A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction.

BACKGROUND: Error analysis plays a crucial role in clinical concept extraction, a fundamental subtask within clinical natural language processing (NLP). The process typically involves a manual review of error types, such as contextual and linguistic factors contributing to their occurrence, and the identification of underlying causes to refine the NLP model and improve its performance. Conducting error analysis can be complex, requiring a combination of NLP expertise and domain-specific knowledge. Due to the high heterogeneity of electronic health record (EHR) settings across different institutions, challenges may arise when attempting to standardize and reproduce the error analysis process. OBJECTIVES: This study aims to facilitate a collaborative effort to establish common definitions and taxonomies for capturing diverse error types, fostering community consensus on error analysis for clinical concept extraction tasks. MATERIALS AND METHODS: We iteratively developed and evaluated an error taxonomy based on existing literature, standards, real-world data, multisite case evaluations, and community feedback. The finalized taxonomy was released in both .dtd and .owl formats at the Open Health Natural Language Processing Consortium. The taxonomy is compatible with several different open-source annotation tools, including MAE, Brat, and MedTator. RESULTS: The resulting error taxonomy comprises 43 distinct error classes, organized into 6 error dimensions and 4 properties, including model type (symbolic and statistical machine learning), evaluation subject (model and human), evaluation level (patient, document, sentence, and concept), and annotation examples. Internal and external evaluations revealed strong variations in error types across methodological approaches, tasks, and EHR settings. Key points emerged from community feedback, including the need to enhancing clarity, generalizability, and usability of the taxonomy, along with dissemination strategies. CONCLUSION: The proposed taxonomy can facilitate the acceleration and standardization of the error analysis process in multi-site settings, thus improving the provenance, interpretability, and portability of NLP models. Future researchers could explore the potential direction of developing automated or semi-automated methods to assist in the classification and standardization of error analysis.

Small RNAs, spermatogenesis, and male infertility: a decade of retrospect.

Small non-coding RNAs (sncRNAs), being the top regulators of gene expression, have been thoroughly studied in various biological systems, including the testis. Research over the last decade has generated significant evidence in support of the crucial roles of sncRNAs in male reproduction, particularly in the maintenance of primordial germ cells, meiosis, spermiogenesis, sperm fertility, and early post-fertilization development. The most commonly studied small RNAs in spermatogenesis are microRNAs (miRNAs), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), and transfer RNA-derived small RNAs (ts-RNAs). Small non-coding RNAs are crucial in regulating the dynamic, spatial, and temporal gene expression profiles in developing germ cells. A number of small RNAs, particularly miRNAs and tsRNAs, are loaded on spermatozoa during their epididymal maturation. With regard to their roles in fertility, miRNAs have been studied most often, followed by piRNAs and tsRNAs. Dysregulation of more than 100 miRNAs has been shown to correlate with infertility. piRNA and tsRNA dysregulations in infertility have been studied in only 3-5 studies. Sperm-borne small RNAs hold great potential to act as biomarkers of sperm quality and fertility. In this article, we review the role of small RNAs in spermatogenesis, their association with infertility, and their potential as biomarkers of sperm quality and fertility.

Strategies and challenges to enhance commercial viability of algal biorefineries for biofuel production.

The rise in energy consumption would quadruple in the coming century and the, existing energy resources might be insufficient to meet the demand of the growing population. An alternative and sustainable energy resource is therefore needed to address the fossil fuel deficiency. The utility of microalgae strains in the aspect of biorefinery has been in research for quite some time. Algal biorefinery is an alternate way of renewable energy however even after decades of research it still suffers from commercialization bottlenecks. The current manuscript reviews the scenarios where the innovation needs an ignition for its commercialization. This review discusses the prospects of up-scale cultivation, and harvesting algal biomass for biorefineries. It narrates algal biorefinery hurdles that can be solved using integrated technology approach, life cycle assessment and applications of nanotechnology. The review also sheds light upon the ties of algal biorefineries with its economic viability.

The curious case of genome packaging and assembly in RNA viruses infecting plants.

Genome packaging is the crucial step for maturation of plant viruses containing an RNA genome. Viruses exhibit a remarkable degree of packaging specificity, despite the probability of co-packaging cellular RNAs. Three different types of viral genome packaging systems are reported so far. The recently upgraded type I genome packaging system involves nucleation and encapsidation of RNA genomes in an energy-dependent manner, which have been observed in most of the plant RNA viruses with a smaller genome size, while type II and III packaging systems, majorly discovered in bacteriophages and large eukaryotic DNA viruses, involve genome translocation and packaging inside the prohead in an energy-dependent manner, i.e., utilizing ATP. Although ATP is essential for all three packaging systems, each machinery system employs a unique mode of ATP hydrolysis and genome packaging mechanism. Plant RNA viruses are serious threats to agricultural and horticultural crops and account for huge economic losses. Developing control strategies against plant RNA viruses requires a deep understanding of their genome assembly and packaging mechanism. On the basis of our previous studies and meticulously planned experiments, we have revealed their molecular mechanisms and proposed a hypothetical model for the type I packaging system with an emphasis on smaller plant RNA viruses. Here, in this review, we apprise researchers the technical breakthroughs that have facilitated the dissection of genome packaging and virion assembly processes in plant RNA viruses.

Comparative diagnostic utility of different urinary biomarkers during pre-albuminuric stages of non-hypertensive type 2 diabetic nephropathy.

Background & objectives: Activation of renin-angiotensin system and tubulointerstitial damage might be seen in pre-albuminuria stage of diabetic nephropathy (DN). Here, diagnostic utility of four urinary biomarkers [Angiotensinogen (Angio), Interleukin (IL)-18, Neutrophil Gelatinase-Associated Lipocalin (NGAL) and Cystatin] during pre-albuminuria stages of non-hypertensive type 2 diabetes patients was studied. Methods: A total of 952 type 2 diabetes mellitus (T2DM) patients were screened for nephropathy [estimated glomerular filtration rate (eGFR) ≥120 ml/min and albumin-creatinine ratio (ACR) ≥30], and 120 patients were followed up for one year. At one year, they were classified into hyperfiltration (43), normoalbuminuria (29) and microalbuminuria (48) groups. Another 63 T2DM patients without nephropathy were included as controls. Hypertension, patients on angiotensin-converting enzyme inhibitor/angiotensin receptor blocker, eGFR <60 ml/min/1.73 m2 and all proteinuric conditions were excluded. All were subjected to testing for urine protein, ACR, HbA1C, eGFR, along with urinary biomarkers (IL-18, cystatin-C, NGAL and AGT). Comparative analysis of all the diagnostic tests among different subgroups, correlation and logistic regression was done. Results: Urinary IL-18/Cr, cystatin/creatinine (Cr) and AGT/Cr levels were higher in groups of hyperfiltration (13.47, 12.11 and 8.43 mg/g), normoalbuminuria (9.24, 11.74 and 9.15 mg/g) and microalbuminuria (11.59, 14.48 and 10.24 mg/g) than controls (7.38, 8.39 and 1.26 mg/g), but NGAL/Cr was comparable. The area under receiver operating characteristic curve (AUC) and sensitivity of AGT to detect early CKD were higher than ACR and eGFR (0.91 and 90.4%, 0.6 and 40% and 0.6 and 37%, respectively). AUC values of other biomarkers, namely IL-18/Cr, cystatin/Cr and NGAL/Cr, were 0.65, 0.64 and 0.51, respectively. Angio/Cr and IL-18/Cr showed correlation with log albuminuria (r=0.3, P=0.00, and r=0.28, P=0.00, respectively). NGAL showed correlation with log eGFR (r=0.28 P=0.00). Multivariate logistic analysis showed that odds ratio of developing nephropathy was 7.5 times with higher values of log Angio/Cr. Interpretation & conclusions: Urinary AGT showed a higher diagnostic value than ACR and eGFR followed by IL-18 and cystatin to diagnose DN during pre-albuminuric stages.

Synthesis, characterization, and applications of gold nanoparticles in development of plasmonic optical fiber-based sensors.

Gold nanoparticles (Au-NPs) are readily used nanoparticles which finds applications in fields like biosensors, drug delivery, optical bioimaging and many state of art systems used for detection. In the recent years fiber optic sensors have seen utilization of Au-NPs along with other nanoparticles for implementation of sensors for sensing various biomolecules like cholesterol, glucose, and uric acid. The cancer cells, creatinine and bacteria can also be detected with the fiber optic sensors. Given the significance of Au-NPs in fiber optic sensors, the current work is a review of the synthesis, the common methods used for characterization, and the applications of Au-NPs. It is important to discuss and analyse the work reported in the literature to understand the trend and gaps in developing plasmonic optical fiber sensors.

Transient State Kinetics of Plasmodium falciparum Apicoplast DNA Polymerase Suggests the Involvement of Accessory Factors for Efficient and Accurate DNA Synthesis.

Plasmodium, the causative agent of malaria, belongs to the phylum Apicomplexa. Most apicomplexans, including Plasmodium, contain an essential nonphotosynthetic plastid called the apicoplast that harbors its own genome that is replicated by a dedicated organellar replisome. This replisome employs a single DNA polymerase (apPol), which is expected to perform both replicative and translesion synthesis. Unlike other replicative polymerases, no processivity factor for apPol has been identified. While preliminary structural and biochemical studies have provided an overall characterization of apPol, the kinetic mechanism of apPol's activity remains unknown. We have used transient state methods to determine the kinetics of replicative and translesion synthesis by apPol and show that apPol has low processivity and efficiency while copying undamaged DNA. Moreover, while apPol can bypass oxidatively damaged lesions, the bypass is error-prone. Taken together, our results raise the following question─how does a polymerase with low processivity, efficiency, and fidelity (for translesion synthesis) faithfully replicate the apicoplast organellar DNA within the hostile environment of the human host? We hypothesize that interactions with putative components of the apicoplast replisome and/or an as-yet-undiscovered processivity factor transform apPol into an efficient and accurate enzyme.

Risk Factors, Clinical Features, and Outcomes of Acute Pancreatitis in Children in Endemic Zone of Ascariasis in Eastern Bihar: A Hospital-Based Study.

Objective This study aims to describe the etiology, clinical features, and outcomes of acute pancreatitis (AP) in children in an endemic area of hepatobiliary ascariasis. Methods This retrospective observational study included acute pancreatitis (AP) patients in the age group of 2-15 years from January 2019 to January 2022. Demographic profile, risk factors, clinical features, laboratory imaging, and outcome data were collected and analyzed. Results A total of 40 patients comprising of 21 males (52.5%) and 19 females (47.5%) were included. The median age of the diagnosis of AP was 8.3 years (range: 4-14 years). Biliary ascariasis was the most frequent etiology of AP (n=18, 45%), followed by gallbladder (GB) stone (n=6, 12%), trauma (n=1, 2.5%), hepatitis (n=1, 2.5%), valproate drug (n=1, 2.5%), and GB sludge (n=1, 2.5%). In clinical features, all cases had pain in the abdomen (n=40, 100%), followed by fever (n=9, 22.5%), nausea/vomiting (n=33, 82.5%), jaundice (n=2, 5%), and anemia (n=2, 5%). Three (7.5%) patients developed complications such as shock, pseudocyst, and necrotizing pancreatitis, respectively. The average median hospital stay was nine days (range: 4-20 days). No mortality occurred in our study. Conclusions This study revealed a high prevalence (12-13 cases/year) of AP in children in this area. Biliary ascariasis (45%) emerged as the commonest risk factor. Most of the cases suffered from mild AP (92%) and so recovered completely without any complication.

Genistein lowers fertility with pronounced effect in males: Meta-analyses on pre-clinical studies.

Genistein, an isoflavonoid, is found in a plethora of plant-based foods, and has been approved for use in various therapies. A couple of studies in adult men observed a negative correlation between genistein exposure and reproductive parameters. To assess the effects of genistein exposure on reproduction and fertility in males and females, we performed quantitative meta-analyses by pooling data from published studies on animals that assessed various reproductive parameters. Pooled analysis showed significant decreases in sperm count in males exposed to genistein during adulthood (Hedges's g = -2.51, p = 0.013) and in utero (Hedges's g = -0.861, p = 0.016) compared with controls. In males exposed to genistein in utero, serum testosterone levels decreased (Hedges's g = -6.301, p = 0.000) and luteinizing hormone (LH) (Hedges's g = 7.127, p = 0.000) and FSH (Hedges's g = 6.19, p = 0.000) levels increased in comparison with controls. In females, the number of corpora lutea (Hedges's g = -2.103, p = 0.019) and the litter size (Hedges's g = -1.773, p-value = 0.000) decreased; however, female reproductive hormones remained unaffected. These meta-analyses show that genistein has detrimental effects on male reproductive system and on the progression and sustenance of pregnancy, with more pronounced adverse impact in males, particularly when exposed in utero.

KTaO3 -The New Kid on the Spintronics Block.

Long after the heady days of high-temperature superconductivity, the oxides came back into the limelight in 2004 with the discovery of the 2D electron gas (2DEG) in SrTiO3 (STO) and several heterostructures based on it. Not only do these materials exhibit interesting physics, but they have also opened up new vistas in oxide electronics and spintronics. However, much of the attention has recently shifted to KTaO3 (KTO), a material with all the "good" properties of STO (simple cubic structure, high mobility, etc.) but with the additional advantage of a much larger spin-orbit coupling. In this state-of-the-art review of the fascinating world of KTO, it is attempted to cover the remarkable progress made, particularly in the last five years. Certain unsolved issues are also indicated, while suggesting future research directions as well as potential applications. The range of physical phenomena associated with the 2DEG trapped at the interfaces of KTO-based heterostructures include spin polarization, superconductivity, quantum oscillations in the magnetoresistance, spin-polarized electron transport, persistent photocurrent, Rashba effect, topological Hall effect, and inverse Edelstein Effect. It is aimed to discuss, on a single platform, the various fabrication techniques, the exciting physical properties and future application possibilities of this family of materials.

Continuing arteriovenous fistula creation by nephrologist and its outcome during COVID pandemic-Analysis of 376 cases.

There has been a significant reduction of elective surgeries including creation of arteriovenous fistulas (AVF) during the ongoing pandemic by the surgeons. Here, we report the retrospective observational data of AVF creation by nephrologists in a single center, during a period of 8 months. A total of 376 fistulae were created in 310 patients. Patients were followed up at 2, 6, and 12 weeks. Twenty-eight patients required fistula creation twice, 16 patients thrice, and two patients underwent fistula creation four times. Of the total, 259 (68.8%) fistulae were radio-cephalic while 99 (26.3%) and 18 (4.79%) were brachio-cephalic and brachio-basilic, respectively. A total of 207 (67%) patients were already on hemodialysis whereas 103 (33%) were planned for elective initiation after fistula maturation. Of the 211 (69%) patients who completed 3 months of follow-up, 31 (15%) expired and 7 (3.3%) were lost to follow-up. Primary failure was observed in 70 (33.2%) fistulae. Fifteen (7.1%) patients were noted to be COVID positive during the follow-up. A total of 279 (90%) patients were alive at last follow-up. Amongst 20 dialysis staffs with 10 nephrologists, only two have developed COVID. Both were having mild illness and recovered completely. This study demonstrates that AVF creation can be performed safely with careful screening and by using adequate personal protective equipment.

Advances in electrochemical and optical sensing techniques for vitamins detection: a review.

Vitamins are essential nutrients that aid in metabolism, cell growth, and the appropriate functioning of other biomolecules. They are required for the proper functioning of various systems in human body. Both vitamin shortage and excess can pave the way for a variety of illnesses. They enter the body via food and supplements eaten, making it critical to measure the vitamin concentrations in food, medicines, and biological fluids. The concentrations of these vitamins are determined using a variety of techniques. The performance measure of the techniques like selectivity, sensitivity, and limit of detection is crucial in their utilization. Among the many techniques of determination, electrochemical sensing and optical sensing have garnered widespread interest because of their potential to improve performance. Additionally, the introduction of innovative materials has added a lot of benefits to sensing. The aim of this article is to summarize significant work toward recent improvements in electrochemical and optical methods for detecting different vitamins. Additionally, it attempts to assess the gaps in vitamin sensing in order to encourage researchers to fill such gaps that will benefit the community.

Effect of Vitamin D on Urinary Angiotensinogen Level in Early Diabetic Nephropathy.

BACKGROUND: Urinary angiotensinogen (UAGT) is supposed to be a marker of activation of the intrarenal renin- angiotensin system (RAS) system in early diabetic nnephropathy (EDN). Vitamin D has been studied as a negative regulator of the circulating and tissue RAS activity, so its supplementation may prevent the progression of diabetic nephropathy (DN). This study was planned to assess the RAS activation and effect of vitamin D supplementation in EDN progression by estimating the UAGT level. METHODS: A total of 103 EDN subjects were randomized in two groups to receive either cholecalciferol (54) or matching placebo (49) in a double-blind manner. All were subjected to routine investigations, urinary albumin-to-creatinine ratio (UACR), UAGT, vitamin D, and intact parathyroid hormone (iPTH) at the 0 and 6 months. A total 40 healthy controls were also included for assessment of the same investigations at 0 month. RESULTS: Significant reduction of UACR, UAGT, and iPTH level were corroborated with an increase in 25(OH) vitamin D level from 0 to 6 months (all four P < 0.001). After 6 months, the median [interquartile range (IQR)] of UAGT and UACR levels was significantly lower in the cholecalciferol group as compared to placebo group (p < 0.001 and P = 0.04, respectively). The median UAGT level was significantly higher in patients with EDN (cholecalciferol & placebo Group) than control group at 0 month (p = 0.001). CONCLUSION: Significantly higher UAGT levels in EDN supports the role of intrarenal RAS activation. A significant decrease in UAGT level in the cholecalciferol group supports the beneficial role of vitamin D supplementation in the progression of EDN.