bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical methods for analysing biosensor performance
Authors: Eddowes Mark J 
Published: November 2023

Abstract
Theory, along with experiment, forms a vital part of a practical scientific approach. Though perhaps redundant on its own, theory enables the most efficient use of time spent performing experiments. This is important since experiments are often difficult and time consuming and will not always be successful. Proper use of theory assists effective planning of experiments and enables the researcher to gain the maximum amount of information from each experiment performed. In applied work, such as biosensor research and development, theory used in a predictive manner can identify which, of perhaps a multitude of approaches, is most likely to yield the desired result. It is therefore important that proper consideration be given to theory and its application to the solution of practical problems involving real systems. The aim of this chapter is to demonstrate how, in practice, the problem of the provision of a theoretical description of biosensors may be approached and illustrate this approach by way of some examples commonly encountered.
Methods for the study of anaerobic microflora
Authors: Drasar B S , Roberts April K 
Published: November 2023

Abstract
This chapter is about the study of the microbial ecology of the bacteria associated with the human body. This is among the most intensively studied of microbial habitats and includes a number of distinct ecosystems of particular interest. Attention has focused on the microbial flora of the mouth (1), the skin (2), the genital tract (3), and the intestine (4 6). These themes have on occasion been drawn together in more systematic treatments of the whole system (7-9). Systematic studies of animals other than man have concentrated on the bovine rumen (10, l l). Many studies have been concerned to describe these habitats in terms of their bacterial inhabitants while others have concentrated on examining the metabolic potential of the bacterial microflora and its impact on the host (12, 13).
The combinatorial approach
Authors: Cohen Fred E , Presnell scott R 
Published: November 2023

Abstract
With the advent of protein X-ray crystallography in the 1950s and the more recent use of multidimensional NMR spectroscopy, biologists have become familiar with the detailed organization of protein structures at the atomic level. These structures have fundamentally changed our understanding of mechanistic enzymology and molecular recognition in the immune system. More recently, the ability of structural studies to influence drug discovery and design has become clear (1). In spite of these advances, the rate of pro tein sequence determination via DNA sequencing vastly exceeds the rate of structure determination. How can this gap between sequence and structure be bridged? With an increase in the number of proteins of known structure, the likelihood that a new sequence will be similar to a known structure increases. Currently, ∼20% of the sequences identified in genome sequencing efforts are related to well-characterized proteins (2).
Recent developments in affinity separation technologies
Authors: Mohan Sudesh B , Lyddiatt Andrew 
Published: November 2023

Abstract
Since the innovative work of Porath et al. (1) in the 1960s, and the seminal texts of Lowe and Dean (2) and Dean et al. (3), the technologies of affinity separation have become widely accepted-perhaps now to the extent of being taken for granted. Practitioners range widely from laboratories interested in the isolation of bioactive probes and tools for biological research, to large manufacturing plants active in the production of diagnostic and therapeutic agents.
Immunoaffinity arid IgG receptor technologies
Authors: Godfrey Miguel A J 
Published: November 2023

Abstract
Historically, affinity chromatographic techniques have exploited the presence of naturally occurring biospecific interactions found in nature. Perhaps the most useful of these to biomedical science is the binding of antibodies to antigens, especially as the presence and binding specificities of antibodies may be manipulated by selective operator intervention. This chapter aims to introduce the laboratory scientist to affinity chromatographic methods of purifying antibodies and to demonstrate the use of immobilized antibodies as a tool in preparative affinity chromatography.
Designer affinity purifications of recombinant proteins
Authors: Sharma Satish K 
Published: November 2023

Abstract
During the last five years, tailoring recombinant proteins to facilitate their purification has proven to be a very useful strategy in recombinant DNA technology. DNA encoding peptide or protein tags (also called, among other names, affinity tails, cleavable linkers, and marker sequences) is attached to the gene of interest at its 5’ or 3’ end. The resulting gene fusions are expressed in a host and the encoded recombinant protein can be isolated from contaminating host proteins based on properties of the engineered tag. A schematic representation of this genetic approach, called designer affinity purification, is shown in Figure 1.
Counting integral numbers of residues by chemical modification
Authors: Hollecker Michelle 
Published: November 2023

Abstract
Proteins have integral numbers of each of the 20 amino adds, hut all the currently accepted methods of determining this number measure only a nonintegral ratio of moles of amino acid per mole of protein. This value is rarely found to be close to an integer, due to experimental error and uncertainty about the molecular weight of the protein (1-3).
Analysis of protein conformation by gel electrophoresis
Authors: Goldenberg David P 
Published: November 2023

Abstract
Electrophoresis through polyacrylamide gels (PAGE) is one of the simplest and most commonly used methods for characterizing protein molecules (1,2). As described in Chapter l, gel electrophoresis in the presence of the detergent sodium dodecyl sulfate (SOS) is widely used to determine the molecular weights of polypeptides. Electrophoretic methods can also be used to determine the isoelectric point of a protein and to count the number of reactive groups (Chapter 6). This chapter describes the use of non-denaturing, or ‘native’, gel electrophoresis to analyse the conformations of proteins as well as a method for studying protein folding-unfolding reactions using gels containing transverse gradients of denaturants.
Glutathione Transferase Photoaffinity Labeling Displays GST Induction by Safeners and Pathogen Infection
Authors: Font Farre Maria , Brown Daniel , König Maurice , Killinger Brian J , Kaschani Farnusch , Kaiser Markus , Wright Aaron T , Burton Jonathan , van der Hoorn Renier A L 
Published: November 2023

Abstract
Glutathione transferases (GSTs) represent a large and diverse enzyme family involved in the detoxification of small molecules by glutathione conjugation in crops, weeds and model plants. In this study, we introduce an easy and quick assay for photoaffinity labeling of GSTs to study GSTs globally in various plant species. The small-molecule probe contains glutathione, a photoreactive group and a minitag for coupling to reporter tags via click chemistry. Under UV irradiation, this probe quickly and robustly labels GSTs in crude protein extracts of different plant species. Purification and mass spectrometry (MS) analysis of labeled proteins from Arabidopsis identified 10 enriched GSTs from the Phi(F) and Tau(U) classes. Photoaffinity labeling of GSTs demonstrated GST induction in wheat seedlings upon treatment with safeners and in Arabidopsis leaves upon infection with avirulent bacteria. Treatment of Arabidopsis with salicylic acid (SA) analog benzothiadiazole (BTH) induces GST labeling independent of NPR1, the master regulator of SA. Six Phi- and Tau-class GSTs that are induced upon BTH treatment were identified, and their labeling was confirmed upon transient overexpression. These data demonstrate that GST photoaffinity labeling is a useful approach to studying GST induction in crude extracts of different plant species upon different types of stress.
Real-world comparative study of the efficacy of Janus kinase inhibitors in patients with rheumatoid arthritis: the ANSWER cohort study
Authors: Hayashi Shinya , Tachibana Shotaro , Maeda Toshihisa , Yamashita Mai , Shirasugi Iku , Yamamoto Yuzuru , Yamada Hirotaka , Okano Takaichi , Nishimura Keisuke , Ueda Yo , Jinno Sadao , Saegusa Jun , Yamamoto Wataru , Murata Koichi , Fujii Takayuki , Hata Kenichiro , Yoshikawa Ayaka , Ebina Kosuke , Etani Yuki , Yoshida Naofumi , Amuro Hideki , Hashimoto Motomu , Hara Ryota , Katayama Masaki , Okano Tadashi , Kuroda Ryosuke 
Published: November 2023

Abstract

Objective
This multicentre, retrospective study compared the efficacy and safety of tofacitinib, baricitinib, peficitinib and upadacitinib in real-world clinical settings after minimizing selection bias and adjusting the confounding patient characteristics.

Method
The 622 patients were selected from the ANSWER cohort database and treated with tofacitinib (TOF), baricitinib (BAR), peficitinib (PEF) or upadacitinib (UPA). The patient’s background was matched using propensity score-based inverse probability of treatment weighting (IPTW) among four treatment groups. The values of Clinical Disease Activity Index (CDAI), C-reactive protein (CRP), and modified Health Assessment Questionnaire (mHAQ) after drug initiation and the remission or low disease activity (LDA) rates of CDAI at 6 months after drug initiation were compared among the four groups. Further, the predictive factor for TOF and BAR efficacy was analysed.

Results
The retention and discontinuation rates until 6 months after drug initiations were not significantly different among the four JAK inhibitors treatment groups. Mean CDAI value, CDAI remission rate, and CDAI-LDA rate at 6 months after drug initiation were not significantly different among treatment groups. Baseline CDAI (TOFA: OR 1.09, P &lt; 0.001; BARI: OR 1.07, P &lt; 0.001), baseline CRP (TOFA: OR 1.32, P = 0.049), baseline glucocorticoid dose (BARI: OR 1.18, 95% CI 1.01–1.38, P = 0.035), a number of previous biological or targeted synthetic disease-modifying antirheumatic drugs (biological/targeted synthetic DMARDs) (BARI: OR 1.36, P = 0.004) were predictive factors for resistance to CDAI-LDA achievement to JAK inhibitor treatment.

Conclusion
The efficacy and safety of TOF, BAR, PEF and UPA were not significantly different for the treatment of patients with rheumatoid arthritis.
Comparison of short-term outcomes between robotic and laparoscopic liver resection: a meta-analysis of propensity score-matched studies
Authors: Gao Feng-wei , Zhao Xin , Xie Qing-yun , Jiang Kang-yi , Mao Tian-yang , Yang Man-yu , Wu Hong 
Published: November 2023

Objective:
This meta-analysis aimed to compare short-term outcomes between robotic liver resection (RLR) and laparoscopic liver resection (LLR) using data collected from propensity score-matched studies (PSM).

Methods:
The PubMed, Cochrane Library, and Embase databases were searched to collect propensity score-matched studies comparing RLR and LLR. Relevant data were extracted and analyzed. Odds ratios (OR) and standardized mean differences (SMDs) with 95% confidence intervals (CIs) were calculated using fixed-effect or random-effect models. Meta-regression analysis was performed for primary outcome measures. Subgroup analyses and sensitivity analyses were performed for outcomes exhibiting high heterogeneity. Quality of evidence was evaluated using the Grading of Recommendations, Assessment, Development and Evaluation framework.

Results:
Twenty-two propensity score-matched studies were included to comprise 5272 patients (RLR group, 2422 cases; LLR group, 2850 cases). Intraoperative blood loss (SMD=−0.31 mL, 95% CI −0.48 to −0.14; P=0.0005), open conversion (OR= 0.46, 95% CI 0.37 to 0.58; P<0.0001), and severe complications (OR=0.76, 95% CI 0.61 to 0.95; P=0.02) were significantly lower in the RLR group. Operation time, odds of use and duration of Pringle maneuver, length of hospital stay, and odds of intraoperative blood transfusion, overall complications, R0 resection, reoperation, 30-day readmission, 30-day mortality, and 90-day mortality did not significantly differ between the groups. Further subgroup and sensitivity analyses suggested that the results were stable. Meta regression analysis did not suggest a correlation between primary outcomes and study characteristics. The quality of evidence for the primary outcomes was medium or low, while that for the secondary outcomes was medium, low, or very low.

Conclusion:
Although some short-term outcomes are similar between RLR and LLR, RLR is superior in terms of less blood loss and lower odds of open conversion and severe complications. In the future, RLR may become a safe and effective replacement for LLR.
Natural History of Pediatric Patients With Crohn’s Disease Treated With Mesalamine Therapy
Authors: Young Denise D. , Perry Sharon , Malay Sindhoosha , Sferra Thomas J. , Finkler Michael , Moses Jonathan 
Published: November 2023

Background:
5-aminosalicylates (5-ASA) are used to treat mild to moderate ulcerative colitis. Despite their lack of efficacy in Crohn disease (CD), they are still used in real-world practice. Additionally, when patients have progressive disease, they may escalate to biologic therapy, at which time 5-ASA may or may not be discontinued.

Objectives:
The aim of this study is to assess the clinical outcomes of patients started on 5-ASA for the treatment of pediatric CD. The secondary aims were to evaluate the outcomes of those who continue 5-ASA to those who discontinue 5-ASA upon biologic escalation.

Methods:
We performed a single-center retrospective chart review of pediatric CD patients from 2010 to 2019 who were initially treated with 5-ASA. Demographics, medication and laboratory data, and clinical disease activity were collected.

Results:
Sixty-one patients were included in the study; the majority had inflammatory CD with ileocolonic involvement. Twenty-four patients were on a concomitant immunomodulator. The majority of patients (85.2%) required escalation to biologics. Thirty-two patients (61.5%) who escalated to biologic therapy continued on 5-ASA. Eighty percent of patients achieved clinical remission at 1 year, and there was no difference between those who continued 5-ASA at time of biologic initiation compared to those who did not continue the medication. Patients who discontinued 5-ASA had an average annual cost savings of $6741.

Conclusion:
5-ASA is not a durable monotherapy for the treatment of pediatric CD. Patients who require escalation from 5-ASA to biologic therapy do not benefit from concomitant 5-ASA therapy. Further prospective studies are needed to confirm these findings.
Development and validation of a multivariable risk prediction model for hepatic steatosis in patients with HIV infection
Authors: Wirth Marielle , Ruckes Christian , Michel Maurice , Schattenberg Jörn M. 
Published: November 2023

Objective:
Early detection of hepatic steatosis in people with HIV (PWH) could prevent progression and inflammation. The aim was to develop and validate a multivariable risk prediction model for hepatic steatosis in German PWH.

Design:
In this cohort study, 282 PWH were prospectively enrolled, and hepatic steatosis was defined via controlled attenuation parameter (CAP; ≥275 dB/m) using vibration-controlled transient elastography.

Methods:
Three multivariable logistic regression models were conducted. Missing values were imputed with multiple imputation. Cut-offs were derived based on Youden-Indices. Performance was assessed via discriminatory and calibrative ability and accuracy via Brier Skill Score. Sensitivity, specificity, and predictive values were calculated. Internal validation was performed via bootstrapping.

Results:
The prevalence of hepatic steatosis was 35.3% (100/282). Univariate analyses revealed associations with age, waist circumference, BMI, hypertension, hyperlipidemia and gamma-gt. In multivariable analyses, male sex [odds ratio (OR) 2.07, 95% confidence interval (CI) 1.42–3.00, P = 0.001] and BMI (OR 1.27, 95% CI 1.18–1.36, P < 0.001) were identified as independent predictors of hepatic steatosis. The naive and optimism-corrected c-statistic of 79% showed a good discriminatory ability, the calibration was well with a slight tendency for overestimation for predicted probabilities above 70%. At the cutoff of 1.95, the specificity was 71% and the negative-predictive value 82.3%. Twenty-seven percent of the 282 patients would be misclassified, 17% as false positives and 10% as false negatives.

Conclusion:
The developed prediction model contributes to the lack of validated noninvasive tools to predict hepatic steatosis in people with HIV. Future studies should include more candidate predictors and externally validate the model.
SimReadUntil for Benchmarking Selective Sequencing Algorithms on ONT Devices
Authors: Mordig Maximilian , Rätsch Gunnar , Kahles André 
Published: November 2023

AbstractMotivationThe Oxford Nanopore Technologies (ONT) ReadUntil API enables selective sequencing, which aims to reduce time spent on sequencing uninteresting reads in favor of more interesting reads, e.g., to deplete or enrich certain genomic regions. The performance gain depends on the selective sequencing decision-making algorithm (SSDA) which decides whether to reject a read, stop receiving a read or wait for more data. Since real runs are time-consuming and costly (at scale), simulating the ONT device with support for the ReadUntil API is highly beneficial to compare and optimize the parameters of SSDAs. Existing software like MinKNOW and UNCALLED only return raw signal data, are memory-intensive, require huge and often unavailable multi-fast5 files (≥100GB) and are not clearly documented.ResultsWe present the ONT device simulatorSimReadUntilthat takes a set of full (real or simulated) reads as input, distributes them to channels and plays them back in real time including mux scans, channel gaps and blockages, and allows to unblock (reject) reads as well as stop receiving data from them (imitating the ReadUntil API). Our modified ReadUntil API provides the basecalled reads rather than the raw signal to reduce computational load and focus on the SSDA rather than basecalling. Tuning the parameters of tools like ReadFish and ReadBouncer becomes easier because no GPU is required anymore for basecalling. We offer various methods to extract simulation parameters from a sequencing summary file and compare them.SimReadUntil‘s gRPC interface allows standardized interaction with a wide range of programming languages.AvailabilityThe code is freely available on GitHub (https://github.com/ratschlab/sim_read_until) along with a fully worked use case that combines the simulator with ReadFish (and optionally NanoSim).Supplementary informationSupplementary data are available at Bioinformatics online.
Senescent cells impair fracture repair through elevating ubiquitin-proteasome system activity in aged mice
Authors: Zhang Jun , Xu Jiongnan , Liu Jiatong , Lipe Brea , Wu Tao , Boyce Brendan F. , Shen Jie , Xing Lianping , Zhang Hengwei 
Published: November 2023

AbstractSenescent cells accumulate in multiple tissues with aging. Depletion of senescent cells benefits the aging related disease, such as aging bone fracture. However, the molecular mechanisms by which senescent cells regulate their neighboring bone cells are still not well-known. We reported that proteasome inhibitor enhanced fracture repair in aged mice. Senescent cells are major source of chronic inflammatory cytokines, which in turn induced protein ubiquitination. We reported that PDGFRβ was one of the highly ubiquitinated proteins in mesenchymal progenitors (MPCs) and TGFβ was the most increased SASP. In the current study, we found TGFβ induced PDGFRβ ubiquitination and proteasomal degradation through its E3 ligases. TGFβ neutralizing antibody blocked the inhibited callus derived MPC growth and increased Ub-PDGFRβ by senescent cells, which could be further prevented PDGFRβ inhibitor. These findings suggested senescent cells derived TGFβ impaired fracture repair in aged mice through elevating ubiquitination of PDGFRβ. The discovery of TGFβ-PDGFRβ pathway triggered by senescent cells opens avenues for optimizing treatment strategies for aging related disease by combination with the ligand of PDGFRβ.
Melanophilin mediates the association of myosin-5a with melanosome via three distinct interactions
Authors: Pan Jiabin , Zhou Rui , Yao Lin-Lin , Zhang Jie , Zhang Ning , Cao Qin-Juan , Sun Shaopeng , Li Xiang-dong 
Published: November 2023

ABSTRACTTransport and localization of melanosome at the periphery region of melanocyte are depended on myosin-5a (Myo5a), which associates with melanosome by interacting with its adaptor protein melanophilin (Mlph). Mlph contains four functional regions, including Rab27a-binding domain, Myo5a GTD-binding motif (GTBM), Myo5a exon F-binding domain (EFBD), and actin-binding domain (ABD). The association of Myo5a with Mlph is known to be mediated by two specific interactions: the interaction between the exon-F-encoded region of Myo5a and Mlph-EFBD and that between Myo5a-GTD and Mlph-GTBM. Here, we identify a third interaction between Myo5a and Mlph, i.e., the interaction between the exon-G-encoded region of Myo5a and Mlph-ABD. The exon-G/ABD interaction is independent from the exon-F/EFBD interaction and is required for the association of Myo5a with melanosome. Moreover, we demonstrate that Mlph-ABD interacts with either the exon-G or actin filament, but cannot interact with both of them simultaneously. Based on above findings, we propose a new model for the Mlph-mediated Myo5a transportation of melanosomes.
Extralimital Terrestrials: A reassessment of range limits in Alaska’s land mammals
Authors: Baltensperger A. P. , Lanier H. C. , Olson L. E. 
Published: November 2023

ABSTRACTUnderstanding and mitigating the effects of anthropogenic climate change and development on species requires the ability to track distributional changes over time. This is particularly true for species occupying high-latitude regions, which are experiencing a greater magnitude of climate change than the rest of the world. In North America, ranges of many mammals reach their northernmost extent in Alaska, positioning this region at the leading edge of climate-induced distribution change. Over a decade has elapsed since the publication of the last spatial assessments of terrestrial mammals in the state. We compared public occurrence records against commonly referenced range maps to evaluate potential extralimital records and develop repeatable baseline range maps. We compared occurrence records from the Global Biodiversity Information Facility for 64 terrestrial mammals native to mainland Alaska against a variety of range estimates (International Union for the Conservation of Nature, Alaska Gap Analysis Project, and the published literature). We mapped extralimital records and calculated proportions of occurrences encompassed by range extents. We also evaluated extralimital records against published species models, highlighted extralimital observations on U.S. Department of Interior lands, and report on two species of bats new to Alaska since 2014. Range comparisons identified 6,848 extralimital records belonging to 39 of 112 (34.8%) Alaskan species. On average, the Alaska Gap Analysis Project encompassed 95.5% of occurrence records and ranges were deemed accurate (> 90.0% correct) for 31 of 37 species, but overestimated extents for 13 species. International Union for Conservation of Nature range maps encompassed 68.1% of occurrence records and were > 90% accurate for 17 of 39 species. Results are either the product of improved sampling and digitization or represent actual geographic range expansions. Here we provide new data-driven range maps, update standards for the archival of museum-quality locational records and offer recommendations for mapping range changes for monitoring and conservation.