bluuebunny/crossref_metadata_2025 huggingface dataset:
Techniques for elucidating the secretory process: from Ca2+ entry to exocytosis
Authors: Fisher Thomas e. , Oberhauser andres f.
Published: November 2023

Technical innovation has always been central to progress in the study of neurotransmission. The first demonstration of chemical neurotransmission was in fact made possible by a novel and ingenious experimental approach. In 1921 Otto Loewi rushed to his laboratory in the middle of the night to perform an experiment that had occurred to him in a dream. It had been known for some time that stimulation of the vagal nerve causes slowing of the frog heart. Loewi’s insight was to stimulate the vagus of a perfused frog heart and then add the perfusate to the solution bathing a second frog heart in a separate vessel. This caused the slowing of the second heart, demonstrating that the vagal action was caused by release of a chemical substance, later shown to be acetylcholine. From this simple, elegant beginning the techniques for studying neurotransmission have developed to the point where it is now possible to measure exocytosis at the level of a single neuron, with the precision to detect the fusion of a single synaptic vesicle with the neuronal membrane.
Sequence analysis of expressed proteins
Authors: Keen Jeff N , Ashcroft Alison E
Published: November 2023

The generation of recombinant proteins may be considered a relatively facile process nowadays. The wide range of expression systems available, and the marketing of specialized molecular biological kits by a number of manufacturers, virtually ensure that reasonable quantities of recombinant proteins can be produced in most biochemistry laboratories, although there are notable exceptions such as some integral membrane proteins. The engineering of appropriate ‘tags’ (e.g. hexa-His, StrepTag) into the DNA sequence encoding any particular protein frequently enables single-step affinity purification of the expressed polypeptide. Similarly, the creation of a fusion protein, with the desired polypeptide linked to glutathione S-transferase for example, allows ready expression and purification of the protein. The incorporation of a unique protease-sensitive site (e.g. for Factor Xa) into the linking region between the two polypeptide domains enables the desired product to be removed from the fusion protein. However, unequivocal proof of the identity of the expressed protein and detailed analysis of the synthetic fidelity are essential prerequisites for its use in experimental systems, particularly in structural and functional analysis, and are absolutely critical prior to release of the protein into the environment in numerous biotechnological applications. The confirmation of N- and C-termini is of paramount importance, and amino acid sequence analysis remains the most unambiguous technique for this. This is complemented by mass spectrometric methods, particularly utilizing electrospray ionization, for accurate mass measurement of the expressed protein. This in turn enables a comparison to be made with the theoretical value, which may indicate the presence of post-translational modifications and lead to their identification.
Protein degradation in mammalian cells
Authors: Ciechanover Aaron , Wiederanders Bernd
Published: November 2023

Recent experimental evidence implicates the ubiquitin system in the specific and programmed degradation of many key regulatory and short-lived cellular proteins. Among these are mitotic cyclins, transcriptional activators, tumour suppressors, and growth regulators, as well as membrane receptors involved in signal transduction and the immune and inflammatory responses. It is also involved in processing of antigens for presentation via class I MHC molecules. The system can specifically target abnormal, misfolded, and unassembled proteins that may result from mutations, environmental damage, or non stoichiometric synthesis of subunits of complex proteins. It is clear therefore that ubiquitin-mediated proteolysis plays important roles in the regulation of basic pathophysiological cellular processes such as regulation of cell cycle and division, development and differentiation, malignant transformation, modulation of the immune system, and neurodegeneration. With the multitude of substrates targeted, it is not surprising that recent studies have implicated the system in the pathogenesis of several disease states as well. For example, the inability to degrade the kidney Na+ channel leads to stabilization of the protein, accumulation of the channel subunits, excessive reabsorption of the cation and water, and a severe form of hypertension (1). Mutations in the gene that encodes E6-AP, a ubiquitin-protein substrate ligase, lead to the Angelman syndrome that is characterized by mental retardation, seizures, and abnormal gait (2). It is predicted that the list of ubiquitin-related pathological derangements will grow significantly in the future.
Epidemiological methods for studies of genetic factors that influence infectious diseases
Authors: Engels Eric A , O’Brien Thomas R
Published: November 2023

Epidemiological studies are concerned with the relationship within populations between exposures and outcomes. A strong relationship between an exposure and outcome provides evidence that the exposure, at least in part, is a cause of the outcome. Numerous types of exposures are of potential interest to epidemiologists. These types include, but are not limited to, environmental exposures (e.g. toxic chemicals or radiation), exposures defined by socioeconomic status or occupation (which can be markers for more specific exposures that are difficult to measure), and endogenous exposures (e.g. blood pressure or hormone levels). An additional type of exposure is provided by infectious agents, i.e. micro-organisms such as viruses, bacteria, or parasites. Infectious diseases, by definition, require exposure to an infecting organism for the development of disease. Nonetheless, although contact with the micro-organism is necessary for infectious diseases, it is often not sufficient. Not everyone who is exposed to an infectious organism becomes infected, and not everyone who becomes infected develops disease.
Introduction to the principles of flow cytometry
Authors: Carter Nigel P , Ormerodt Michael G
Published: November 2023

1 Introduction

Flow cytometry is a technique for making rapid measurements on particles or cells as they flow in a fluid stream one by one through a sensing point. The important feature of flow cytometric analysis is that measurements are made separately on each particle within the suspension in turn, and not just as average values for the whole population. The ability of laser- and arc lamp-based flow cytometers to measure multiple cellular parameters, based on light scatter and fluorescence, and to purify physically subpopulations of cells has led to the increasingly widespread use of this instrumentation in biology and medicine. The applications of flow cytometry and cell sorting are numerous. A wide range of fluorescent probes is available for directly estimating cellular parameters such as nucleic acid content, enzyme activity, calcium flux, membrane potential, and pH. Conjugation of fluorescent dyes to ligands and to polyclonal and mono clonal antibodies has enabled the density and distribution of cell-surface and cytoplasmic determinants and receptors to be studied, as well as allowing functional subpopulations of cells to be identified. Many of these fluorescent dyes and reagents can be used in combination to produce multiple correlated measurements. For example, it is now commonplace in immunology to measure two light-scatter and three immunofluorescence parameters on each cell.
Microinjection
Authors: Knoblauch Michael
Published: November 2023

During recent decades, microinjection has developed into an important method used by cell biologists, and there have been several thousand papers published describing applications of this technique. The main advantage of microinjection is that it enables the direct introduction of substances into individual cells or organelles whilst being observed. Microinjection can be used in intact tissue of whole plants as well as in tissue cultures or tissue slices. In essence, for micro injection a glass pipette (needle) with a tip size of about 1 µm is filled with the substance to be introduced. The substance is forced from the capillary by hydro static pressure (pressure injection) or by an electric current (iontophoresis) into the cell. The main problem is that the method is technically demanding. On the other hand, it is inexpensive, costs being mainly associated with purchase of the experimental hardware.
Patterning and Positional Information
Authors: Wolpert L , Kerszberg M
Published: November 2023

Pattern formation is a key process in embryonic development (1). When a fertilized egg divides, the resulting cells become different and give rise to a variety of structures such as the main body and its appendages. These structures have a well-defined spatial organization-the vertebrate limb is a good example—which is brought about by the process of pattern formation. There are three other related processes: (1) cell differentiation is the process by which different specialized adult cell types such as muscle, cartilage, and neurons are generated; (2) morphogenesis, or a change in form, such as neural tube formation; and (3) growth—it is a general feature of pattern formation that it is initially only specified for any organ on a small scale—rarely greater than more than 100 cell diameters. These processes are related to one another but, in general, pattern formation is the primary event in that it specifies the other processes. Thus patterning in vertebrate limb development specifies where cartilage will form and how it will grow; it also specifies ectodermal cells such as the apical ridge, which controls the overall form of the limb.
Narrow Roads Of Gene Land
Authors: Hamilton W D
Published: November 2023

Why is `blood thicker than water’? Are we innately violent or pacific? What is the best sex ratio? Why are plants and animals sexual? Why do we grow old and die? Over what do our chromosomes quarrel? Such questions have motivated the life-work of W.D. Hamilton, widely acknowledged as the most important theoretical biologist of the 20th century. His papers continue to exert an enormous influence and they are now being republished for the first time. Each one is introduced by an autobiographical essay written especially for this collection. This first volume contains all of Hamilton's publications prior to 1981, a set especially relevant to social behaviour, kinship theory, sociobiology, and the notion of `selfish genes'. It includes several of the most read and famous papers of modern biology. A forthcoming volume will be devoted to the second half of Hamilton's life's work, on sex and sexual selection. Narrow Roads of Gene Land will be welcomed by professionals, graduate students, and undergraduates from a variety of disciplines, including evolution, population genetics, animal behaviour, genetics, anthropology, and ecology. The essays are accessible to non-specialists and will fascinate and entertain general readers with an interest in evolution and behaviour.
Clinical utility of the forward-viewing echoendoscope in patients after pancreatoduodenectomy: A prospective study
Authors: Ishiwatari Hirotoshi , Kaneko Junichi , Sato Junya , Satoh Tatsunori , Ishikawa Kazuma , Niiya Fumitaka , Matsubayashi Hiroyuki , Minamide Tatsunori , Maeda Yuki , Yamamoto Youichi , Kishida Yoshihiro , Yoshida Masao , Ito Sayo , Kawata Noboru , Imai Kenichiro , Hotta Kinichi , Imamura Taisuke , Sugiura Teiichi , Uesaka Katsuhiko , Ono Hiroyuki
Published: November 2023

Background and Objectives

Endoscopic treatment of obstructive jaundice and pancreatitis due to hepaticojejunostomy (H-J), pancreatojejunostomy (P-J) strictures, and tumor recurrence after pancreatoduodenectomy (PD) is technically challenging. Treatment of P-J strictures results in poor outcomes. Although conventional EUS that has an oblique view is not suitable for such patients, forward-viewing EUS (FV-EUS) may become a useful option. This study aimed to evaluate the feasibility and efficacy of FV-EUS in patients who have undergone PD.

Methods

Patients with PD who were scheduled to undergo diagnosis and treatment using FV-EUS for H-J or P-J lesions were enrolled in this single-center prospective study. After observation of the P-J and H-J using FV-EUS according to a predetermined protocol, treatment using FV-EUS was performed as needed.

Results

A total of 30 patients were enrolled, and FV-EUS was used to observe P-J and H-J in 24 and 28 patients, respectively. The detection rates of P-J and H-J by endoscopy were 50% (12/24) and 96.4% (27/28), respectively, and by EUS were 70.8% (17/24) and 100% (28/28), respectively. Of these, P-J and H-J were found by endoscopy only after EUS observation in 3 and 1 patient, respectively. The success rates of endoscopic treatment using FV-EUS were 66.7% (2/3), 95.2% (20/21), and 25% (1/4) for benign P-J strictures, benign H-J strictures, and tumor recurrence, respectively.

Conclusions

Endoscopic treatment using FV-EUS is feasible and effective for patients after PD. Moreover, FV-EUS increases the P-J lesion detection rate by adding EUS observation.
Feasibility of Surveillance for Mucinous Cystic Neoplasm of the Pancreas
Authors: Hozaka Yuto , Ohtsuka Takao , Nakamura Masafumi , Hijioka Susumu , Unno Michiaki , Shimizu Yasuhiro , Tanabe Minoru , Nagakawa Yuichi , Hatano Etsuro , Kawai Manabu , Sano Tsuyoshi , Koshita Shinsuke , Katanuma Akio , Kita Emiri , Hanada Keiji , Nakai Yousuke , Aoki Takeshi , Serikawa Masahiro , Okamoto Kojun , Takeyama Yoshifumi
Published: November 2023

Objective

We aimed to elucidate the feasibility of surveillance of patients with mucinous cystic neoplasm (MCN).

Methods

We performed a retrospective, multi-institutional study of 328 patients who underwent surgery for MCN at 18 Japanese institutions. Patients with MCN were divided into an immediate surgery group and a surveillance group, which underwent surgery after surveillance.

Results

The median surveillance period until surgery in the surveillance group was 27 months (range, 7–165 months). Compared with the immediate surgery group, the surveillance group showed smaller tumor diameter (46 vs 50 mm, P = 0.01), more frequent laparoscopic approach (58% vs 37%, P < 0.01), and less frequent malignancy (7% vs 15%, P = 0.03). The new appearance of mural nodules and elevation of serum tumor markers were associated with malignancy in the surveillance group. Two patients in the surveillance group experienced postoperative recurrence, although there was no significant difference in recurrence or disease-free survival between the two groups. In the surveillance group, the 1-, 5-, and 10-year cumulative incidence rates of malignant MCN were 0.8%, 5.6%, and 36.5%, respectively.

Conclusion

As the risk of progression to malignant MCNs increases over the long term, MCNs should be resected rather than subjected to unnecessary surveillance.
Daily Pain Experiences in Chronic Pancreatitis
Authors: Han Samuel , Li Rui , Palermo Tonya M.
Published: November 2023

Objectives

Pain, the hallmark symptom of chronic pancreatitis (CP), remains difficult to assess. To capture the variability of pain that patients can experience day to day, this study used pain diaries to describe daily pain experiences and identify pain phenotypes.

Methods

This study is a secondary data analysis from a pilot trial examining cognitive behavioral therapy for pain treatment in CP. Before treatment, patients completed an online daily pain diary using the Brief Pain Inventory for 7 days. Using indicators of pain magnitude, pain variability, pain synchrony along with least, worst, and average pain intensity levels, we identified pain patterns using K-means clustering.

Results

Of 30 patients in the pilot trial, a total of 27 patients (mean age of 49.8 years, 80% women) had complete data to include in this report. Four clusters were identified: cluster 1, lowest pain magnitude (n = 3); cluster 2, moderate pain magnitude and high pain variability (n = 4); cluster 3, moderate pain magnitude and low pain variability (n = 9); and cluster 4, highest pain magnitude and lowest pain variability (n = 11).

Conclusions

Daily pain diaries offer a novel way of evaluating the dynamic pain experiences in CP. Although 4 distinct pain patterns were identified, further studies are needed to validate these findings.
The Association Between Human Immunodeficiency Virus and Bacterial Vaginosis and Metronidazole Treatment Failure for Trichomonas vaginalis
Authors: Frechtling Dan , Chopra Shubam , Ratnayake Aneeka , Kissinger Patricia J.
Published: November 2023

Background

Trichomonas vaginalis (TV) is a common sexually transmitted infection. High rates of repeated infections have been observed, particularly among women living with human immunodeficiency virus (HIV). Trichomonas vaginalis frequently cooccurs with bacterial vaginosis (BV). The purpose of this study was to determine if coinfections with TV, BV, and HIV could lead to differential treatment failure outcomes.

Methods

Data were pooled from 2 prior randomized control trials comparing 2 g oral single-dose versus 500-mg twice daily oral 7-day dose metronidazole for the treatment of TV in HIV infected and HIV uninfected women. Trichomonas vaginalis rates 1-month postcompletion of treatment were compared by arm, HIV and BV status after removing those who had sexual reexposure, and/or did not complete their treatment.

Results

Data for 795 subjects were included in the study, of which 76 (9.6%) experienced treatment failure. In the final multivariable model, which included treatment dose, HIV status, and BV status, odds of treatment failure infection in the 7-day dose group were lower than the odds in the single dose group (odds ratio, 040; 95% confidence interval, 0.23–0.68). Treatment failure was lower in the multidose arm compared with single dose for both HIV-infected (4.0% vs 10.3%; P = 0.0568) and HIV-uninfected (7.3% vs 15.4%; P = 0.0037). Neither HIV nor BV was associated with higher treatment failure.

Conclusions

Human immunodeficiency virus infection and BV status did not significantly alter the rate of repeat infection for either single dose or 7-day dose metronidazole. Among all women, 7-day metronidazole lowered the odds of treatment failure.
The longitudinal effect of disseminating handwashing public health education to children in India via co-created, culturally relevant resources.
Authors: Crosby Sapphire , Younie Sarah , Ujenia Harnesh Vijay , Laird Katie
Published: November 2023

Infectious diseases are a leading cause of death for children from Low-and Middle-Income-Countries (LMICs), often due to inadequate hand-hygiene. This study evaluates culturally-relevant educational resources as a vehicle to disseminate the importance of handwashing amongst children in India. Employing a Participatory Action Research (PAR) model and mixed methods, this follow-up longitudinal study evaluates a set of innovate educational handwashing resources and workshops specifically co-created for use in the State of Gujarat, and how they aid teachers in the teaching of hand-hygiene over a three-year period. Working alongside local NGOs on-the-ground, teacher questionnaires (n=58) and focus groups including a brief questionnaire with teachers (n=35) were conducted to assess the impact of trainer workshops. In addition, pre- and post-workshop worksheets were conducted with children (n=98). Percentage change was calculated between children’s pre and post worksheet scores and a cumulative frequency of responses to each questionnaire criterion was measured. Data from the focus group found that the resources had been used in over 200 schools by more than 5000 children. In addition, 92.28% of teachers said they would use the resources within their classrooms in India, with 58.16% of pupils having an increased understanding of germs/handwashing directly after the workshop. Teachers reported that they are able to teach microbiology and handwashing more effectively. Furthermore, following a focus group, 100% of teachers noted a reduction in childhood vomiting and diarrhoeal illnesses linked with insufficient hand-hygiene across 46 schools in the State of Gujarat since using the Germ’s Journey resources.
DystoGen Compendium: A comprehensive resource of ACMG annotated movement disorder associated genetic variants
Authors: Saikia Bhaskar Jyoti , Gaharwar Utkarsh , Poojary Mukta , Mhaske Aditi , Paul Sangita , Kumar Mukesh , Sharma Srishti , Pandhare Kavita , Rastogi Shivanshi , Karal Medhavi , Rophina Mercy , Scaria Vinod , BK Binukumar
Published: November 2023

Purpose

In recent years, the advent of high throughput sequencing techniques has led to the identification of a number of genetic variants across different genes that are associated with movement disorders. However, the under-appreciation of the variant spectrum in movement disorders and the lack of consolidated and systematic evidence-based annotation of these variants has long undermined the true potential of genomic approaches to expedite precision medicine.

Methods

We manually curated the genetic variants from a panel of 118 genes that have been associated with monogenic causes of movement disorders and systematically annotated them according to ACMG & AMP (American College of Medical Genetics and the Association of Molecular Pathologists) guidelines.

Results

Data integration after systematic classification of variants according to ACMG & AMP guidelines showed 5118 pathogenic/likely pathogenic variants accounting for 18.03% of the total unique variants being annotated. This data and annotations are available in a comprehensive online compendium DystoGen.

Conclusion

To the best of our knowledge, this is the most comprehensive compendium of genetic variants in movement disorders annotated as per the ACMG & AMP guidelines for pathogenicity. The compendium indexes 28377 variants along with a wide array of information including the geographical origin of the variant, global distribution, and population allele frequency. The resource has been made available in the URLhttps://clingen.igib.res.in/dystogen/.
Early-life immune activation is a vulnerability factor for adult epileptogenesis in neurofibromatosis type 1
Authors: Faidi Rania , Reid Aylin Y
Published: November 2023

Introduction

Patients with Neurofibromatosis type 1 (NF1), the most common neurocutaneous disorder, can develop several neurological manifestations that include cognitive impairments and epilepsy over their lifetime. It is unclear why certain patients with NF1 develop these conditions while others do not. Early-life immune activation promotes later-life seizure susceptibility, neurocognitive impairments, and leads to spontaneous seizures in some animal models of neurodevelopmental disorders, but the central nervous system immune profile and the enduring consequences of early-life immune activation on the developmental trajectory of the brain in NF1 have not yet been explored. We tested the hypothesis that early-life immune activation promotes the development of spatial memory impairments and epileptogenesis in a mouse model of NF1.

Methods

Male wild-type (WT) andNf1+/-mice received systemic lipopolysaccharide (LPS) or saline at post-natal day 10 and were assessed in adulthood for learning and memory deficits in the Barnes maze and underwent EEG recordings to look for spontaneous epileptiform abnormalities and susceptibility to challenge with pentylenetetrazole (PTZ).

Results

Whereas early-life immune activation by a single injection of LPS acutely elicited a comparable brain cytokine signature in WT andNf1+/-mice, it promoted spontaneous seizure activity in adulthood only in theNf1+/-mice. Early-life immune activation affected susceptibility to PTZ-induced seizures similarly in both WT andNf1+/-mice. There was no effect on spatial learning and memory regardless of mouse genotype.

Discussion

Our findings suggestsecond-hitenvironmental events such as early-life immune activation may promote epileptogenesis in theNf1+/-mouse and may be a risk-factor for NF1-associated epilepsy.
Molecular Connectomics Reveals a Glucagon-Like Peptide 1 Sensitive Neural Circuit for Satiety
Authors: Webster Addison Nicole , Becker Jordan J. , Li Chia , Schwalbe Dana Catharine , Kerspern Damien , Karolczak Eva O. , Bundon Catherine , Onoharigho Roberta A. , Crook Maisie , Jalil Maira , Godschall Elizabeth Nora , Dame Emily G. , Dawer Adam , Belmont-Rausch Dylan Matthew , Pers Tune H. , Lutas Andrew , Habib Naomi , Guler Ali D. , Krashes Michael J. , Campbell John Nelson
Published: November 2023

Liraglutide and other agonists of the glucagon-like peptide 1 receptor (GLP-1RAs) are effective weight loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons which inhibit hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nuclei transcriptomics. Applying this method to AgRP neurons predicted at least 21 afferent subtypes in the mouse mediobasal and paraventricular hypothalamus. Among these are Trh+ Arc neurons, inhibitory neurons which express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating Trh+ Arc neurons inhibits AgRP neurons and feeding in an AgRP neuron-dependent manner. Silencing Trh+ Arc neurons causes over-eating and weight gain and attenuates liraglutide's effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons, and reveal a circuit through which GLP-1RAs suppress appetite.
Land, carbon and biodiversity data for supply chain impact calculations
Authors: Gassert Francis , Stela Biel , Palao Elena , Harfoot Mike
Published: November 2023

Monitoring, halting and reversing land conversion is fundamental to meeting international biodiversity and climate targets, and agriculture is the major driver of land conversion. We present an open access set of global data for calculating land use change impacts of agricultural supply chains. These data, originally prepared for the LandGriffon service, include indicators of deforestation, conversion of natural ecosystems, greenhouse gas emissions, and loss of intact or high integrity ecosystems following international standards and guidelines for reporting and target setting in the agriculture, forestry, and land use sector. In order to assign impacts to agricultural production, we prepare data using a spatial adaptation of the statistical Land Use Change (sLUC) accounting approach distributing impact to human activities across the local area using a 50km radius. The results are high resolution global maps of impact per hectare of land occupation. These can then be combined with land footprint data, cropland extent, or productivity maps to calculate land use change related impacts for specific crop volumes sourced from specific regions. Carbon and deforestation results are validated against FAO statistics at the national level.
Confounding Fuels Misinterpretation in Human Genetics
Authors: Benning John W. , Carlson Jedidiah , Smith Olivia S. , Shaw Ruth G. , Harpak Arbel
Published: November 2023

The scientific literature has seen a resurgence of interest in genetic influences on human behavior and socioeconomic outcomes. Such studies face the central difficulty of distinguishing possible causal influences, in particular genetic and non-genetic ones. When confounding between possible influences is not rigorously addressed, it invites over- and misinterpretation of data. We illustrate the breadth of this problem through a discussion of the literature and a reanalysis of two examples. Clark (2023) suggested that patterns of similarity in social status between relatives indicate that social status is largely determined by one’s DNA. We show that the paper’s conclusions are based on the conflation of genetic and non-genetic transmission, such as wealth, within families. Song & Zhang (2024) posited that genetic variants underlying bisexual behavior are maintained in the population because they also affect risk-taking behavior, thereby conferring an evolutionary fitness advantage through increased sexual promiscuity. In this case, too, we show that possible explanations cannot be distinguished, but only one is chosen and presented as a conclusion. We discuss how issues of confounding apply more broadly to studies that claim to establish genetic underpinnings to human behavior and societal outcomes.
Unveiling Driver Modules in Lung Cancer: A Clustering-Based Gene-Gene Interaction Network Analysis
Authors: Taheri Golnaz , Szalai Marcell , Habibi Mahnaz , Papapetrou Panagiotis
Published: November 2023

Lung cancer, which is the leading cause of cancer-related death worldwide and is characterized by genetic changes and hetero-geneity, presents a significant treatment challenge. Existing approaches utilizing Machine Learning (ML) techniques for identifying driver modules lack specificity, particularly for lung cancer. This study addresses this limitation by proposing a novel method that combines gene-gene interaction network construction with ML-based clustering to identify lung cancer-specific driver modules. The methodology involves mapping biological processes to genes and constructing a weighted gene-gene interaction network to identify correlations within gene clusters. A clustering algorithm is then applied to identify potential cancer-driver modules, focusing on biologically relevant modules that contribute to lung cancer development. The results highlight the effectiveness and robustness of the clustering approach, identifying 110 unique clusters ranging in size from 4 to 10. These clusters surpass evaluation requirements and demonstrate significant relevance to critical cancer-related pathways. The identified driver modules hold promise for influencing future approaches to lung cancer diagnosis, prognosis, and treatment. This research expands our understanding of lung cancer and sets the stage for further investigations and potential clinical advancements.
Small-molecule binding and sensing with a designed protein family
Authors: Lee Gyu Rie , Pellock Samuel J. , Norn Christoffer , Tischer Doug , Dauparas Justas , Anischenko Ivan , Mercer Jaron A. M. , Kang Alex , Bera Asim , Nguyen Hannah , Goreshnik Inna , Vafeados Dionne , Roullier Nicole , Han Hannah L. , Coventry Brian , Haddox Hugh K. , Liu David R. , Yeh Andy Hsien-Wei , Baker David
Published: November 2023

Despite transformative advances in protein design with deep learning, the design of small-molecule–binding proteins and sensors for arbitrary ligands remains a grand challenge. Here we combine deep learning and physics-based methods to generate a family of proteins with diverse and designable pocket geometries, which we employ to computationally design binders for six chemically and structurally distinct small-molecule targets. Biophysical characterization of the designed binders revealed nanomolar to low micromolar binding affinities and atomic-level design accuracy. The bound ligands are exposed at one edge of the binding pocket, enabling thede novodesign of chemically induced dimerization (CID) systems; we take advantage of this to create a biosensor with nanomolar sensitivity for cortisol. Our approach provides a general method to design proteins that bind and sense small molecules for a wide range of analytical, environmental, and biomedical applications.
Uromonitor®: Clinical Validation and Performance Assessment of a Urinary Biomarker for Recurrence Surveillance in Non-Muscle Invasive Bladder Cancer Patients
Authors: Ramos Pedro , Brás João Paulo , Dias Carolina , Bessa-Gonçalves Mafalda , Prazeres Hugo , Botelho Francisco , Silva João , Silva Carlos , Pacheco-Figueiredo Luís
Published: November 2023

Introduction

Bladder cancer (BC) remains the most common malignancy of the urinary tract, with non-muscle invasive BC (NMIBC) representing the vast majority of bladder cancer patients. The current standard of care (SOC) follow-up in NMIBC patients demands an intensive schedule and requires costly and burdensome methods, driving the development of alternative, non-invasive, cost-effective methods that may complement or serve as substitutes to cystoscopy and cytology. Uromonitor® is a urine biomarker test that detects hotspot mutations in three genes (TERT, FGFR3, andKRAS) for the evaluation of disease recurrence. The aim of the current study was to assess its performance comparing it to the current SOC methods.

Materials and Methods

A total of 528 NMIBC surveillances from 439 individual patients were enrolled from December 2021 to June 2023. All subjects underwent SOC methods and provided an urine sample before undergoing cystoscopy for Uromonitor® analysis. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for recurrence and compared to the gold-standard cystoscopy plus trans-urethral resection (TURBT) pathology.

Results

Uromonitor® displayed a sensitivity of 87.2%, with only 6 recurrences failing to be detected by the urinary biomarker test, a specificity of 99.2%, a positive predictive value (PPV) of 93.2% and a negative predictive value (NPV) of 98.8%. Cystoscopy showed a total of 22 (31,88%) false positives not confirmed by TURBT, while Uromonitor® presented only 3 positive tests where no suspected lesions were found in cystoscopy. Sensitivity, specificity and NPV values for Uromonitor® also remained high across all NMIBC grades and stages.

Conclusion

In the present study, we confirmed that the Uromonitor® biomarker test represents a reliable tool in the detection of NMIBC recurrence in patients undergoing routine surveillance, regardless of stage and grade. It offers either an alternative or a complement to the current SOC methods, providing rapid results and a non-invasive option, potentially improving patients’ quality of life and helping reduce the economic burden of NMIBC follow-up. To our knowledge, this is the largest single-center study assessing Uromonitor®’s performance and thus validating its usefulness in clinical practice.
COMPARISON BETWEEN SANGER, ILLUMINA AND NANOPORE SEQUENCING EVIDENCING INTRA-HOST VARIATION OF FELINE LEUKEMIA VIRUS THAT INFECTS DOMESTIC CATS
Authors: Castillo-Aliaga Cristobal , Blanchard Adam Mark , Castro-Seriche Susana , Hidalgo-Hermoso Ezequiel , Jerez-Morales Alonso , Loose Matthew W , Tarlinton Rachael E
Published: November 2023

Knowledge of Feline Leukemia Virus (FeLV) sequence variation has mainly been developed using Sanger sequencing methods. However, advances in next generation sequencing methods and their broad use in laboratories has been changing our understanding of viral genetics. FeLV sequencing has specific complications with the presence of both exogenous (exFeLV) and endogenous (enFeLV) virus with frequent recombination between them, limiting sequencing approaches. Here we report an FeLV-A and FeLV-B amplicon-based comparison between Sanger, Illumina, and Oxford Nanopore sequencing methods in Chilean domestic cats. We analysed the hypervariable envelope gene, where a higher number of variants as well as recombination with endogenous strains occurs. We detected multiple variants and viral quasispecies infecting the cats. We compared these three methods to evaluate the advantages and disadvantages between them. Although the Sanger method is highly reliable, it showed a high fail rate (many amplicons did not produce useable sequence) and the sequences obtained showed artificial sequence clustering when compared with the NGS methods. Illumina sequencing showed a lower error rate but could not discriminate between exogenous and endogenous viruses. Finally, Oxford Nanopore (MinION) sequencing could successfully detect low-abundance sequences and discriminate between FeLV-A and FeLV-B sequences, although its higher error-rate requires caution in interpretation of the results. Our results indicate advantages and disadvantages for each method, with the purpose of sequencing needing to be considered in the choice of method. Results of large viral phylogenetic trees combing sequences derived from mixed sequencing methods, such as those combining historical and contemporary sequencing need to be considered with some caution as artificial clustering by sequencing method may occur.
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9
Authors: Eaton Joshua D , Board Jessica , Davidson Lee , Estell Chris , West Steven
Published: November 2023

RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial directionality. After transcription begins, the opposing functions of Integrator (INTS11) and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.
Rab27 in tick extracellular vesicle biogenesis and infection
Authors: Butler L. Rainer , Singh Nisha , Marnin Liron , Valencia Luisa M. , O’Neal Anya J. , Cabrera Paz Francy E. , Shaw Dana K. , Oliva Chavez Adela S. , Pedra Joao H.F.
Published: November 2023

Background

The blacklegged tick,Ixodes scapularis, transmits most vector-borne diseases in the United States. It vectors seven pathogens of public health relevance, including the emerging human pathogenAnaplasma phagocytophilum. Nevertheless, it remains critically understudied when compared to other arthropod vectors.I. scapularisreleases a variety of molecules that assist in the modulation of host responses. Recently, it was found that extracellular vesicles (EVs) carry several of these molecules and may impact microbial transmission to the mammalian host. EV biogenesis has been studied in mammalian systems and is relatively well understood, but the molecular players important for the formation and secretion of EVs in arthropods of public health relevance remain elusive. RabGTPases are among the major molecular players in mammalian EV biogenesis. They influence membrane identity and vesicle budding, uncoating, and motility.

Methods

Using BLAST, anin-silicopathway for EV biogenesis in ticks was re-constructed. We identified Rab27 for further study. EVs were collected from ISE6 tick cells after knocking downrab27to examine its role in tick EV biogenesis.I. scapularisnymphs were injected with small interfering RNAs to knock downrab27then fed on naïve andA. phagocytophiluminfected mice to explore the importance ofrab27in tick feeding and bacterial acquisition.

Results

Our BLAST analysis identified several of the proteins involved in EV biogenesis in ticks, including Rab27. We show that silencingrab27inI. scapularisimpacts tick fitness. Additionally, ticks acquire lessA. phagocytophilumafterrab27silencing. Experiments in the tick ISE6 cell line show that silencing ofrab27causes a distinct range profile of tick EVs, indicating that Rab27 is needed to regulate EV biogenesis.

Conclusions

Rab27 is needed for successful tick feeding and may be important for acquiringA. phagocytophilumduring a blood meal. Additionally, silencingrab27in tick cells results in a shift of extracellular vesicle size. Overall, we have observed that Rab27 plays a key role in tick EV biogenesis and the tripartite interactions among the vector, the mammalian host, and a microbe it encounters.
Learning about what is most important: incorporating values into the design of learning experiences
Authors: Campana Kathleen , Kociubuk Jacqueline , Mills J. Elizabeth , Martin Michelle H.
Published: November 2023

Purpose

The purpose of this study was to bring library practitioners and researchers together to develop two co-designed tools for helping library practitioners gain a more holistic understanding of families in underserved groups and identify their values with the goal of developing more relevant learning experiences for them. The co-designed tools were then tested with Master’s of Library and Information Science (MLIS) students at two universities, whose feedback yielded several valuable findings and informed revisions to the tools.

Design/methodology/approach

A participatory, design-based approach was used throughout the study, both with engaging library practitioners in the co-design of different tools and processes introduced in the Toolkit, and to help MLIS students and library practitioners test the tools and provide feedback on the tool revisions.

Findings

Students indicated that the tools helped them develop a deeper understanding of underserved groups and their values and gave the students the time and space to reflect on their understanding of the socio-cultural and value contexts of their communities and the values they hold.

Originality/value

This study can help libraries more effectively design strengths-based learning experiences that are meaningful and relevant to underserved groups and their values, particularly for children and families from underserved communities.
Resource sustainability in the water, energy and food nexus: role of technological innovation
Authors: David Love Opeyemi , Nwulu Nnamdi Ikechi , Aigbavboa Clinton Ohis , Adepoju Omoseni Oyindamola
Published: November 2023

Purpose

This paper aims to examine the role of technological Innovation in ensuring resource sustainability in the water, energy and food (WEF) nexus, as there exists a shortage of statistical research on the extent of the influence of technological Innovation on the WEF nexus.

Design/methodology/approach

The study used a quantitative research method, using a well-structured questionnaire to collect data from management staff in the WEF departments in South Africa. The collected data were analyzed by using mean score ranking, exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) for structural equation modelling (SEM).

Findings

The findings show that the technological process of technological innovation is significant for resource sustainability. The result also showed that technological innovations directly and statistically significantly affect WEF nexus. The EFA resulted in three components of WEF nexus product innovation, WEF nexus process innovation and WEF nexus novel innovations. Furthermore, the CFA and SEM analysis reveals that six technological innovation indicators influence the sustainability of the nexus: smart water metering technology, smart metering technology, food quality monitoring technology, agricultural technology solutions, new technological design and eco-friendly WEF products.

Originality/value

The sustainability of these three inevitable resources for man’s survival is dependent on technological innovations, and this study has shown the major categories of innovations needed, thus establishing a pathway for engineering design.
The influence of openness to change on academics' research publication in public higher education institutions in Tanzania
Authors: Ndiango Sinyati , Kumburu Neema P. , Jaffu Richard
Published: November 2023

Purpose

The major purpose of this paper is to examine the influence of openness to change on research publication in higher education institutions (HEI) in Tanzania.

Design/methodology/approach

With a sample of 247 academics, a cross-sectional survey design was used and questionnaires were the primary data collection tool. The collected data were tested using mean and standard deviations, and the causal–effect relationship between the independent and dependent variables was tested using simple linear regression.

Findings

The findings of this study revealed that openness to change positively and significantly influence research publication in higher education (β = 0.598 and p < 0.001).

Practical implications

The study recommends that HEI should consider openness to change value as one among criteria for hiring academics as well as developing good programs that will help academics develop the academics' self-awareness with regard to what takes for one to be a productive researcher.

Originality/value

This is the first study to examine the influence of openness to change as a personal value on academics’ research publication in Tanzanian HEI. In this instance, the study contributes to the existing literature on the influence of academics' personal values in terms of openness to change on research publication.
How true is the truth? A study of the factors affecting honest response behaviour of patients in hospital settings
Authors: Darzi Mushtaq Ahmad , Islam Sheikh Basharul , Bhat Suhail Ahmad , Khursheed Syed Owais
Published: November 2023

Purpose

The current study is aimed at identifying the prominent influencers that affect the response behaviour of patients in a hospital environment.

Design/methodology/approach

The research is based on the data collected through the participant observation method while interviewing patients about the quality of healthcare services in nine community health centres of the Kashmir division. Thematic analysis was performed on the information collected from patients admitted to various hospital sections.

Findings

The analysis of the qualitative data revealed that the presence of hospital staff near respondents, perceived risk of maltreatment, social desirability, the sensitivity of the topic, risk of information sharing and attitude towards surveys are the most frequently observed factors that modulate the patient's tendency to truthfully report critical facts about the problem understudy.

Originality/value

These results can help researchers to exercise caution while communicating with respondents and collecting data related to serious issues in a natural setting.
Skeletal muscle DNA methylation: Effects of exercise and HIV
Authors: Jankowski Catherine M. , Konigsberg Iain R. , Wilson Melissa P. , Sun Jing , Brown Todd T. , Julian Colleen G. , Erlandson Kristine M.
Published: November 2023

Aging, human immunodeficiency virus (HIV) infection, and antiretroviral therapy modify the epigenetic profile and function of cells and tissues, including skeletal muscle (SkM). In some cells, accelerated epigenetic aging begins very soon after the initial HIV infection, potentially setting the stage for the early onset of frailty. Exercise imparts epigenetic modifications in SkM that may underpin some health benefits, including delayed frailty, in people living with HIV (PWH). In this first report of exercise‐related changes in SkM DNA methylation among PWH, we investigated the impact of 24 weeks of aerobic and resistance exercise training on SkM (vastus lateralis) DNA methylation profiles and epigenetic age acceleration (EAA) in older, virally suppressed PWH (n = 12) and uninfected controls (n = 18), and associations of EAA with physical function at baseline. We identified 983 differentially methylated positions (DMPs) in PWH and controls at baseline and 237 DMPs after training. The influence of HIV serostatus on SkM methylation was more pronounced than that of exercise training. There was little overlap in the genes associated with the probes most significantly differentiated by exercise training within each group. Baseline EAA (mean ± SD) was similar between PWH (−0.4 ± 2.5 years) and controls (0.2 ± 2.6 years), and the exercise effect was not significant (p = 0.79). EAA and physical function at baseline were not significantly correlated (all p ≥ 0.10). This preliminary investigation suggests HIV‐specific epigenetic adaptations in SkM with exercise training but confirmation in a larger study that includes transcriptomic analysis is warranted.