jimnoneill/paper-to-field-training huggingface dataset:
Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

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

Abstract Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations 1 . The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution 2,3 . However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved 4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive 7 . Here we present the genome of the inshore hagfish, Eptatretus burgeri . Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity 7 .
Post‐treatment effects of token reinforcement, verbal praise, and self‐monitoring in a residential psychiatric program

Field: Psychology (Social Sciences)

Abstract The present study was designed to investigate the effects of token reinforcement, verbal praise, and self‐monitoring on post‐treatment performance of bedroom preparation tasks by adult clients in a residential psychiatric program. Twenty‐four clients were randomly assigned to six experimental conditions (four subjects per condition) as follows: (1) contingent token reinforcement, (2) contingent verbal praise, (3) contingent token reinforcement plus contingent verbal praise, (4) self‐monitoring, (5) self‐monitoring plus contingent token reinforcement, and (6) control. All participants were exposed to a one week initial baseline period, then one week of their experimental condition, and finally, one week of a second baseline period. Research participants who received contingent token reinforcement engaged in bedroom‐area preparation tasks significantly less during the second baseline period of the study than during the initial baseline period. Verbal praise, however, produced a significant increase in performance from Baseline 1 to Baseline 2. The presence of both contingent token reinforcement and verbal praise produced a significant increase in performance during the second baseline period as compared to the control condition. This increase, however, was not found with concomitant token reinforcement and self‐monitoring. Changes in performance from Baseline 1 to Baseline 2 for participants assigned to the token reinforcement plus self‐monitoring condition were not significantly different from those found for participants assigned to the control condition. Implications of these results for clinical settings using token economies are presented.
Decision Support Framework for Sustainable and Fire Resilient Buildings (SAFR-B)

Field: Decision Sciences (Social Sciences)

Abstract Buildings of all types are increasingly becoming complex ‘systems of systems.’ They are subject to evolving societal objectives, new and innovative materials, and in many countries, regulatory ecosystems are having difficulty keeping pace with rapidly changing societal, environmental and technological changes. Two evolving objectives that are stimulating changes to buildings and communities are the desire for a more environmentally sustainable built environment and the need to become more resilient to the many increasingly hazardous impacts of climate change. Unfortunately, in some building designs these objectives are in conflict. As a first step toward a more integrated, holistic tool to aid in the design of sustainable and fire resilient buildings (SAFR-B), this paper develops and applies a first-order decision framework for a midrise apartment building. The SAFR-B framework is built on an analysis of design and regulatory objectives for fire safety and sustainability for buildings, and of risk and decision methods that can support design decisions. It makes use of risk indexing and the analytical hierarchy process (AHP), with initial scoring and weighting of attributes and strategies derived from international experts in the field of fire safety and sustainability through a Delphi process.
Gauge unification in higher dimensions

Field: Physics and Astronomy (Physical Sciences)

A complete 5-dimensional SU(5) unified theory is constructed which, on compactification on the orbifold with two different Z{sub 2}'s (Z{sub 2} and Z{sub 2}{prime}), yields the minimal supersymmetric standard model. The orbifold accomplishes SU(5) gauge symmetry breaking, doublet-triplet splitting, and a vanishing of proton decay from operators of dimension 5. Until 4d supersymmetry is broken, all proton decay from dimension 4 and dimension 5 operators is forced to vanish by an exact U(1){sub R} symmetry. Quarks and leptons and their Yukawa interactions are located at the Z{sub 2} orbifold fixed points, where SU(5) is unbroken. A new mechanism for introducing SU(5) breaking into the quark and lepton masses is introduced, which originates from the SU(5) violation in the zero-mode structure of bulk multiplets. Even though SU(5) is absent at the Z{sub 2}{prime} orbifold fixed point, the brane threshold corrections to gauge coupling unification are argued to be negligibly small, while the logarithmic corrections are small and in a direction which improves the agreement with the experimental measurements of the gauge couplings. Furthermore, the X gauge boson mass is lowered, so that p {yields} e{sup +}{pi}{sup 0} is expected with a rate within about one order of magnitude of the current limit. Supersymmetry breaking occurs on the Z{sub 2}{prime} orbifold fixed point, and is felt directly by the gauge and Higgs sectors, while squarks and sleptons acquire mass via gaugino mediation, solving the supersymmetric flavor problem.
Degenerate electron gas effects in the modulation spectroscopy of pseudomorphic Al0.32Ga0.68As/In0.15Ga0.85As/GaAs high electron mobility transistor structures

Field: Physics and Astronomy (Physical Sciences)

The effects of a degenerate two-dimensional electron gas on the interband optical excitations, occurring in the active channel of Al0.32Ga0.68As/In0.15Ga0.85As/GaAs high electron mobility transistor structures, were investigated by using phototransmittance spectroscopy. The ground state transition at room temperature exhibited a characteristic steplike line shape, which was considered to be an effect of the screening of excitons by the degenerate electron gas. A line shape fitting by using a first derivative of the absorption coefficient with respect to the electron sheet concentration ns, allowed an estimation of the latter quantity by phototransmittance. An observed temperature-sensitive excitonlike signal, associated with the second electron subband was attributed to the modulation of the many-body correlation-enhanced excitonic absorption, known as the Fermi-edge singularity.
Algebraic reachability of rational systems

Field: Mathematics (Physical Sciences)

The concept of algebraic reachability refers to the property of a system that every state from a sufficiently big subset of a state-space can be reached from a given inital state by applying an admissible input to the system. In this paper we study algebraic reachability of rational systems. We provide necessary and sufficient conditions for a rational system to be algebraically reachable (from an initial state). These conditions are formulated in terms of ideals of polynomials which makes checking algebraic reachability of a system computationally feasible. We relate the notion of algebraic reachability to the notion of controllability of linear systems, (local and local strong) accessibility and controllability of nonlinear systems.
Our Knowledge of Immunity to Schistosomiasis

Field: Immunology and Microbiology (Life Sciences)

Investigations on immunity to schistosomiasis have dealt principally with two main topics: with immunodiagnosis and with methods for producing resistance either by the use of vaccines or by previous infection with irradiated cercariae and with nonhuman strains.As far as immunodiagnosis is concerned, a large number of serologic tests have been devised that seem to be of help in the diagnosis of chronic infections in which eggs are difficult to find in feces or urine. All of these tests can be carried on with relative simplicity; antigens have been purified to some extent, and the actual tests are very simplified so that they can be used under field conditions. Antigens prepared from cercariae and from adult worms are the most commonly used. The intradermal reaction is also used extensively, and since the nitrogen content of antigens has been standardized, a definite area of the wheal formed after injection can be called a positive reaction.
“Safeguarding the Right to Data Protection in the EU”, 30th and 31st October 2014, Paris, France

Field: Social Sciences (Social Sciences)

This contribution is based on presentations and discussions at the conference “Safeguarding the Right to Data Protection”, held in Paris on the 30th and 31st October, 2014. Vladimir Marinescu, of the Academy of European Law (hereafter: ERA), in cooperation with the Cour de Cassation, organised the event. The conference looked at developments in EU data protection law with a focus on data protection as a fundamental right. Speakers discussed recent jurisprudence from the Court of Justice of the European Union (hereafter: CJEU or the Court), the European Court of Human Rights (hereafter: ECtHR) and national courts. The conference covered four main focus areas: EU data protection law; civil and criminal law aspects of data protection and the internet; data protection as a cornerstone of European fundamental rights protection; and data protection remedies. This contribution elaborates upon some of the most pertinent issues speakers discussed.
Physiology and Rheology of Arteries

Field: Medicine (Health Sciences)

Anatomical descriptions of the human and other mammalian arterial trees can be found in many textbooks. For the purpose of illustrating the blood perfusion and pressure pulse transmission path, the major branches of the arterial tree are shown in Fig. 2–1. There are considerable similarities among the corresponding anatomical sites of the arterial circulation in mammals (Li, 1996). The root of the aorta begins immediately at the aortic valve. The outlet of the aortic valve sits in the ascending aorta, which has the largest diameter of the aorta. The first branches off the aorta are the left and right main coronary arteries. The aortic arch junction is formed by the ascending aorta, the brachiocephalic artery, the left subclavian artery, and the descending thoracic aorta.
[Surgical treatment of cervical spondylotic myelopathy. A follow-up study].

Field: Medicine (Health Sciences)

The effect of operative treatment of spondylotic cervical myelopathy (SCM) was assessed by a follow up investigation of 33 patients submitted consecutively to operation. The patients were followed up on an average two years and two months after operation. As compared with the preoperative status, 39% of the patients had improved, 27% remained unchanged and 33% had a clinical status which was poorer than preoperatively. Age and sex were not found to be of significance for the prognosis. Patients with brief case histories had better effects of operation than patients with prolonged duration of the condition. The best results were found in patients in whom the duration of the condition was less than one year. Although 66% patients had obtained improved clinical condition or in whom progression of the condition has been arrested, 82% of the patients had been awarded social pensions at follow up examination as compared with 48% preoperatively. It is concluded that treatment of SCM should be instituted as early as possible in the course of the condition in the form of operative decompression of the cervical medulla.
Apoptosis of Motor Neurons in the Spinal Cord after Ischemia Reperfusion Injury Delayed Paraplegia in Rabbits

Field: Neuroscience (Life Sciences)

Objective To clarify the pathologic change of the motor neuron on spinal cord ischemia reperfusion injury delayed paraplegia. Methods The infrarenal aorta of White New Zealand rabbits (n = 24) was occluded for 26 minutes using two bulldog clamps. Rabbits were killed after 8, 24, 72, or 168 hours (n=6 per group), respectively. The clamps was placed but never clamped in sham-operated rabbits (n=24). The lumbar segment of the spinal cord (L5 to L7) was used for morphological studies, including hematoxylin and eosin staining, the expression of bcl-2 and bax proteins in spinal cord was detected with immunohistochemistry. The apoptotic neurons in spinal cord were measured with terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end-labeling of DNA fragments (TUNEL) staining. Results Delayed paraplegia occurred in all rabbits of ischemia reperfusion group at 16-24 hours, but not in sham groups. Motor neurons were selectively lost at 7 days after transient ischemia. After ischemia, the positive expression of bcl-2 protein were in the sham controls but decreased significantly as compared with that of the IR group (P＜0.01), especially in 72 hours reperfusion. The positive expression of bax protein were also in the sham controls, but increased in the IR group, especially in 72 hours reperfusion In addition, TUNEL study demonstrated that no cells were positively labeled until 24 hours after ischemia, but nuclei of some motor neurons were positively labeled at peak after ischemia reperfusion at 72 hours. Conclusion Spinal cord ischemia in rabbits induces morphological and biochemical changes suggestive of apoptosis. These data raise the possibility that apoptosis contributes to neuronal cell death after spinal cord ischemia reperfusion.
Financial circumstances of the elderly in Denmark--now and in the coming years. Pension systems and other economic possibilities.

Field: Economics, Econometrics and Finance (Social Sciences)

The situation concerning pensions in Denmark has been changing in recent years. There is a trend for the population itself has to pay into private pension to ensure a satisfactory financial situation after retirement. There are three categories of pensions and supplementary grants influencing the financial situation of the elderly: social-political grants, labour market political grants, and private arrangements. The national retirement pension is paid to everyone in accordance with certain rules. One condition is residence in Denmark for 40 years after reaching the age of 15. The pension age is 67 years. It is possible to receive early retirement pay or to obtain partial pension from the age of 60. This means that the age for retirement from the labour market on average is 62 years. Supplements to the national pension can be given as a net sum. Such a payment, however, makes it more difficult for the elderly person to overview his or her financial circumstances in retirement. The partial pension is a new form of pension which was introduced in 1986. About 2% of the 60-66 year-olds have taken advantage of this possibility, most of them independent trade men. In contrast, 105,000 wage earners are receiving early retirement pay, which is based on unemployment insurance. Certain considerations apply when the social pension is paid in a gross amount. This amount will not be free of tax. A number of special grants for the elderly will be included in the gross amount of the social pension. A system of that sort will make the financial circumstances of the retired person more clear.(ABSTRACT TRUNCATED AT 250 WORDS)
Peptide binding affinity redistributes preassembled repeat protein fragments

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

Abstract Designed armadillo repeat proteins (dArmRPs) are modular peptide binders composed of N- and C-terminal capping repeats Y and A and a variable number of internal modules M that each specifically recognize two amino acids of the target peptide. Complementary fragments of dArmRPs obtained by splitting the protein between helices H1 and H2 of an internal module show conditional and specific assembly only in the presence of a target peptide (Michel, E., Plückthun, A., and Zerbe, O. (2018). Peptide-guided assembly of repeat protein fragments. Angew. Chem. Int. Ed. 57, 4576–4579). Here, we investigate dArmRP fragments that already spontaneously assemble with high affinity, e.g. those obtained from splits between entire modules or between helices H2 and H3. We find that the interaction of the peptide with the assembled fragments induces distal conformational rearrangements that suggest an induced fit on a global protein level. A population analysis of an equimolar mixture of an N-terminal and three C-terminal fragments with various affinities for the target peptide revealed predominant assembly of the weakest peptide binder. However, adding a target peptide to this mixture altered the population of the protein complexes such that the combination with the highest affinity for the peptide increased and becomes predominant when adding excess of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.
Pregnancy Tradition "Ngapati" in Javanese Society Based on Perspective of the Qur'an and Hadith

Field: Arts and Humanities (Social Sciences)

Traditions and customs are an inseparable part of Javanese society. Traditipns four months of pregnancy or known as ngapati is one of the traditions carried out by the Javanese people until now. But nowadays, the tradition of ngapati is much abandoned by the Society. Some people consider the tradition to be out of order in the Qur'an and the Hadith, and even prohibit it. By comparing various exposures from the literature, the authors analyze, identify and review many literatures, this article discusses in depth the tradition of ngapati done by the community and its relation in the Qur'an and Hadith. Research reveals that the tradition of the regent is not in conflict with the Qur'an and the Hadith.
Enabling Lipidomic Biomarker Studies for Protected Populations by Combining Noninvasive Fingerprint Sampling with MS Analysis and Machine Learning

Field: Medicine (Health Sciences)

Triacylglycerols and wax esters are two lipid classes that have been linked to diseases, including autism, Alzheimer's disease, dementia, cardiovascular disease, dry eye disease, and diabetes, and thus are molecules worthy of biomarker exploration studies. Since triacylglycerols and wax esters make up the majority of skin-surface lipid secretions, a viable sampling method for these potential biomarkers would be that of groomed latent fingerprints. Currently, however, blood-based sampling protocols predominate in the field. The invasiveness of a blood draw limits its utility to protected populations, including children and the elderly. Herein we describe a noninvasive means for sample collection (from fingerprints) paired with fast MS data-acquisition (MassIVE data set MSV000092742) and efficient data analysis via machine learning. Using both supervised and unsupervised classification, we demonstrate the usefulness of this method in determining whether a variable of interest imparts measurable change within the lipidomic data set. As a proof-of-concept, we show that the method is capable of distinguishing between the fingerprints of different individuals as well as between anatomical sebum collection regions. This noninvasive, high-throughput approach enables future lipidomic biomarker researchers to more easily include underrepresented, protected populations, such as children and the elderly, thus moving the field closer to definitive disease diagnoses that apply to all.
An Analysis of Classroom Management in Social Science Learning to Strengthen Character Education in Class V at SD Negeri Kandangan 1 Sleman Yogyakarta

Field: Social Sciences (Social Sciences)

This research aims to, (1) describe the class management process in social studies learning to strengthen social care character education, (2) describe the class management process in social studies learning to strengthen responsible character education, (3) describe the supporting and inhibiting factors in classroom management in social studies learning to strengthen character education, (4) describe solutions to classroom management obstacles in social studies learning to strengthen character education. This research is descriptive qualitative research. The research sample was determined using purposive sampling. The data collection process uses observation, interview and documentation techniques. Data validity techniques use data triangulation which includes source triangulation, technique triangulation, and time triangulation. This research consists of four steps of data analysis: data collection, data reduction, data presentation, and drawing conclusions. The results of the research show that (1) teachers carry out classroom management in social studies learning to strengthen social care character education. The teacher forms students into several groups then looks for community activities around their neighborhood, and also makes donations if there are people affected by natural disasters. (2) To strengthen the character of responsibility, teachers give students individual assignments with time limits, and students carry out class pickets according to their respective schedules. (3) Supporting factors for classroom management in social studies learning to strengthen character education are good communication between teachers and parents, social studies material that is relevant to everyday life, students who are active in discussions and teachers who use technology. Inhibiting factors include the large number of students and not all students being easy to manage. (4) Solutions to these obstacles include schools creating additional tutoring programs, singing national songs or regional songs before learning, and carrying out 3S habits (senyum, sapa, salam/ smile, say hello, greet).
A simulation study of a wireless bandwidth reservation multiple access protocol for multimedia traffic

Field: Computer Science (Physical Sciences)

Bandwidth reservation multiple access protocol (BRMA) resolves access contentions for mobile users in wireless local networks. Bandwidth is assigned to each user dynamically at frame level. In each frame, request channels are deterministically assigned to each user and are therefore contention-free. Data channels are assigned dynamically by base station and are therefore collision-free. In this paper, BRMA is studied for multimedia traffic through simulations. Traffic patterns of different kinds, such as voice, data, real time high activity video (MPEG movie Star Wars) are used to study the protocol performance. With a proper admission control and with proper design of protocol parameters (service ratio, frame length, etc), traffic with different quality of service (QoS) requirements can be supported.