Miracle-dz/UniFAR-FTUs huggingface dataset:
Designing NLP applications to support ICD coding: an impact analysis and guidelines to enhance baseline performance when processing patient discharge notes

Financial costs are a major concern in the healthcare system, with medical billing and coding playing a key role in facilitating transactions and financing procedures. Billing involves filing claims with insurance companies and requires scrutiny of clinical summaries and electronic health records to correctly match diagnoses, prescriptions, and procedures to standardized codes. Accuracy in assigning International Classification of Diseases (ICD) codes is critical to proper reimbursement of care. Incorrect codes waste time and resources, and cause administrative and financial problems for hospitals, insurance companies and patients. Manual medical coding is a labor-intensive and error-prone process that creates additional administrative burden and inconvenience for hospitals, insurance companies, and patients. To simplify the process, clinical records are often processed to automatically identify and extract clinical concepts and corresponding ICD codes. Deep learning and natural language processing techniques have shown promise in a variety of tasks but applying them to medical coding has been challenging. Accurate coding requires a deep understanding of medical terminology, context, and guidelines that may be difficult to capture with traditional deep learning methods. Although deep learning shows promise in healthcare, its specific impact on ICD coding is not fully understood, and translating scalable deep learning methods into practical improvements in ICD coding remains a challenge. Evaluating deep learning models under the scenarios of real-world coding and comparing them to established practice is critical to determining their true effectiveness. In this work, we address the automation of ICD coding by highlighting pitfalls and contrasting different perspectives. We investigated automatic ICD coding using baseline machine learning models, with a focus on identifying ICD-9 codes in discharge notes from Medical Information Mart for Intensive Care (MIMIC) database. A thorough evaluation of different models and approaches is crucial to avoid over-reliance on any method. Our findings show that simpler methods can achieve comparable results to deep learning models while still requiring fewer computational resources.
PASSERINES MIGRATION ALONG THE HABITATS FROM THE DANUBE DELTA BIOSPHERE RESERVATION

� + + + + + + + + + + + + + + + � + � � � + + + + + + + + + + + + + + + � � + + � � + + + + � � � + + � � + + + + + � + + � + � � � + � + + + + + + + + + + + + + + + + + + � � � + � � � � � + + + � � � + + + � � + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + � � + + + + � � + + + + + + + + + + + + + + + + + � + � � + + � + � + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + � � � + � + � � � + + + + + + + � � � � + � � + + � + + � + � + � � � � + + � + � + + + + � � � � � � � � + + + + + + + � + + + + + + + + + + + + + + + + � + + � + � + + + + + + + + + + + � � � � � + + + + + + + + + + + + + � � � + + + + + + + + + + + + + + + + + + + + + + + + � � + � + + + + + + + + + + + + � � � � � + + � + � + + � � � + + + � � + + + + + + + + + + + + + + � + � � + + � � � � + + � � + + + + + + + + + + + + + + + + + + + + � + + + + + + + + + + + + + + + + + + + + + + + � + � � � + + + + + + + + + � � � + � � � + + + � � � +
Explicating Numerical Information: When and How Fingers Support (or Hinder) Number Comprehension and Handling

Numbers are of enormous significance for modern society. They form the basis of currency and economic systems, of measurement and calculation, of engineering and the natural sciences, and, as a matter of course, lie at the heart of mathematics. Therefore, teaching mathematical skills plays an important role in preschool and school education. However, before children are able to perform their first symbolic algorithms such as multi-digit addition and multiplication they must have mastered two representational number systems: a verbal system (e.g., English number words) and a notational system (e.g., Arabic digits). The main competence that children have to acquire with these systems is to represent and handle the numerical information internally (Zhang and Norman, 1995). Using one's fingers for numerical tasks may indicate that parts of the internal processes still require external support and are not mastered adequately, but it would be erroneous to infer that finger strategies are not worthy of support. On the contrary: we argue that one's fingers, applied properly, provide a natural, and readily available toolkit for modeling numerical information and reflecting on numerical concepts (cf. Fuson and Secada, 1986; Carpenter et al., 1999; Wright et al., 2002; Guha, 2006; Andres et al., 2008). This position is exemplified for the acquisition of the verbal number system and for verbal processes involved in counting and calculating. Following Zhang and Norman's (1995) representational analysis of notational systems, we analyze which features of the verbal system can be accessed externally, which have to be represented internally, and how this may be supported – or hindered – by finger counting strategies.
Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs

Desensitization of nicotinic acetylcholine receptors (nAChRs) can be induced by overstimulation with acetylcholine (ACh) caused by an insufficient degradation of ACh after poisoning with organophosphorus compounds (OPCs). Currently, there is no generally applicable treatment for OPC poisoning that directly targets the desensitized nAChR. The bispyridinium compound MB327, an allosteric modulator of nAChR, has been shown to act as a resensitizer of nAChRs, indicating that drugs binding directly to nAChRs can have beneficial effects after OPC poisoning. However, MB327 also acts as an inhibitor of nAChRs at higher concentrations and can thus not be used for OPC poisoning treatment. Consequently, novel, more potent resensitizers are required. To successfully design novel ligands, the knowledge of the binding site is of utmost importance. Recently, we performed in silico studies to identify a new potential binding site of MB327, MB327-PAM-1, for which a more affine ligand, UNC0646, has been described. In this work, we performed ligand-based screening approaches to identify novel analogs of UNC0646 to help further understand the structure-affinity relationship of this compound class. Furthermore, we used structure-based screenings and identified compounds representing four new chemotypes binding to MB327-PAM-1. One of these compounds, cycloguanil, is the active metabolite of the antimalaria drug proguanil and shows a higher affinity towards MB327-PAM-1 than MB327. Furthermore, cycloguanil can reestablish the muscle force in soman-inhibited rat muscles. These results can act as a starting point to develop more potent resensitizers of nAChR and to close the gap in the treatment after OPC poisoning.
Ion Channels in Peripheral Blood Mononuclear Cells– Effect of Culture and Ascorbic Acid.

Peripheral blood mononuclear cells which include lymphocytes and monocytes play important role in the adaptive and innate immune responses. Cell mediated immunity is sub served by lymphocytes and innate immunity by granulocytes, monocytes and macrophages. Ion channels on the cell membrane play significant roles during activation of these immune cells The activation of lymphocytes is dependent on function of voltage gated potassium channels, calcium activated potassium channels and calcium release activated channels(CRAC) channels. Similarly, voltage gated proton currents play a key role in the respiratory burst of phagocytic cells. The expression of these ion channels on the membrane may change when the cells are exposed to culture environment in which they may undergo differentiation. Further, the function of these ion channels can be modulated by certain drugs for therapeutic purposes. Drugs may also alter the expression of ion channels on the cell membrane Vitamins act as immunomodulants and are known to alter gene expression in immune cells. The present work involves study of the changes in two ionic currents in peripheral blood mononuclear cells during culture and the effect of vitamin C on these currents when it is present in supraphysiological concentrations in the culture environment. The proton currents in peripheral blood monocytes were characteristically similar to proton currents reported in other mammalian phagocytes in terms of their voltage dependence and gating kinetics. The currents recorded in peripheral blood monocytes were larger than those reported in THP-1 monocytes. The proton current density decreased during culture when the cells differentiated into macrophages or dendritic cells. The changes can be correlated to a certain extent to decreased NADPH oxidase in monocyte derived cells reported earlier, though a functional significance cannot be clearly stated with the experiments done in this study.
DISABILIT Y-ADJUSTED LIFE YEARS OF LEUKEMIA CANCER IN CHILDREN 0-14 YEAR IN ASIA FROM 2010 TO 2019: A SYSTEMATIC ANALYSIS FOR THE GLOBAL BURDEN OF DISEASE STUDY 2019

– Objective: Childhood leukemia is the most frequent form of cancer in children. Despite the fact that most children diagnosed with leukemia are cured, many of them experience long-term complications. Materials and Methods: An ecological study was conducted utilizing data related to healthy life years lost due to disability (YLDs), years of life lost due to premature death (YLLs), and disability-adjusted life years (DALYs) caused by leukemia cancer (chronic and acute) in children from the Global Burden of Disease (GBD). We used correlation tests at the 0.05 level to examine the correlation between these indicators and the human development index. Results: The highest DALYs and YLLs in 2010 and 2019 were associated with Low Socio-Demographic Index (SDI) regions, while the highest number of YLDs in 2010 and 2019 were related to High-middle SDI regions in the continent. In Asia, the burden of disease, YLDs and premature death were higher in men than in women from 2010 to 2019. Our results demonstrated a negative and significant correlation between DALY (r=-0.563, p =0.0001) and YLL (r=-0.571, p =0.0001) with the human development index in Asian countries. However, the correlation between the index of YLD (r=- 0.108, p =0.483) and the human development index was not significant. Conclusions: To reduce the risks associated with leukemia cancer, policymakers
Identification of Candidate Genes, Governing Gynoecy In Bitter Gourd (Momordica Charantia L. ) by In-Silico Gene Expression Analysis

Bitter gourd (Momordica charantia L.) is both medicinally and economically highly valued cucurbit. Hybrid vigor has been well exploited for early maturity, higher yields and other genetic and agronomic traits. However, hybrid seed production in bitter gourd is labor-intensive requiring manual bagging and hand pollination. Use of gynoecious lines as female parent that produce only female flowers have not only reduced the labor requirement, but also have increased yields in hybrids and have good combining ability. However, early phenotypic detection of gynoecy in breeding lines is difficult as gynoecy is highly influenced by environment. To identify the candidate genes governing gynoecy, differentially expressing gene between a gynoecious (Gy323) and a monoecious line (DRAR-1) were explored. 7865 genes were differentially regulated between two lines and 4131 genes were up regulated in gynoecious lines. Up regulated genes in gynoecious line; BTB/POZ domain-containing protein that regulate floral development and previously reported ethylene biosynthesis and regulation genes in cucumber and melon; 1-aminocyclopropane-1-carboxylate oxidases and 1aminocyclopropane-1-carboxylate synthase and ethylene receptor and ethylene responsive proteins were identified as putative candidate genes for gynoecy in bitter gourd.
Scale-sensitive Psi-dimensions: the Capacity Measures for Classifiers Taking Values in R^Q

Bounds on the risk play a crucial role in statistical learning theory. They usually involve as capacity measure of the model studied the VC dimension or one of its extensions. In classification, such "VC dimensions" exist for models taking values in {0, 1}, {1,. , Q} and R. We introduce the generalizations appropriate for the missing case, the one of models with values in R^Q. This provides us with a new guaranteed risk for M-SVMs which appears superior to the existing one.
Rank-Based Inference over Web Databases

In recent years, there has been much research in Ranked Retrieval model in structured databases, especially those in web databases. With this model, a search query returns top-k tuples according to not just exact matches of selection conditions, but a suitable ranking function. This paper studies a novel problem on the privacy implications of database ranking. The motivation is a novel yet serious privacy leakage we found on real-world web databases which is caused by the ranking function design. Many such databases feature private attributes - e.g., a social network allows users to specify certain attributes as only visible to him/herself, but not to others. While these websites generally respect the privacy settings by not directly displaying private attribute values in search query answers, many of them nevertheless take into account such private attributes in the ranking function design. The conventional belief might be that tuple ranks alone are not enough to reveal the private attribute values. Our investigation, however, shows that this is not the case in reality. To address the problem, we introduce a taxonomy of the problem space with two dimensions, (1) the type of query interface and (2) the capability of adversaries. For each subspace, we develop a novel technique which either guarantees the successful inference of private attributes, or does so for a significant portion of real-world tuples. We demonstrate the effectiveness and efficiency of our techniques through theoretical analysis, extensive experiments over real-world datasets, as well as successful online attacks over websites with tens to hundreds of millions of users - e.g., Amazon Goodreads and Renren.com.
What Agriculture Can Learn from Native Ecosystems in Building Soil Organic Matter: A Review

Over the last century, researchers and practitioners with diverse backgrounds have articulated the importance of improving soil organic matter (SOM) contents in agricultural soils. More recently, climate change scientists interested in CO2 sinks, and agroecologists interested in ecological intensification have converged on the goal of building SOM stocks in croplands. The challenge is that agriculture itself is responsible for dramatic losses of SOM. When grassland or forest ecosystems are first converted to agriculture, multiple mechanisms result in SOM declines of between 20% and 70%. Two of the most important mechanisms are the reduction in organic matter inputs from roots following the replacement of perennial vegetation with annual crop species, and increases in microbial respiration when tillage breaks open soil aggregates exposing previously protected organic matter. Many agricultural practices such as conservation tillage and integration of cover crops have been shown to achieve some degree of SOM improvement, but in general adoption of these practices falls short of accumulating the SOM stocks maintained by grasslands, forests or other native ecosystems that agriculture replaced. Two of the overarching reasons why native terrestrial ecosystems have achieved greater soil organic matter levels than human agroecosystems are because they direct a greater percentage of productivity belowground in perennial roots, and they do not require frequent soil disturbance. A growing body of research including that presented in this review suggests that developing perennial grain agroecosystems may hold the greatest promise for agriculture to approach the SOM levels that accumulate in native ecosystems. We present calculations that estimate potential soil organic carbon accumulation rates in fields converted from annual to perennial grains of between 0.13 and 1.70 t ha−1 year−1.
First assessment of the diversity of coralline species forming maerl and rhodoliths in Guadeloupe, Caribbean using an integrative systematic approach

The present study documents species of coralline algae that form maerl and rhodoliths in Guadeloupe, Caribbean using an integrative systematic approach of combining molecular (COI-5P, psb A) and morphological/anatomical data. Maerl and rhodoliths were collected by SCUBA and dredging from six localities in Guadeloupe during the Karubenthos Expedition , which was coordinated by the Parc National de la Guadeloupe and the Museum National d´Histoire Naturelle. Of the twelve maerl and rhodolith specimens collected and sequenced, eight specific entities were delimitated based on the analysis of molecular data: Lithothamnion cf. ruptile, five species of the genus Lithothamnion , one species of the genus Spongites , and the remaining one was either assigned to the genus Lithoporella or Mastophora . Morphological/anatomical data are presented for each of these species. Molecular analyses revealed that Lithothamnion . cf ruptile and other four species ( Lithothamnion spp.1–4) were resolved in a distinct lineage than the other Lithothamnion species examined. Nevertheless, these five species were provisionally remained in the genus Lithothamnion based on the presence of flared epithallial cells. Previously, only three species of Lithothamnion have been cited in the Caribbean. Till this study species belonging to the genus Spongites have not been hitherto reported for this region. The specimen identified as either Lithoporella or Mastophora shared anatomical features with both genera. Further examination of reproductive material is required to identify this specimen to a lower taxonomical rank. This study is the first to report the occurrence of maerl and rhodoliths belonging to the genus Lithothamnion at 110 m depth; this record being the deepest for the genus in the Caribbean Sea. Our results have revealed that species diversity of Caribbean maerl has been underestimated and further surveys coupled with an integrative taxonomic approach on this biodiversity hotspot are necessary.
Diet and feeding niches of juvenile Gadus morhua, Melanogrammus aeglefinus and Merlangius merlangus during the settlement transition in the northern North Sea.

A study on the feeding ecology of juvenile cod Gadus morhua, haddock Melanogrammus aeglefinus and whiting Merlangius merlangus during the pelagic to demersal transition was carried out on fishes sampled throughout their settlement season at a local nursery ground in the north-western North Sea, off the Scottish east coast. A comprehensive quantitative taxonomic analysis of the diets, as described in the paper, showed the emergence of distinctive feeding niches, minimizing the potential for competition between species and size categories. The diet of the juveniles changed with fish size, water depth, time of year and distance offshore. Small G. morhua were present in the study area earlier in the season, settled further inshore and ate a higher proportion of pelagic prey (copepods) and as size increased they moved into deeper waters and targeted larger, more benthic prey. As M. aeglefinus grew larger and moved into deeper waters, a diet of largely copepods, amphipods, pelagic Ammodytes spp. , cyprids and pelagic gastropods evolved to one dominated predominantly by fishes and benthic invertebrates. In the case of M. merlangus, widespread ages and sizes throughout the sampling season, a consequence of their more protracted spawning season, resulted in dietary changes which were more likely to be influenced by seasonal changes in the prey field, in addition to developmental (size) changes, than the diets of the other two species.
A New Cecal Slurry Preparation Protocol with Improved Long-Term Reproducibility for Animal Models of Sepsis

Sepsis, a life-threatening systemic inflammatory response syndrome induced by infection, is widely studied using laboratory animal models. While cecal-ligation and puncture (CLP) is considered the gold standard model for sepsis research, it may not be preferable for experiments comparing animals of different size or under different dietary regimens. By comparing cecum size, shape, and cecal content characteristics in mice under different experimental conditions (aging, diabetes, pancreatitis), we show that cecum variability could be problematic for some CLP experiments. The cecal slurry (CS) injection model, in which the cecal contents of a laboratory animal are injected intraperitoneally to other animals, is an alternative method for inducing polymicrobial sepsis; however, the CS must be freshly prepared under conventional protocols, which is a major disadvantage with respect to reproducibility and convenience. The objective of this study was to develop an improved CS preparation protocol that allows for long-term storage of CS with reproducible results. Using our new CS preparation protocol we found that bacterial viability is maintained for at least 6 months when the CS is prepared in 15% glycerol-PBS and stored at -80°C. To test sepsis-inducing efficacy of stored CS stocks, various amounts of CS were injected to young (4–6 months old), middle-aged (12–14 months old), and aged (24–26 months old) male C57BL/6 mice. Dose- and age-dependent mortality was observed with high reproducibility. Circulating bacteria levels strongly correlated with mortality suggesting an infection-mediated death. Further, injection with heat-inactivated CS resulted in acute hypothermia without mortality, indicating that CS-mediated death is not due to endotoxic shock. This new CS preparation protocol results in CS stocks which are durable for freezing preservation without loss of bacterial viability, allowing experiments to be performed more conveniently and with higher reproducibility than before.