 nM) were similar to those determined from equilibrium binding studies. Kinetic parameters for factor X activation by factor IXa showed that the K. and k,1 were identical for normal and patient platelets in the absence of factor VIlla. In the presence of factor VIIIa, and k,,1, for patient platelets (163 min-') was only 33% of that for normal platelets (491 min-')This result can be explained by the difference in affinity for factor IXa between normal and patient platelets in the presence of factor VIIIa, suggesting impaired factor VIIIa binding to Scott syndrome platelets.
Treatment Approaches for Amyotrophic Lateral Sclerosis

Field: Medicine (Health Sciences)

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that impairs motor neuron function, causing progressive muscle weakness and paralysis. ALS is extremely rare, affecting only around 30,000 people in the United States. However, it has a very low survival rate; only 10% of patients survive 10 years after disease onset. While the cause is typically unknown, 5-10% of ALS cases are caused by genetic mutations in the SOD1 and C9orf72 genes. Currently, several FDA-approved therapies for ALS exist. These drugs aim to partially correct the SOD1 mutation, or block cellular and neurological pathways related to motor neuron damage. In clinical studies to date, these drugs either unsuccessfully treat ALS, or are only able to prolong a patient's lifespan up to several months. Scientists are exploring novel therapies that target the root cause of ALS, whether it be damaged neurons, genetic factors, or muscle dysfunction. These therapies include gene therapy, monoclonal antibody therapy, and stem cell therapy. While further research is needed, current data show significant promise, as these treatments directly target the underlying mechanisms of ALS, rather than focusing on select symptoms like conventional approaches, ultimately making new approaches to ALS therapy more sustainable for the future. This paper will discuss and evaluate current FDA-approved therapies for ALS and explore the potential efficacy of novel treatments.
Intravenous Immunoglobulins for Recurrent Chronic Histiocytic Intervillositis: A Series of Case Studies

Field: Medicine (Health Sciences)

ABSTRACT Introduction Chronic histiocytic intervillositis (CHI) is a rare inflammatory placental disease characterized by diffuse infiltration of monocytes into the intervillous space and is associated with adverse pregnancy outcomes. No treatment is currently validated and although in some small reports, steroids with hydroxychloroquine have been described. There are no data for other therapies in refractory cases. Patients and Methods We here report four cases of patients with a history of CHI treated with immunoglobulins during a subsequent pregnancy. The four patients with recurrent CHI had failed to previous immunomodulatory therapies with steroids and hydroxychloroquine. All patients had at least four pregnancy losses with histopathological confirmation of CHI for at least one pregnancy loss. The usual pregnancy‐loss etiology screening and immunological screening were negative for all the patients. Results For three patients, intravenous immunoglobulins were initiated at the βHCG positivity at 1 g/kg every 15 days until delivery. In one case with combined therapy since the beginning of the pregnancy, intravenous immunoglobulins were introduced at 20 WG because of severe growth restriction. Two patients had live births at 36 WG and one patient at 39 WG. One patient, who presented early first‐trimester hypertension and severe placental lesions, failed to intravenous immunoglobulins and had a pregnancy loss at 15 WG. Conclusion This is the first report demonstrating the potential benefit of intravenous immunoglobulins in recurrent chronic intervillositis. Larger studies are needed to confirm this potential benefit for patients presenting severe cases of recurrent CHI.
Who is afraid of biosimilars? Openness to biosimilars in an Australian cohort of patients with rheumatoid arthritis

Field: Medicine (Health Sciences)

Abstract Biosimilars are increasingly adopted to improve affordability of biologics. An effective introduction of biosimilars requires an understanding of patient acceptance of these agents. We performed a cross‐sectional study of 132 patients with rheumatoid arthritis prior to the introduction of biosimilar switching or prescribing in this cohort. Despite being unfamiliar with biosimilars, most patients are willing to accept biosimilar medicines if recommended by their rheumatologist. Patient concerns about biosimilar uptake mainly focus on concerns about its efficacy. There is a significant correlation between patient attitudes towards biosimilar and generic medicines.
Classification Scheme for Root Cause and Failure Modes and Effects Analysis (FMEA) of Passenger Vehicle Recalls

Field: Engineering (Physical Sciences)

This study analysed 345 passenger vehicle recalls that were reported to the National Highway Traffic Safety Administration. The root cause analysis was applied to analyse each recall event in order to derive the cause of the recall, i.e., the defect type. Classification schemes were developed to organize the defective components and defect type into useful categories. The defect types were classified into manufacturing defects, design flaws, and mislabelling. Each of the above categories was expanded into smaller subcategories and items. Following the root cause analysis, the functional block diagram, and failure modes and effects analysis (FMEA) were applied to translate defective recall cases into FMEA tabular statements. Cramer's V and Phi coefficient analyses were applied to identify significant associations between defective components and defect types to prevent the future recurrence of recalls and improve vehicle quality. This study demonstrated that root cause and FMEA, based on an orthogonal classification scheme, can be applied to derive feasible solutions for reducing vehicle safety recalls, and such analysis can be generalized to other products or manufacturing processes.
The NMDA receptor expression and significance in the pulmonary after acute spinal cord injury causing lung injury in rats

Field: Medicine (Health Sciences)

Objective To investigate the NMDA receptor expression and significance in the lung injury caused by acute spinal cord injury.Methods 36 rats were divided into two groups:model group(group A)and MK-801 treated group(group B)which were divided into subgroups of 12h,1,3 days after injury respectively(each subgroup,n=6).All animals were sacrificed at the time points(12h,1d,3d)after injury.Group B were treated with 0.1 ms/kg MK-801 6h before sacrificed.The lung W/D,the content of cells and the total protein in bronchoalveolar lavage fluid(BALF)were determined.Results In group A,pulmonary hemorrhage and edema were observed at the 12th hour,and reached peak at the 3rd day after injury.Those parameters determined in group B were significantly improved than that in group A(P<0.05).Conclusions Pulmonary hemorrhage and edema appear in the early stage after spinal cord injury in rats,which may be the pathological basic of the early respiratory failure and pulmonary infection,and it may induce the acute lung injury through the activation of NMDA receptor.

Key words:
Spinal cord injuries/CO; Respiratory distress syndrome,adult/CO; Receptors,N-methyl-D-Aspartate/ME
Leffingwell Odor Dataset

Field: Computer Science (Physical Sciences)

NOTE: It's easier to download this dataset from pyrfume. Here's how:

# First install pyrfume in your Python environment. This can be done easily with pip. # pip install pyrfume import pyrfume molecules = pyrfume.load_data('leffingwell/molecules.csv', remote=True) behavior = pyrfume.load_data('leffingwell/behavior.csv', remote=True) # e.g. to count the number of molecules with each descriptor behavior.sum().sort_values(ascending=False).astype(int)

Predicting properties of molecules is an area of growing research in machine learning, particularly as models for learning from graph-valued inputs improve in sophistication and robustness. A molecular property prediction problem that has received comparatively little attention during this surge in research activity is building Structure-Odor Relationships (SOR) models (as opposed to Quantitative Structure-Activity Relationships, a term from medicinal chemistry). This is a 70+ year-old problem straddling chemistry, physics, neuroscience, and machine learning. To spur development on the SOR problem, we curated and cleaned a dataset of 3523 molecules associated with expert-labeled odor descriptors from the Leffingwell PMP 2001 database. We provide featurizations of all molecules in the dataset using bit-based and count-based fingerprints, Mordred molecular descriptors, and the embeddings from our trained GNN model (Sanchez-Lengeling et al., 2019). This dataset is comprised of two files: leffingwell_data.csv: this contains molecular structures, and what they smell like, along with train, test, and cross-validation splits. More detail on the file structure is found in leffingwell_readme.pdf. leffingwell_embeddings.npz: this contains several featurizations of the molecules in the dataset. leffingwell_readme.pdf: a more detailed description of the data and its provenance, including expected performance metrics. LICENSE: a copy of the CC-BY-NC license language. The dataset, and all associated features, is freely available for research use under the CC-BY-NC license. If you use the data in a publication, please cite:

@article{sanchez2019machine, title={Machine learning for scent: Learning generalizable perceptual representations of small molecules}, author={Sanchez-Lengeling, Benjamin and Wei, Jennifer N and Lee, Brian K and Gerkin, Richard C and Aspuru-Guzik, Al{\'a}n and Wiltschko, Alexander B}, journal={arXiv preprint arXiv:1910.10685}, year={2019} }
Serial Point‐Prevalence Studies to Investigate Hospital Antimicrobial Prescribing

Field: Health Professions (Health Sciences)

ABSTRACT Aim To investigate antimicrobial prescribing patterns using a validated point‐prevalence approach and to identify intervention targets to optimise antimicrobial use. Method 3 prospective point‐prevalence studies were conducted over 4‐day periods in April 2005, September 2005 and April 2006 at a tertiary hospital using a previously published method. Clinical pharmacists used a standardised data collection form on an allocated day to record details of all patients who were prescribed systemic antimicrobials (antivirals, antifungals, antibacterials) and the total number of patients seen. The appropriateness of the IV route was assessed using pre‐defined criteria. Results Over the 3 study periods 1515 drug charts were reviewed. Of these, 508 (34%) patients were prescribed 832 antimicrobial courses. The mean patient age was 67.5 (SD 32.3) years and 55% were males. Treatment accounted for 730 (88%) courses and prophylaxis for 102 (12%). The most frequently prescribed antimicrobials were ceftriaxone (9.7%) and amoxycillin/clavulanate (7.5%). The most commonly prescribed antimicrobial classes were penicillins (26%) and cephalosporins (20%). 342 (41%) courses were restricted antimicrobials and 85% of these had appropriate approval. 478 (58%) courses were given IV with clinical pharmacists identifying that 2.9% of these could have been given orally. Conclusion Serial point‐prevalence studies proved to be an effective tool for examining baseline patterns of antimicrobial use. This efficient and reproducible tool would be appropriate for other hospitals to use as a component of their antimicrobial usage monitoring.
A Critical Analysis On Margaret E. Roberts (2018), Censored: Distraction And Diversion Inside China's Great Firewall

Field: Social Sciences (Social Sciences)

Margaret E. Robert book builds on a foundation of the basic law of economy which is the relationship between supply and demand. She argues that censorship Chinese government censorship has violated free market law. In her book, she specified three mechanisms of censorship; fear, friction, and flooding (Roberts 2018). She explained in detail how Chinese’s people reactions toward the censorship in chapter four, five and six. In this paper, I challenged Roberts idea that fear is not part of the censorship mechanism. I have two arguments; first fear is emotion it needs stimuli to appear. Second fear and curiosity are motivation behind information seeking. Fear appeared from negative experience while curiosity appeared from positive outcomes. Fear is part of information behavior, it works like a brake system (Heinstrom 2010). Through fear, the disappointment and punishment will be evaluated by individuals to decide the next move. Fear is something dynamic, as time evolve it creates sensitivity, but it does not stop the basic need of information. American astronaut Thomas P. Stafford mentioned that evolution made us the ultimate learning machine, and the ultimate learning machine needs to be oiled by curiosity (Stafford 2012). At the end of my paper, I suggested Roberts to consider using word threat as one of censorship mechanism rather than fear.
Fine structure of the cyrtophorid ciliate Chlamydodon mnemosyne Ehrenberg, 1837

Field: Agricultural and Biological Sciences (Life Sciences)

Summary. Chlamydodon mnemosyne is a bottom-dwelling cyrtophorid ciliate found in brackish water ponds. The morphology of nondividers is described based upon light microscopy of living and silver stained cells. In addition we provide a detailed descrip tion of the ultrastructure of the cells. C. mnemosyne is dorsoventrally flattened and ciliated only on the ventral surface which is separated from the dorsal surface by a peculiar transversally striped band at the margin of the cells. This band consists of regularly arranged C- shaped clasps with a complex multilayered fine structure. The somatic ciliature is subdivided in right and left fields of kineties flanking a medial field of 4 postoral kineties. The somatic monokinetids are associated with tubular and fibrillar cytoskeletal elements according to the phyllopharyngid pattern, the most pronounced feature being a pack of subkinetal microtubules. Similar to other cyrtophorid ciliates the oral ci liature consists of an inner and an outer circumoral kinety as well as a preoral kinety all of which are built up from dikinetids with their ant erior kinetosome bearing the cilium. The oral apparatus consists of an inner ring of cytopharyngeal lamellae and an outer ring of 9 large and 2 small anteriorly positioned nematodesmal rods resulting in the bilateral appearance of the cytopharyngeal basket. The rods are capped with so ca lled dentes which harbour a barren kinetosome each. The detailed ultrastructural description provided here serves as a basis for studies on the morphogenesis of C. mnemosyne, part of which are presented in an accompanying paper (Bardele and Kurth 2001).
Environmental and Location Effects on Nut Set, Nut Characteristics, and Yield of ‘Ka'u’, ‘Kea'au’, and ‘Keauhou’ Macadamia (Macadamia Integrifolia Maiden and Betche)

Field: Agricultural and Biological Sciences (Life Sciences)

This three-year study was undertaken to determine the effects of temperature, rainfall, and tree age on nut set, percent kernel, percent grade 1 kernel, and yield of three macadamia cultivars at eight locations in Hawaii. Initial nut set two weeks after anthesis was highest with maximum temperatiires from 18 to 24°C for macadamia cultivars Keauhou, Ka'u, and Kea'au. Increased rainfall in the two weeks after anthesis was associated with a reduction in initial nut set of 'Keauhou' and 'Ka'u', within a range of 1 tb 95 cm of rainfall. Final nut set of 'Keauhou' appeared optimum with a rainfall of 100 cm within a range of 1 to 215 cm during the eight weeks from anthesis to final nut set. As rainfall increased from 1 to 215 cm during the eight weeks from anthesis to final nut set, final nut set of 'Ka'u' and 'Kea'au' was reduced. Final nut set was highest at a minimum temperature of 14°C for all three cultivars. A slight increase of percent kernel of 'Keauhou' and 'Ka'u' was associated with increasing maximum temperatures from 20 to 25°C in the 90 days after anthesis. A reduction in percent kernel of 'Keauhou' and 'Ka'u' was related to maximum temperatures above 26°C. Increasing minimum temperature from 13 to 17°C was related to an increase of percent grade 1 kernels for 'Keauhou'. Percent grade l kernels of 'Keauhou' decreased with increasing age of trees. An increase in percent grade 1 kernels occurred for 'Ka'u' up to 12 years of age, followed by a decline up to 17 years when a more rapid decline occurred. Increasing minimum temperature from 13 to 19°C was associated with increased percent grade 1 kernels of 'Ka'u'. 'Keauhou' had higher yields with rainfall averaging 30 cm per month. Rainfall averaging 10 cm per month for 'Ka'u' and 'Kea'au' was related to higher yields. Average yearly minimum temperatures of about 14.5°C appeared optimum for yield of 'Keauhou'. 'Ka'u' and 'Kea'au' appeared to yield better with about 16 to 18°C average yearly minimum temperature.
Uncooled SWIR detection using conjugated polymers

Field: Materials Science (Physical Sciences)

III-V and II-VI compound semiconductors have long dominated high sensitivity IR detection applications. In recent years, technologies such as strained layer superlattices have emerged, but they still require cooling. We have recently demonstrated uncooled detection in predominantly the SWIR with residual detection in the MWIR and LWIR. The devices operate at uncooled, ambient temperatures and exhibit mA/W responsivities when measured against a cavity blackbody radiator, have low-kHz -3 dB electronic bandwidths, but with specific detectivities comparable to III-V and II-VI semiconductors. In one example, a polymer with an undoped SWIR bandgap well beyond 1 μm—a first for any polymer system—demonstrated broadband responsivity of 6.5 mA/W against a cavity blackbody radiator. An introduction to conjugated polymers is included that provides a bridge between the polymer and semiconductor communities.