jimnoneill/paper-to-field-training huggingface dataset:
Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma

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

DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase γ (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of metal cofactor, typically magnesium (Mg2+) or manganese (Mn2+), influences its structural stability, enzymatic activity, and fidelity. In this study, we employed molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how Mg2+ and Mn2+ affect the flexibility, active site stabilization, and catalytic efficiency of Pol γ. Intermolecular interaction analysis of individual residues is consistent with experimental mutagenesis reports and highlights the importance of specific residues, many of which are evolutionarily conserved, and some are involved in pathogenic mutations. It is also observed that Mn2+ enhances catalytic efficiency, exhibiting higher exoergicity (-3.65 kcal mol-1 vs -1.61 kcal mol-1 for Mg2+) and a lower activation barrier. Intermolecular interaction analysis reveals that Mn2+ provides larger stabilization of the transition state and product complex, favoring reaction progression. Investigation of the effects of the electric field in the active site suggests that the O3' atom on the DNA primer base experiences larger polarization in the system with Mn2+ ions when compared to Mg2+, with dipole directions consistent with the catalytic reaction progress. Our findings highlight a trade-off between structural stability and catalytic efficiency, providing insights into the role of metal ions in mitochondrial polymerase function and their implications for mutagenesis and mitochondrial disorders.
Stigma Associated With Postprostatectomy Urinary Incontinence

Field: Health Professions (Health Sciences)

In Brief Purpose This collective case study explored the social implications of postprostatectomy urinary incontinence (UI). Design Collective case study. Settings and subjects Three men older than age 60 years dwelling in the community who had urinary incontinence following prostatectomy. Methods Unstructured, in-depth interviews were thematically analyzed and presented in the form of a collective case study. Results Participants articulated two separate entities: a private and public identity. In their public identity, the participants went to great lengths to appear as a person who was continent of urine, and they expressed fear that their UI would be exposed. In revising their private identity, men used knowledge of their anatomy and physiology, family history, and life events to reject the cultural attitudes towards UI and renegotiate a new sense of self that was accepting of their leaking body. Conclusion A stigma exists for men who experience UI following prostatectomy; this stigma affects public and private identity. Naturalistic inquiry methods such as the collective case study described here provide new knowledge for continence nurses as they assist these patients to manage their UI within a social context. A collective case study explores social aspects of urinary incontinence following radical prostatectomy.
The Word ‘Lebai’ and Its Ethnic Origins: Reassessing an Early Designation for Muslim Religious Officials in the Malay World

Field: Arts and Humanities (Social Sciences)

This article proposes a new etymon for the Malay word lebai (minor religious official/scholar), namely the Sino-Muslim term libai (禮拜, worship or religious service conducted in a mosque). Scholars have traditionally argued that lebai, a loanword introduced during the early stages of Islamization, derives from the Tamil leppai (or lebbai), likewise signifying (amongst other things) a minor religious official/scholar. On this basis, it has been argued that Tamil Muslims acted as Southeast Asia’s earliest Islamic officials. This article critically reassesses the evidence underlying this attribution. By tracing the earliest known Malay usage of lebai to Java –where it emerged alongside Sino-Muslim influences associated with Cirebon, Gresik and Demak– the etymon libai is proposed: since the Song dynasty (960-1279), Sino-Muslims have used the noun libai as a designate for religious affairs (particularly prayers) conducted in a mosque. This study suggests that lebai originates with this term, making it indicative of Sino-Muslim influence during Java’s Islamization.
Fatty Acid-Binding Protein 4-Mediated Regulation Is Pivotally Involved in Retinal Pathophysiology: A Review

Field: Medicine (Health Sciences)

Fatty acid-binding proteins (FABPs), a family of lipid chaperone molecules that are involved in intracellular lipid transportation to specific cellular compartments, stimulate lipid-associated responses such as biological signaling, membrane synthesis, transcriptional regulation, and lipid synthesis. Previous studies have shown that FABP4, a member of this family of proteins that are expressed in adipocytes and macrophages, plays pivotal roles in the pathogenesis of various cardiovascular and metabolic diseases, including diabetes mellitus (DM) and hypertension (HT). Since significant increases in the serum levels of FABP4 were detected in those patients, FABP4 has been identified as a crucial biomarker for these systemic diseases. In addition, in the field of ophthalmology, our group found that intraocular levels of FABP4 (ioFABP4) and free fatty acids (ioFFA) were substantially elevated in patients with retinal vascular diseases (RVDs) including proliferative diabetic retinopathy (PDR) and retinal vein occlusion (RVO), for which DM and HT are also recognized as significant risk factors. Recent studies have also revealed that ioFABP4 plays important roles in both retinal physiology and pathogenesis, and the results of these studies have suggested potential molecular targets for retinal diseases that might lead to future new therapeutic strategies.
Content Based Image Retrieval Using Combined Features of Shape, Color and Relevance Feedback

Field: Computer Science (Physical Sciences)

Content based image retrieval is increasingly gaining popularity among image repository systems as images are a big source of digital communication and information sharing.Identification of image content is done through feature extraction which is the key operation for a successful content based image retrieval system.In this paper content based image retrieval system has been developed by adopting a strategy of combining multiple features of shape, color and relevance feedback.Shape is served as a primary operation to identify images whereas color and relevance feedback have been used as supporting features to make the system more efficient and accurate.Shape features are estimated through second derivative, least square polynomial and shapes coding methods.Color is estimated through max-min mean of neighborhood intensities.A new technique has been introduced for relevance feedback without bothering the user.
Kymlicka on cultural rights and liberalism

Field: Arts and Humanities (Social Sciences)

Kymlicka’s Liberalism, Community, and Culture originated a highly influential argument about the ethical foundations of minority cultural rights. The argument is explained and assessed in its original context and in the more developed form it took in his later book, Multicultural Citizenship. In its original version the argument was seriously underspecified, but the later version cleared up some problems only to create others. Minority cultural rights were either classed as the rights to self-government of national minorities or the rights of immigrants to integration into the receiving society, a form of incorporation that welcomes the retention of hyphenated cultural identities. The argument still left ample room to doubt that nationality suffices to justify self-government and that reasons derived from the value of multicultural integration could really support immigrant rights. Alan Patten’s recent book, Equal Recognition, goes far to remedy these shortcomings while remaining firmly within the liberal paradigm of cultural rights that Kymlicka established with his first book.
Exploring the Potential for Students to Develop Self-Awareness through Personalized Learning

Field: Social Sciences (Social Sciences)

Personalized learning (PL) and social-emotional learning (SEL) are areas of increasing emphasis in U.S. educational policy and practice. With the goal of examining how these initiatives may be mutually supportive, this exploratory study investigates the potential for a PL experience to help middle school students develop the SEL skill of “self-awareness.” Using qualitative inquiry, we analyze reflective interviews with eleven students engaged in PL using an original self-awareness coding scheme. Our findings offer promising evidence that PL can promote self-awareness, including specific student examples, followed by recommendations for how PL and SEL efforts can be more strategically aligned.
DD-001 Evaluation of the implementation of the automated medication organisation (2009–2015)

Field: Health Professions (Health Sciences)

Background

The increasing attention to patient safety and the rejected medication organisation by the healthcare inspection in 2008 has led to implementation of an automated medication organisation. Medication distribution is based on a computerised physician order entry (CPOE) and individual medication is distributed daily by the pharmacy. The centralised pharmacy is organised using ARX-ROWA to store medication and Sinteco to produce individual medication rings. The medication for a therapy change or a new patient is provided by a computerised medication cabinet (VANAS).

Purpose

This investigation aimed to compare the organisation of medication distribution before (2009) and after implementation (2015) of an automated medication distribution system.

Material and methods

Medication organisation audits were performed in 2009 and 2015. The legal requirements of the prescription, administration schedule, agreement between prescription and administration schedule, patient medication on the nurse ward (the correct identification of the medication name, dose, expiry date and patient name), medication administration and distribution were investigated. The obtained data were processed in Excel.

Results

The prescriptions that fulfilled the legal requirements increased: 4/87 (4.6%) in 2009, 195/236 (83%) in 2015. The correct administration schedules increased: 45/87 (52%) in 2009, 220/236 (93%) in 2015. Implementation of the CPOE resulted in complete agreement between the prescription and administration schedule. The correct medication identification on the nurse ward increased: 21/87 (24%) in 2009, 65/87 (79%) in 2015. No expired medicines were detected. The administration registration increased: 74/87 (85%) in 2009, 224/236 (95%) in 2015. In 2015 the administration time was verified. In 2015, 285/338 (84%) of the medication was distributed patient specific, 22/338 (7%) provided by the computerised medication cabinet and 31/338 (9%) provided by the nurse ward.

Conclusion

Implementation of the automated medication distribution resulted in complete agreement between the prescription and the administration schedule and an increased presence of correct medication on the nurse ward. The automated medication organisation contributed to improved patient safety. In future, bedside scanning should be implemented to close the medication circle, and efforts have to be made to increase the results obtained. No conflict of interest
Application of maximum entropy method to density profile measurement via microwave reflectometry on GAMMA 10

Field: Physics and Astronomy (Physical Sciences)

The electron density profile has been analysed using the maximum entropy method (MEM) in signal processing of the X-mode microwave reflectometry carried out in the GAMMA 10 tandem mirror. Although the detected reflectometry signals included the noise components due to density fluctuations in addition to signal components, the signal components were spectrally separated from the noise components using MEM. Reconstructed density profiles are consistent with that obtained from the millimetre wave interferometry measurements assuming a parabolic profile. The present MEM analysis will also be applicable to microwave reflectometry experiments on tokamaks or stellarators where signal levels were significantly affected by plasma movement or density perturbations.
Polymorphism and Gene Conversion in Mouse α-Globin Haplotypes

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

We have cloned and characterized three distinct α-globin haplotypes obtained from inbred strains of the mouse, Mus domesticus. We report here the complete nucleotide sequence of the six α-globin genes that the haplotypes contain. Our analysis of these genes and those from one other previously described haplotype indicates that recurrent gene conversion events have played a major role in their history. The pattern of nucleotide substitutions suggests that conversions have occurred both within and between haplotypes. Limited segments of coding and noncoding DNA have been involved in these gene conversion events. In two of the haplotypes, the nonallelic genes of each maintain DNA sequence identity over discrete intervals and encode the same α-globin polypeptide. On the other hand, the coding regions of some genes have accumulated replacement changes that result in distinct α-globins. In one instance, these changes appear to reflect positive selection of advantageous mutations.
MALIGNANT MELANOMAS OF THE HUMAN CHOROID AND CILIARY BODY

Field: Medicine (Health Sciences)

The ultrastructure of fifty malignant melanomas of the choroid and ciliary body has been studied over a period of ten years. Based upon twenty tumours embedded in epoxy resins, a comparison between their light microscopical morphology and ultrastructure revealed that the types established by Callender have characteristic ultrastructural features. The material comprised two spindle A, four spindle B, twelve mixed, one epithelioid, and one fascicular tumour. The fascicular tumour is the first tumour ultrastructurally studied belonging to this cell type. Its ultrastructure may support previous suggestions that the cells have their origin in special parts of the neural crest. In view of the prognostic practice of grouping together the fascicular and spindle B tumours, it is remarkable that cells from both these tumours contained cytoplasmic filaments not observed in spindle A or in the epithelioid tumours, and not previously found in choroidal malignant melanomas. The epithelioid tumour was found to be composed of only one type of cell, whereas the tumours of the mixed type appeared to be linked together as a group only by their differing from other types, although features of either spindle or epithelioid cells could be seen to a certain extent in some cells. This type probably expresses a certain degree of anaplasia and is not a mixture of spindle and epithelioid cells. The authors finally sum up the ultrastructural features which they consider characteristic of highly differentiated and of anaplastic malignant choroidal melanomas.
Joint Attention and Toddler Characteristics: Race, Sex and Socioeconomic Status

Field: Psychology (Social Sciences)

In studies of joint attention and sequences of interaction that foster joint attention, limited focus has been placed on toddler characteristics such as race, sex and socioeconomic status (SES). The purpose of the present study was to investigate the relationship between joint attention and toddler's race, sex and SES. Eighty‐four dyads of diverse race, sex and SES were videotaped playing, and joint attention and initiating matemal bid sequences were coded. Joint attention related to a "persisting" mother, whether or not the toddler accepted the initial maternal bid. No race differences were found; however, females engaged in more frequent bouts of joint attention and had more frequent nonpersistent maternal responses after the bid was accepted. Finally, SES was generally unrelated to joint attention. The manner in which bids for joint attention transpired and the amount of joint attention that occurred was largely independent of the dyad's SES as measured here.
Analysis of Timing Error Due to Supply and Substrate Noise in an Inverter Based High-Speed Comparator

Field: Engineering (Physical Sciences)

This paper presents the timing error and power supply induced jitter (PSIJ) analyses of an inverter based high-speed comparator, including the design of common-mode body biasing feedback circuitry. Both the main circuit and the supporting circuitry have been designed and implemented in a standard 28 nm CMOS technology with power supply of 0.9 V. The closed-form transfer function of the comparator including biasing circuitry, used in PSIJ analysis, is derived using symbolic admittance method. The mathematical model shows an agreement with the simulation and exhibits 7.4% of mean percentage error (MPE).
Inferring axon diameters using magnetic resonance imaging oscillating gradient spin echo sequences

Field: Neuroscience (Life Sciences)

A new diffusion magnetic resonance imaging method was developed and optimized to probe the smallest structures to date (0.54 ± 0.06 µm), micron-sized tissue structures, such as small axon diameters (AxD). This method relies on probing the shortest possible diffusion time scales. Current temporal diffusion spectroscopy methods cannot distinguish small structures because the pulse sequences limit the ability to probe the shortest diffusion times. This method circumvents those limitations using oscillating gradients in lieu of pulsed gradients and will have important neuroscience applications such as probing AxD distributions. The required imaging time will need to be shortened in order for the method to be clinically useful. The thesis presents three sets of experiments that guided the selection of pulse sequence and imaging parameters needed for measuring micron-sized restrictions. Measurements were made on water diffusing between 3 μm polystyrene spheres. The gradient frequencies and amplitudes used were appropriate to infer the pore sizes between the 3 μm beads while the fit results indicated a better signal-to-noise ratio would help make the results more accurate. Measurements made on water diffusing inside various tubes indicated the gradient frequency range was not appropriate for inferences of tube diameters that were 250 μm and larger. The second set of experiments used information from the first set to choose imaging and gradient parameters for measurements of water diffusing between 3, 6, and 10 μm beads and 150 μm tubes. Pore sizes, surface-to-volume ratio and diameters could be inferred from these samples with this method. The results indicated that the method had a resolution limit which is greater than 0.5 μm given that the pore sizes between the 3 μm and 6 μm beads were indistinguishable. The more accurate inferences of diameters of the bead rather than diameters of the tubes suggest the method is better optimized for micron-sized samples rather than 150 μm-sized samples. The final experiment tested the method on human corpus callosum. The results suggest that the resolution limit of the method needs to be decreased and careful attention to the axon direction would be needed. Suggestions for improvements to the model are made.
RPS: Repeats in Protein Sequences

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

Repeats are two or more contiguous segments of amino acid residues that are believed to have arisen as a result of intragenic duplication, recombination and mutation events. These repeats can be utilized for protein structure prediction and can provide insights into the protein evolution and phylogenetic relationship. Therefore, to aid structural biologists and phylogeneticists in their research, a computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats (of varying lengths) in protein sequences. In addition, users can check the frequency of occurrence of the repeats in sequence databases such as the Genome Database, PIR and SWISS-PROT and among the protein sequences available in the Protein Data Bank archive. Furthermore, users can view the three-dimensional structure of the repeats using the Java visualization plug-in Jmol . The proposed computing resource can be accessed over the World Wide Web at http://bioserver1.physics.iisc.ernet.in/rps/.
Sharing, Giving or Reselling: An Economic Analysis

Field: Economics, Econometrics and Finance (Social Sciences)

We consider the non-linear properties \ and boundaries in the three forms of sharing, gift, \ and reselling economy. We decode the economic \ rationality and marketplace mechanisms in today’s \ ever booming sharing/gifting/reselling networks. \ We contribute to the fundamental economics literature \ by decomposing a merchandise into two \ parts: the ownership good and the detached good. \ The ownership good can be utilized or shared \ by the owner. The detached good can either be \ given as a gift or be resold for an income. The \ separation is bounded by considering the estimated \ finite life of the good and a future time stamp \ of detachment. We consider owner’s holding cost, \ various transaction costs, rewards, as well as the \ incentive mechanism from the network. We find \ that there exist various conditions when certain \ ownership form is more preferred to the others. \ Our results also indicate that governmental and \ marketplaces’ incentive policies play an important \ role when consumers make decisions among the \ three economic forms and consequently adjusting \ the total social welfare.
Failure of Case-Carburized Gear and Its Prognosis(Machine Elements, Design and Manufacturing)

Field: Engineering (Physical Sciences)

A transmission gear failure affects function and performance of the entire machine. Meanwhile, gears may break before expected service life even if bending strength, surface durability and scuffing strength, which are evaluated in the desigh process of gears, are fulfilled. So it is extremely important to establish a gear failure prognosis technology. The existing gear failure prognosis method through vibration, acoustic and temperature measurement can't be universally applied because it can only catch limited sort of signal. Our experiments with case-carburized gears were conducted for the purpose of establishing a practical method. Gear fault progressed from micro pitting to flaking and finally to tooth crack. During the test, gear condition was observed and vibration data was recorded in detail. In this study, Mahalanobis distance was calculated from the vibration data in order to evaluate the gear condition. The result shows that Mahalanobis distance could be an indicator which shows gear condition quantitatively. There is a possibility that a vibration analysis by Mahalanobis distance could be a practical method to prognose gear fault before machine break down.