jimnoneill/paper-to-field-training huggingface dataset:
Differential expression of CEP128 in amyotrophic lateral sclerosis.

Field: Neuroscience (Life Sciences)

Neurodegenerative diseases that affect the motor neurons, including amyotrophic lateral sclerosis (ALS), have little treatment options and are generally rapidly fatal (1, 2). We harnessed the power of unbiased, whole transcriptome differential gene expression analysis, utilizing primary patient cells and tissues to discover genes whose expression defines ALS using published data (3, 4). We found significant differential expression of CEP128, encoding centrosomal protein 128, in induced pluripotent stem cell (iPSC)-derived motor neurons from patients with ALS. Analysis of a second public microarray dataset demonstrated that CEP128 differential expression in iPSC-derived motor neurons was a conserved feature in humans with ALS. CEP128 transcript was present at lower levels in ALS patient motor neurons as compared to control motor neurons. These analyses will begin to define the transcriptional landscape of ALS.
Decision-making in organizations: the new paradigm

Field: Decision Sciences (Social Sciences)

Decision-making is ever present in all forms of organized human activity. Decisions range from the simple to the complex within large organizations, whether in the nonprofit, public or private sectors. Throughout human history, man has sought to control the results of his decisions, to quantify them, to increase their predictability and to reduce their risks. Three current areas of decision making: risk assessment, chaos theory and strategic management are analyzed in this article. Their interconnectedness and potential as a "new paradigm" is its focus.
Afghanistan and beyond: Reflections on the future of warfare

Field: Social Sciences (Social Sciences)

Abstract : The author provides an historical analysis of lessons from the war in Afghanistan so that policymakers and analysts alike will better understand the nature of operations other than war in multiethnic states. Many fear these wars will set the paradigm for future wars and will exert pressure on U.S. forces to conduct peacekeeping, peace enforcement and humanitarian assistance operations in especially dangerous areas. Yugoslavia and Somalia bear out the ubiquity of these wars and the pressures upon the United States to act. Hopefully mechanisms can be devised to forestall and avert future wars, or to bring them to the speediest possible conclusion. Should those mechanisms fail and troops have to be committed, this analysis should enable commanders to have a better grasp of the nature of the war they will fight. Understanding the war and the theater should facilitate a solution more in keeping with U.S. interests and values.
Jingshu Keli and its Components Notoginsenoside R1 and Ginsenoside Rb1 Alleviate the Symptoms of Cervical Myelopathy through Kir3.1 Mediated Mechanisms

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Background & Objective:: Cervical Spondylotic Myelopathy (CSM) is one of the most serious spinal cord disorders in adults. Pharmacological modulation of ion channels is a common strategy to interfere with CSM and prevent neuronal damage. Methods: Here, we investigated the effects of Jingshu Keli (JSKL), a traditional Chinese herbal formula, on CSM-related gait abnormality, mechanical allodynia and thermal hyperalgesia, and assessed the neuronal mechanisms of JSKL on cultured brainstem cells. Behavioral tests and patch clamp recordings were performed to make this assessment. Results: In our study, we found that JSKL significantly recovered the gait performance (P<0.001) and decreased the levels of mechanical pain in 18.9% (P<0.01) and thermal pain in 18.1% (P<0.05). Further investigation suggested that JSKL and its containing ginsenoside Rb1 (GRb1), notoginsenoside R1 (NGR1) reduced the action potential frequency in 38.5%, 27.2%, 25.9%, and hyperpolarized resting membrane potential in 15.0%, 13.8%, 12.1%, respectively. Kir channels, not KV channels and KCa channels, were the major intermediate factors achieving treatment effects. Finally, immunostaining results showed that the phosphorylation of Kir3.1 was promoted, whereas the total expression level did not change. Conclusion: Our study reveals a novel strategy of treating CSM by using Traditional Chinese Medicines (TCMs) containing active components.
Jack Pine Signalling and Responses to Herbivory

Field: Agricultural and Biological Sciences (Life Sciences)

Intra and inter-plant signalling was investigated in jack pine (Pinus banksiana) seedlings in response to jack pine budworm (Choristoneura pinus, Lepidoptera: Tortricidae) feeding. Defoliation was followed by a fungal inoculation by blue stain fungus (Grosmannia clavigera) to assess resistance. Results from greenhouse experiments showed that: 1) intra-plant signalling was mediated by intensity of larval defoliation, 2) intra-plant signalling was not observed with mechanical wounding 3) seedling resistance to a fungal pathogen depended on type of defoliation before inoculation, and 4) volatile-exposure from defoliated seedlings could mediate resistance to subsequent fungal infection. In mature jack pine stands in Ontario, needle monoterpene concentrations decreased on budworm defoliated and nearby branches. Monoterpene concentration in the phloem of mature trees was higher in trees with high budworm infestation. This research contributed to the understanding of inducible responses and volatile signalling in conifer systems. Effects of herbivory on jack pine were investigated though analysis of volatile and tissue monoterpenes, known to mediate multi-organismal ecological interactions.
A Fusion Approach for Water Area Classification Using Visible, Near Infrared and Synthetic Aperture Radar for South Asian Conditions

Field: Earth and Planetary Sciences (Physical Sciences)

Consistent estimation of water surface area from remote sensing remains challenging in regions such as South Asia with vegetation, mountainous topography, and persistent monsoonal cloud cover. High-resolution optical imagery, which is often used for global inundation mapping, is highly impacted by clouds, while synthetic aperture radar (SAR) imagery is not impacted by clouds and is affected by both topographic layover and vegetation. Here, we compare and contrast inundation extent measurements from visible (Landsat-8 and Sentinel-2) and SAR (Sentinel-1) imagery. Each data type (wavelength) has complementary strengths and weaknesses which were gauged separately over selected water bodies in Bangladesh. High-resolution cloud-free PlanetScope imagery at 3-m resolution was used as a reference to check the accuracy of each technique and data type. Next, the optical and radar images were fused for a rule-based water area classification algorithm to derive the optimal decision for the water mask. Results indicate that the fusion approach can improve the overall accuracy by up to 3.8%, 18.2%, and 8.3% during the wet season over using the individual products of Landsat8, Sentinel-1, and Sentinel-2, respectively, at three sites, while providing increased observational frequency. The fusion-derived products resulted in overall accuracy ranging from 85.8% to 98.7% and Kappa coefficient varying from 0.61 to 0.83. The proposed SAR-visible fusion technique has potential for improving satellite-based surface water monitoring and storage changes, especially for smaller water bodies in humid tropical climate of South Asia.
The Impact of Financing on Water Supply Efficiency in Tanzania: A Case of Babati District.

Field: Social Sciences (Social Sciences)

Inefficiencies in water supply systems are a critical challenge in many developing regions, including Babati District, Tanzania. Despite efforts to improve water access, issues such as inadequate government funding, inconsistent development aid, limited community involvement, water leakage, and high energy costs hinder the efficient operation of these systems. These inefficiencies compromise service delivery, leading to unreliable access to clean water and heightened operational costs. Therefore, this study examines the impact of government funding, development aid, and community contributions on the efficiency of water supply systems in Babati District. Utilizing a cross-sectional research design, data were collected from 76 respondents, including government officials, water utility workers, and community leaders. Regression analysis revealed that government funding, development aid, and community contributions have a significant positiveimpact on water supply efficiency. In contrast, water leakage and high energy costs were found to negatively affect efficiency, with population density also presenting a marginally significant challenge. Based on these findings, the study recommends increased public investment in infrastructure, greater community engagement, and the adoption of energy-efficient technologies to improve water service sustainability and performance in the district. These insights provide a framework for policymakers and stakeholders to address water inefficiencies and improve service delivery in similar rural contexts.
From trees to money: the contribution of njansang (Ricinodendron heudelotii) products to value chain stakeholders’ financial assets in the South West Region of Cameroon

Field: Agricultural and Biological Sciences (Life Sciences)

Njansang -Ricinodendron heudelotii (Baill.) Pierre ex Pax.- is a commonly traded non-timber forest product from Central African humid forests, used as a spice. South West Cameroon was selected as major production area and market where little data exist on the contribution of njansang to stakeholders livelihoods in the value chain. Interviews were used to gather information from 261 harvesters, traders and processing enterprises. From 2013 to 2015, 65.8 tons were harvested, with 13.17 tons traded in markets in the South West Region and in Nigeria for a value of €33,511. The ease of accessing markets makes a significant difference to the quantity harvested and contribution to harvesters’ household income. Average profit for harvesters is higher in regional markets than in local ones. Harvester’s profits were higher than buy’amsell’ams, retailers and exporters. Processors add the most value and earn the highest unit profits. Livelihood dependence upon njansang decreases along the chain, with harvesters more dependent than traders. Seasonality, corruption, storage and processing, influence price. Long-term value chain sustainability could be improved by increasing collaboration between stakeholders, collective action, disseminating knowledge about processing and storage techniques, and promoting domestication and cultivation to enable trade in this largely wild harvested NTFP to continue sustainably.
Study of Zr-based metal-organic frameworks for water remediation

Field: Environmental Science (Physical Sciences)

MOFs are a class of crystalline inorganicorganic
hybrid porous materials which show
large surface areas, high porosity and easy
chemical tunability. The MOFs are produced by
a coordination reaction between metal clusters
and organic ligands.1 The interest on these
compounds is mainly due to the outstanding
physical properties they show, which allow
them to access many different uses of
applications (gas separation, catalysis,
biomedical imaging etc).2 MOF-801 and MOF-
808 are two Zr-based MOFs which have shown
a high chemical stability. Therefore, we have
studied the adsorption capacity of both
compounds towards the adsorption of Cr(VI)
from water.
[Quantitative alterations to resorption villi of normal human placentae in the course of gestation (author's transl)].

Field: Medicine (Health Sciences)

A total of 45 placentae of different gestatory age were used to study, after clinically and anamnestically normal pregnancy and by a morphometric method, the quantitative behavior of individual parts of the placental barrier in the course of gestation. For this, hematoxylin-stained preparations and enzyme-incubated semi-thin sections were used. The increase in the percentage of fetal vascular surface with a simultaneous decrease in the relative percentage of villous surface (when determining the ratio of villous surface surrounded by maternal blood to the fetal vascular surface) up to the 28th week of gestation must be considered an expression of an increase in the capability of function. The simultaneous distinct decrease in the average number of Langhans cells and the reduction of their less differentiated forms in favor of those showing a higher degree of differentiation allow to make the conclusion that around the 28th week of gestation conditions in individual villi are, in general, similar to those prevailing in term placentae between the 37th and 41st weeks of gestation. The results obtained from the basis of quantitative studies of the placentae of premature infants and babies born at term after different gestatory risks.
Outcome of Non-Operative/Closed Management of Mandibular Condylar Fractures in Children

Field: Dentistry (Health Sciences)

Objective: To evaluate the outcome of non-surgical treatment of mandibular condylar fractures in growing children using maxillomandibular fixation (MMF) via arch bars, metal wires, elastics and gunning splint (where dentition did not provide support for MMF). Methodology: This prospective study consisted of 67 children of condylar fractures collected at the Oral and Maxillofacial Surgery Departments of King Edward Medical University (KEMU)/Mayo Hospital, Lahore and Fatima Memorial Hospital, Lahore. Maxillomandibular fixation (MMF) with wires was used if there were severe occlusal disturbances. Mild occlusal disturbances were treated with elastic MMF. Mean follow-up period was 4.5 years (follow-ups every 3, 6, 12 & 24 months) and following variables were recorded, i.e. occlusion, mouth opening, degree of lower jaw deviation on rest/mouth opening, temporomandibular joint (TMJ) ankylosis etc. Data analysis was done using SPSS version 24. Results: Fifty one (76.1%) patients showed normal occlusion with normal symmetrical mouth opening. Nine patients (13.5%) had normal occlusion with asymmetrical mouth opening on the affected side. Overall seven (10.4%) patients were diagnosed with TMJ ankylosis during the close follow-up period. Conclusion: Non-operative/closed approach along with regular follow-up in children is a suitable, safe, reliable and non-traumatic treatment modality for growing children having mandibular condylar fractures.
Characterization of the effect of the menstrual cycle, estradiol and Fads2 transcript variants on fatty acid composition and enzyme expression

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

Estrogen is believed to regulate fatty acid composition based on observations of differences between men and women, and changes associated with altered estrogen levels in women during pregnancy, menopause and hormone treatment. Estrogen is consistently associated with increased levels of 18:0, 16:1n-7 and elongase 6, an enzyme in monounsaturated fatty acids (MUFA) biosynthesis. In some, but not all studies, estrogen has also been associated with increased 22:6n-3 and FADS2 expression. FADS2 is responsible for delta-6 desaturase activity, the rate-limiting step in polyunsaturated fatty acid (PUFA) biosynthesis and is necessary for the synthesis of 22:6n-3, which is critical for cardiovascular health and neural development. In this thesis, the effects of subtle changes in estrogen levels during the menstrual cycle in humans, and the estrous cycle in rats, on fatty acid metabolism was examined. In addition, the response of FADS2 to estrogen was examined using MCF7 cells. The presence of multiple FADS2 transcript variants in MCF7 cells was determined, and the role of two variants in PUFA biosynthesis was examined by transfecting them into HEK 293 cells. During the menstrual cycle in women and estrous cycle in rats, increased blood levels of 16:1n-7 and 22:6n-3, and decreased levels of 22:5n-3 were observed when blood estrogen levels were high. The increased 22:6n-3 and decreased 22:5n-3 suggests an effect of estrogen on FADS2 expression and/or activity. In the rat hepatic expression of FADS2 mRNA varied over the cycle, but protein levels did not. However, in estrogen sensitive MCF7 cells, FADS2 mRNA was induced by estrogen. Changes in 22:6n-3 and 22:5n-3 were not observed in the MCF7 cells. Further examination identified multiple transcript variants of FADS2 in MCF7 cells, and demonstrated that the expression of an alternatively spliced transcript variant (FADS2_v2) was considerably higher. Notably, this variant lacked the N-terminal cytochrome-binding domain that is critical for activity, suggesting that it may not be functional. In transfected HEK 293 cells, indirect evidence of delta-6 desaturase activity was observed for the full length wild type variant (FADS2_v0/1) but not for FADS2_v2. When the variants were co-transfected, FADS2_v2 interacted with and inhibited FADS2_v0/1. This work helps further understanding of the relationship between estrogen, lipid biosynthetic enzymes and fatty acid status that is important for determination of dietary requirements of 22:6n-3 for women throughout the lifespan.
BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations

Field: Computer Science (Physical Sciences)

Bayesian Inference of Conformational Populations (BICePs) version 2.0 (v2.0) is a free, open-source Python package that reweights theoretical predictions of conformational state populations using sparse and/or noisy experimental measurements. In this article, we describe the implementation and usage of the latest version of BICePs (v2.0), a powerful, user-friendly and extensible package which makes several improvements upon the previous version. The algorithm now supports many experimental NMR observables (NOE distances, chemical shifts, J-coupling constants, and hydrogen-deuterium exchange protection factors), and enables convenient data preparation and processing. BICePs v2.0 can perform automatic analysis of the sampled posterior, including visualization, and evaluation of statistical significance and sampling convergence. We provide specific coding examples for these topics, and present a detailed example illustrating how to use BICePs v2.0 to reweight a theoretical ensemble using experimental measurements.
Re-Fracturing in Eagle Ford and Bakken to Increase Reserves and Generate Incremental NPV - Field Study

Field: Energy (Physical Sciences)

Abstract Due to the tight nature of the matrix in shale plays, the drainage area does not extend far into the reservoir and is defined by the shape and size of the hydraulic fractures. As a consequence of this, wells typically exhibit steep decline rates and one of the prevalent ways to arrest the decline of a field is to drill and complete more wells. However, re-fracturing is slowly gaining a foothold in the industry, and our study has shown tremendous re-frac potential in the Bakken and Eagle Ford. In this study, we analyzed horizontal wells from the Bakken and Eagle Ford to identify existing re-fractured wells and estimated incremental recovery, followed by an economic analysis, to show re-fracturing as a viable alternative to drilling new wells. Production and completions data was retrieved from public sources for all horizontal wells in the Bakken and the Eagle Ford formations, and a proprietary algorithm was applied to identify wells with a production signature that is consistent with a recompletion event. These wells were individually screened and confirmed as being re-fractured or not. Production metrics were defined to understand the performance of the wells before and after re-fracturing. Cross plots were made between these parameters to understand trends between the ratios of production decline rates and b-factors before and after re-fracturing, taking into account the time of re-completion. Decline curves were fit to the production of these wells to estimate the incremental estimated ultimate recovery (EUR) upon re-fracturing, and a net present value (NPV) analysis was done to determine commercial viability. A majority of the identified potentially re-fractured wells had positive incremental NPV based on the EUR increase, which was 53% and 69%, on an average, for the Eagle Ford and Bakken respectively. From the existing re-fractured wells that were analyzed, it was found that there was no discernible correlation between the time an operator produces a well before being refractured and the various performance metrics that were analyzed. Also, good decline curve fits were found without changing the b-factors post-refrac and secant decline rates were typically lower after re-fracturing. The results show the potential of re-completing wells and increasing reserves without drilling new wells based on actual field examples, showing an alternative field development strategy to the current practice of replacing older wells with newly drilled ones. Also, if re-fracturing is to be implemented on a larger scale, wells must be completed so as to make subsequent recompletions much easier, thereby encouraging use of novel casing and diverting agent technologies. Positive economics shows the huge potential of cost savings with re-stimulation and makes a ‘second wave’ of Eagle Ford/Bakken production possible.
Carotenoid metabolism in phytoplankton

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

Carotenoids are among the natural products with the highest diversity. To date more than 700 different naturally occurring carotenoids have been described (Britton et al., 2004), and they are virtually ubiquitous in living organisms. Carotenoids belong to the compound class of isoprenoids, and the majority of carotenoids are tetraterpenoids with a C40 skeleton as the basic molecular structure. Formally, they can be divided into the carotenes, which are pure hydrocarbons, and the xanthophylls, which are derived from carotenes by introduction of oxygen functions. The ability of de novo biosynthesis of carotenoids is not limited to land plants and algae, but is frequently encountered among prokaryotes (both eubacteria and archaebacteria) and fungi (Britton, 1998). To meet their metabolic demands, animals rely on food-borne uptake of carotenoids which then, however, can be further metabolized. An important example is β-carotene (provitamin A; trivial names for carotenes are used in this chapter – see Data sheets for alternative names such as β,β-carotene in this case) as a precursor of the visual pigment retinal in mammals and animals in general (Goodwin, 1984; von Lintig et al., 2005) or – together with its hydroxylated derivatives – as precursors of ketocarotenoids used as colourants by many crustaceans, various carp species and birds like flamingos or finches (Goodwin, 1984; McGraw et al., 2006). This chapter summarizes our current view on the biosynthesis of carotenoids, termed carotenogenesis, in land plants, cyanobacteria and algae with a focus on recent advances in the genetics of carotenoid biosynthesis. The scope of this review will be limited to oxygenic phototrophs; for details on the carotenogenesis of anoxygenic phototrophic bacteria, readers are referred to an excellent recent review by Maresca, Graham and Bryant (Maresca et al., 2008).