jimnoneill/paper-to-field-training huggingface dataset:
Lysosomal disorders

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

Lysosomes are subcellular membrane-bound organelles containing primary acid hydrolases and other proteins responsible for the catabolism of naturally occurring and phagocytised intracellular macromolecules. Lysosomes are in direct continuity with both endosomal and autophagosomal streams in cells, thus forming what has been referred to as the greater lysosomal system and comprising the predominant recycling system of cells.642 Today, it is recognised that lysosomal involvement is a feature of a wide variety of neurode-generative and neurodevelopmental disorders (see below and Box 8.1). In addition, mutations in genes encoding lysosomal or related proteins are known to result in the accumulation of various molecules within lysosomes, late endosomes and autophagosomes, forming abnormal intracellular inclusions or storage bodies.359 The key mechanism responsible for these so-called lysosomal storage diseases was established in 1963 when HG Hers discovered that, in type II glycogenosis (Pompe disease), glycogen accumulated within vacuoles secondary to a defect of an α-1,4-glucosidase normally present in lysosomes. Based on this finding, Hers hypothesised that other storage disorders known at that time (e.g. Tay–Sachs and Niemann–Pick diseases) could have similar causation.249 Hers's concept of inborn lysosomal disorders included two easily detectable characteristics: a single lysosomal hydrolytic enzyme must be genetically deficient the substrate(s) of that enzyme would, as a consequence, accumulate within pathologically altered secondary lysosomes. In the ensuing years, the concept of lysosomal storage disease evolved to include disorders caused by genetic abnormalities of proteins that are not lysosomal enzymes. These include glycoprotein cofactors for lysosomal enzymes and related soluble proteins essential for lysosomal function, non-lysosomal enzymes involved in the post-translational modification or transport of lysosomal enzymes, and transmembrane proteins responsible for the egress of metabolites out of lysosomes and other functions. It is anticipated that this list will grow as a more detailed understanding of lysosomal diseases emerges.466
The Galveston Technique for L Rod Instrumentation of the Scoliotic Spine

Field: Medicine (Health Sciences)

Many small details of technique are important for achieving an excellent quality L-rod instrumentation of the scoliotic spine. Herein the authors report specifics gleaned from their experience and discuss the basis for them. The optimum approach establishes correctability of the deformity prior to spinal instrumentation, provides secure internal fixation of the spine, and strives for a massive arthrodesis.
Efficacy and Tolerability of Rufinamide in Epileptic Children Younger Than 4 Years

Field: Medicine (Health Sciences)

Background: Rufinamide, a triazole derivative, is a new-generation antiseizure medication with a novel mechanism of action. We evaluated the efficacy and safety of rufinamide treatment in children with epilepsy younger than 4 years at our center. Methods: In this retrospective study, we included children younger than 4 years who had pharmacologically resistant epilepsy and were treated with rufinamide at Boston Children’s Hospital between June 2010 and June 2018. Safety and efficacy of rufinamide treatment were assessed immediately prior to initiation of rufinamide and at the last follow-up visit. Responders were defined as patients who had greater than 50% reduction in seizure frequency on follow-up as compared to baseline. Results: We reviewed records of 128 children and included 103 with complete information. Patients consisted of 60 boys (58%), with a median age of 20 months (interquartile range 13-28, range 2-36). Median treatment duration was 15 months, and median rufinamide dosage at the last follow-up was 42 mg/kg/d (interquartile range 34-56). At the last follow-up, seizure frequency decreased (450 vs 90, P<.001) and overall seizure reduction was 54%. Fifty-one patients (49.5%) were responders with 94% seizure reduction, including 20 (19.4%) who achieved seizure freedom. Treatment retention rate at 12 months was 63%. Thirty patients (29%) developed adverse events and 41 patients (39.8%) discontinued rufinamide because of adverse events (15; 14.5%) and lack of efficacy (26; 25%). Conclusion: Rufinamide is effective in reducing seizure frequency in pediatric epilepsy patients younger than 4 years, and overall well tolerated.
Manipulating Mitochondrial Biogenesis And Cellular Metabolism Via Anaplerosis

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

The transcriptional co-activator PGC1α is sensitive to cellular energy status and nutrient availability. We have recently demonstrated in vitro that chronic elevation of pyruvate decreases TCA cycle flux, down-regulates PGC1·, and results in a metabolic phenotype similar to insulin resistance. PURPOSE: We hypothesized that carbohydrate-induced metabolic dysfunction was due to an impairment in TCA flux; therefore, to test this hypothesis, we determined whether dichloroacetate and anaplerotic amino acids could reverse carbohydrate-induced metabolic dysfunction, increase TCA cycle flux, and improve PGC1αfunction. METHODS: C2C12 myotubes were differentiated for 5 days and then treated for 72h with standard media (CON - 25mM glucose DMEM), high glucose and insulin (HG - 40mM glucose +100nM INS), high fructose and insulin (HF - 25mM fructose+100nM INS), or HG/HF plus glutamine (4mM) and dichloroacetate (DCA; 500uM). Following treatment, we determined cellular respiration and TCA flux using a Seahorse XF-24 metabolic flux analyzer, insulin sensitivity by 2DG uptake, PGC1· expression by real-time qPCR, and PGC1· promoter activity using the luciferase assay system. RESULTS: HG and HF treatments resulted in impaired respiration (HG=57% and HF=35% decrease), basal glucose uptake (HG=34% and HF=32% decrease) and insulin stimulated glucose uptake (HG=49% and HF=47% decrease). Glutamine+DCA increased cell respiration (HG=257% and HF=184%) as well as basal (HG=140% and HF=160%) and insulin stimulated glucose uptake (HG=162% and HF=187%). Finally we observed that 12h treatment of myotubes with 6 anaplerotic amino acids (glutamine, valine, asparagine, aspartate, leucine, and isoleucine) increased PGC1αpromoter activity (range: 84-217%). CONCLUSION: Our data would suggest that mitochondrial metabolism is sensitive to the availability of anaplerotic substrates and that these amino acids mediate their effect in part via activation of PGC1α. Further, the ability of anaplerosis to reverse carbohydrate-induced insulin resistance suggests that it may provide a viable treatment for metabolic disease in vivo.
Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

Field: Agricultural and Biological Sciences (Life Sciences)

Background: The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been found associated with live palm hosts. During the host plant colonization process, a massive transcriptional reorganization helps the fungus evade the host immune response and utilize plant cell wall polysaccharides. Results: A publicly available transcriptome of G. boninense - oil palm interaction was surveyed to profile transcripts that were differentially expressed in planta. Ten percent of the G. boninense transcript loci had altered expression as it colonized oil palm plants one-month post inoculation. Carbohydrate active enzymes (CAZymes), particularly those with a role in lignin degradation, and auxiliary enzymes that facilitate lignin modification, like cytochrome P450s and haloacid dehalogenases, were up-regulated in planta. Several lineage specific proteins and secreted proteins that lack known functional domains were also up-regulated in planta, but their role in the interaction could not be established. A slowdown in G. boninense respiration during the interaction can be inferred from the down-regulation of proteins involved in electron transport chain and mitochondrial biogenesis. Additionally, pathogenicity related genes and chitin degradation machinery were down-regulated during the interaction indicating G. boninense may be evading detection by the host immune system. Conclusions: This analysis offers an overview of the dynamic processes at play in G. boninense - oil palm interaction and provides a framework to investigate biology of Ganoderma fungi across plantations and landscape.
Language Contact in the Arab World: Realities and Implications

Field: Arts and Humanities (Social Sciences)

The Arab world exhibits a fascinating linguistic case that is worth investigating.Likewise Algeria Arab speaking countries implement the policy of Arabization in order to preserve the image of Arabic from any type of threat.Hence, colonialism had not expired without an impact; Linguistic diversity is by far the outcome.The present paper aims at shedding light on the sociolinguistic phenomena such as: Diglossia, bilingualism, and borrowing with reference to the situation of the Arabic language.It tries to raise the question of the utility of the Quran's language in correspondence to our globalized era
Mathematical evaluation of sloped solar chimney power plant for power generation in different regions of Nepal

Field: Energy (Physical Sciences)

Abstract Sloped solar chimney power plant (SSCPP) could be one of the appropriate technologies for powering Nepalese communities. The main components of the plant are chimney, collector and power-generating unit. In this study, the mathematical evaluation of the SSCPP has been conducted for the estimation of the power generation in Nepalese context. For the analysis, the mathematical models have been developed from the governing equations. The parameters such as chimney height and radius, collector radius, ambient temperature and solar insolation have been taken as inputs for simulation of the overall system. The output parameters such as overall system efficiency, chimney efficiency, air velocity, power output from the turbine and electrical power from the proposed system have been evaluated. The results showed that power developed by air, turbine power and electrical power is 120, 66 and 44 kW, respectively. The developed power is estimated when the height and the radius of the chimney were 190 and 5 m, respectively. It is seen that ambient temperature and velocity of air also play an important role in the power generation. The performance influencing the power output based on turbine pressure ratio, thermal conductivity and specific heat capacity of soil and the mass flow rate have also been estimated. Besides, the solar insolation data were taken for five different regions of Nepal to find the power generation and collector efficiency.
Wave attenuation over salt marsh vegetation

Field: Environmental Science (Physical Sciences)

Salt marshes are transitional areas between soil and water. Until recently these areas were usually diked and drained in order to create new agricultural land, but nowadays fortunately more awareness exists about the importance of these inter tidal areas as nature reserves and as natural coastal protections. Although awareness on the coastal protection value of salt marshes has increased in recent years, it is still uncertain how and to what extent waves are reduced by these vegetated intertidal areas. In order to get more insight into the wave damping skills of salt marsh vegetation, it was decided to make SWAN suitable for modelling situations with vegetated foreshores. The numerical description of the effect of vegetation on waves that was used, is based on representing the vegetation by vertical, ridged cylinders and was derived by Dalrymple et al.(1984). The physical vegetation properties that are considered in this formulation are the relative vegetation height, vegetation diameter and density, and the drag coefficient. The calibration parameter in the Dalrymple et al.(1984) formulation, which is of significant importance for determining the wave dissipation due to vegetation, is the drag coefficient (Cd). By varying the drag coefficient different types of vegetation (both stiff and flexible) can be modelled. The value of the drag coefficient is dependent on the Reynolds number and on the shape and orientation of the object. A more severe study of the drag coefficient, first for a single cylinder in flow, subsequently for a multi cylinder array, gave insight in the relation with both wave and vegetation characteristics. A number of processes that are not accounted for in the Dalrymple formulation are also discounted in the drag coefficient. The model was made suitable to model homogeneous, horizontally varying (zoned vegetation) and vertically varying (f.i. Mangroves) vegetation fields. As a final validation the model was applied on field measurement results from the Paulina Marsh in the Westerschelde. In this case all parameters were known except for the drag coefficient, which was calibrated. The results were satisfactory, the value for the drag coefficient ranged between 0.5 and 3.0 and the relation with the vegetation height was as expected. The implementation of vegetation in SWAN was found successful for all types of vegetation. However, due to the dependency of the drag coefficient on wave and vegetation characteristics, the model can only be applied on specific situations where wave and vegetation measurements have been taken. In order to make the model generally applicable, more research needs to be done on the dependency of the drag coefficient on wave and vegetation characteristics. When more is known about these relations, a first prediction can be made on the value of the drag coefficient in a specific situation. This can be accomplished by doing more physical modelling tests and by taking wave measurements over vegetated foreshores.
Binary fission via lnviscid Trajectories

Field: Physics and Astronomy (Physical Sciences)

Abstract We sketch an evolutionary picture which, unlike the classical picture, appears favorable to the hypothesis that close binary stars originate in the fission of a single slowly contracting protostar. The main differences from the classical picture are (1) evolution proceeds along certain families of Riemann ellipsoids, rather than along the Jacobi family and (2) the critical ellipsoid on the evolutionary trajectory suffers a deformation given by an ellipsoidal harmonic of order four, rather than of order three.
On the efficiency of public, welfare and private hospitals in Germany over time: a sectoral data envelopment analysis study

Field: Social Sciences (Social Sciences)

This paper examines the efficiency of the German hospital sector over time and the relative efficiency of public, welfare (both nonprofit) and private (for-profit) hospital sectors using data from the Federal Statistics Office of German hospitals. Efficiency scores were computed using data envelopment analysis. The absolute efficiency of the hospital sector as a whole was found to have improved between 1991 and 1996. In this comparison, the empirical results showed that the hospitals in the public and welfare sector are relatively more efficient than private hospitals. Our results suggest that public, welfare and private hospital sectors have different best-practice frontiers; and that public and welfare hospital sectors appear to use relatively fewer resources than private hospitals. These results suggest differences in quality of care arising from ownership.
Investigation into the effect of antipsychotics on the indices of genital organ and sexual function in male rat

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Objective To assess the effect of antipsychotics on the indices of genital organ and sexual function in male rat. Methods A total of 80, 3-month-old male SD rats were randomly divided into four groups. Three groups of rats were orally administered the following antipsychotics respectively for three or six weeks: quetiapine (20 mg/kg), risperidone (2 mg/kg) and haloperidol (2 mg/kg). The rats in control groups were treated by gavage with vehicle (distilled water). Their mating behaviors were evaluated on the last day of three or six weeks' treatment by using receptive female rats. The following day the rats were killed and the indices of testis, epididymis, seminal vesicle and prostate were also measured.Results~Compared with the control group, quetiapine had no effect on the indices of sexual organ and sexual function both at the third week and sixth week. At the third week, epididymis index was significantly decreased in both risperidone group (t=-3.901; P=0.001) and haloperidol group (t=-3.695; P=0.002). At the sixth week, the indices of epididymis (t=-6.077; P0.001), seminal vesicle (t=-3.984; P=0.01) and prostate (t=-3.765; P=0.01) were significantly reduced in haloperidol group, but not in risperidone group. The following sexual competence was significantly impaired in both risperidone group and haloperidol group at the third week: libido (assessed in numbers of mounting and intromission), sexual arousability/motivation (in terms of latencies for mounting, intromission), orgasm (in terms of latency for ejaculation) (U=6.5—23; P0.05—0.001). At the sixth week, haloperidol also suppressed hit ratio beside above-mentioned parameters, indicating erectile dysfunction (U=19; P=0.019). Risperidone had not significant effect on sexual function at the sixth week.Conclusions Haloperidol and risperidone possibly affect the indices of genital organ and sexual function by the different duration of action in male rats, while quetiapine may have no influence on these indices.
[Diagnostic procedure in cholecystolithiasis. Diagnostic approach, repeat examinations and (incidental) findings].

Field: Medicine (Health Sciences)

If non-surgical methods are to be taken into account in the therapeutic decision-making process in cholecystolithiasis, an expanded diagnostic work-up including not only stone parameters but also gallbladder function, is needed. In 2270 patients (1649 women, 621 men; age: 47.2 +/- 14 years) with (suspected) "cholecystolithiasis" attending the special gallstone outpatient clinic at a university medical department within a period of 5 years the diagnostic procedures most commonly used in both the doctor's office and hospital were abdominal ultrasonography (52%/78%), laboratory investigations (28%/39%) and plain films of the biliary tract (27%/39%). In the doctor's office gallbladder function testing took the form of an cholecystogram (17% of the patients); in the hospital ultrasonography to determine gallbladder contractility (38%). With decreasing frequency, the following additional procedures were carried out (office/hospital): CT 3%/19%, esophagogastroduodenoscopy 7%/3%, intravenous cholegram 6%/0.6%, abdominal X-ray 1%/0.4%, ERCP 1%/0.4%, chest X-ray 0.8%/1.6%. Duplicated examinations showed a relevant frequency only for ultrasonography (39% of the cases), laboratory investigations (18%) and plain films of the gallbladder (4%). Pathologic secondary findings were established in 22% of the cases.
Theoretical studies on the spectroscopic properties of methyl mercaptan (CH3SH)

Field: Chemistry (Physical Sciences)

The properties of the ground and low-lying excited states of methyl mercaptan (CH3SH) are studied by using quantum chemistry methods. The geometric parameters and energies of the ground state and the triplet excited state are calculated in this work. It is shown that the calculated geometries of the ground and triplet state are stable and the triplet state potential energy surface has the repulsive feature. The calculated vertical excitation energies and vertical ionization potentials of methyl mercaptan are in best agreement with the experimental values. In addition, the vertical electron affinity and the adiabatic electron affinity of the CH3SH molecule are also calculated.
Modeling cellular ROS defense in mitochondrial-related diseases

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

Reactive Oxygen Species (ROS) generation is an unavoidable background process during normal cellular function. The main contributor to ROS production is the electron transport chain, which reduces oxygen to water. Some incompletely-reduced oxygen species escape and oxidize a variety of organic molecules, leading to molecular dysfunction and initiating a positive feedback loop of ever increasing active radical production. The increased concentration of ROS damages the mitochondria, therefore further elevating the rate of ROS generation. Healthy cells manage ROS enzymatically and by mitophagy of damaged mitochondria. The precise tuning of the latter mechanism is crucial for cell survival and is controlled by a ROS-induced regulatory network. We have built a set of kinetic models of varying complexity, based on the current understanding of the mechanism of cellular ROS defense. Our models allow simulation of various patho-physiological scenarios related to mitochondrial dysfunction and the failure of the system of ROS regulation in human cells. We employ the models we have constructed to simulate the effects of diseases related to mitochondrial dysfunction and excessive ROS generation, such as Parkinson’s disease, Huntington’s disease and cancer. Experimental evidence is used for model fitting, and we propose model improvements based on incorporation of single-cell experimental measurements. Finally, we discuss the perspective of integrating our kinetic models with genome-scale, constraint-based, tissue-specific models of metabolism, in order to study the effect of ROS misregulation on metabolic phenotype.
Synthesis and absolute configuration of the stereoisomers of [2-(1-diethylaminopropyl)] 1-hydroxy-1,1?-bicyclohexyl-2-carboxylate, a muscarinic antagonist

Field: Chemistry (Physical Sciences)

The compound [2-(1-diethylaminopropyl)] 1-hydroxy-1,1′-bicyclohexyl-2-carboxylate 1 is a muscarinic antagonist characterized by the presence of three chiral atoms and eight possible stereoisomers. The binding affinities to the five cloned m1–m5 muscarinic receptors of the stereoisomers of 1 were previously investigated and proved to be related to the chirality of the molecules. The eight isomers are prepared through the synthesis of their racemates followed by chemical resolution as (+) and (−) tartrate or (+) and (−) dibenzoyltartrate salts. The isomers with cis-configuration of OH and COOH substituents of the cyclohexane are also obtained by coupling optically active (1S, 2S) or (1R,2R)-1-hydroxy-[1,1′-bicyclohexyl]-2-carboxylic acid with (S)- or (R)-1-diethylamino-2-propanol. Chiral GC and HPLC methods are used to determine their optical purity. The absolute configurations of the four cis- and four trans-isomers are established by stereospecific synthesis and X-ray crystallographic data. Chirality 9:713–721, 1997. © 1997 Wiley-Liss, Inc.
Medicinal properties of Cleome viscose: A Critical Review

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Cleome viscose Linn. (Capparidaceae), is an annual, sticky herb found as a common weed all over the plains of India and throughout the tropics of the world. The whole plant and its parts (leaves, seeds,bark and roots) are widely used in traditional and folkloric systems of medicine. In traditional systems of medicine the plant is reported to possess beneficial effects as an anthelmintic, antiseptic, carminative, antiscorbutic, febrifuge. The pharmacological studies have shown that Cleome viscose possesses different biological activities such as, antidiarrheal, hepatoprotective anthelmintic, antimicrobial, analgesic, antiinflammatory, immunomodulatory, antipyretic, psychopharmacological activities. The present review article is an effort to look forward for the traditional medicinal information and advantages on C. viscose for further studies and future prospects.