bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotinylation-based proximity labelling proteomics: basics, applications and technical considerations
Authors: Niinae Tomoya , Ishihama Yasushi , Imami Koshi 
Published: November 2021

Abstract
Recent advances in biotinylation-based proximity labelling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein–protein interactions, protein–nucleic acid interactions, (membraneless) organelle proteomes and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.
The effect of salinity on osmotic regulation and respiratory rate of the prawn Macrobrachium tenellum Smith, 1871 (Decapoda: Caridea: Palaemonidae)
Authors: Hernández-Sandoval Pedro , Díaz Fernando , García-Guerrero Marcelo U 
Published: November 2021

Abstract
The effect of salinity on oxygen consumption rate and hemolymph osmolarity of the palaemonid prawn Macrobrachium tenellum (Smith, 1871) maintained at 0, 5, 10, 15, 20 and 25 psu was analyzed. Oxygen consumption rate was measured in respiratory chambers and osmolality from samples of hemolymph. Oxygen consumption rose significantly beyond 15 psu, with individuals showing hyper regulatory behavior from 0 to 10 psu, being able to maintain its internal solutes concentration (426–504 mmol kg–1) higher than that of the water (153–348 mmol kg–1). They acted as hypo-regulators from 15 to 25 psu as their internal solute concentration (454–562 mmol kg–1) was lower than that of the water (459–744 mmol kg–1). The isosmotic point was 505 mmol kg–1 at 16 psu, and survival was high in all salinities. The osmotic behavior of M. tenellum allows it to successfully invade fresh water by keeping constant the ionic and osmotic concentrations of both extra- and intra-cellular solute concentrations, always above fresh water, but varying its O2 consumption as salinity changes. The implications of such adaptations for the dispersal of the species into freshwater habitats is discussed.
The STL Still Struggles with the Method for Interpreting its Statute
Authors: Di Gianfrancesco Laura 
Published: November 2021

Abstract
This article investigates the Special Tribunal for Lebanon (STL) Trial Chamber’s Ayyash et al. judgment of 2020, focusing on the STL’s novel, domestic-centred solution to the interpretive problems raised by Articles 2 and 3 of its Statute concerning the applicable law. The analysis demonstrates that the Trial Chamber significantly departed from the STL Appeals Chamber’s Interlocutory Decision of 2011. Such divergence derived from a more complete application of the interpretive framework already endorsed in 2011 based on the Vienna Convention on the Law of Treaties (1969) (VCLT). The article shows that, by more comprehensively engaging with the VCLT interpretive method, the Trial Chamber was eventually able to adopt a fair trial-oriented approach to the identification of the applicable law, which led it to exclude the relevance of international criminal law rules. The Ayyash et al. Trial Judgment contributes, in turn, to the broader discussion concerning the ability of the VCLT method to accommodate the interpretive challenges of statutes of criminal tribunals created by virtue of a UN Security Council resolution.
Assessment of spatiotemporal variability of giant clam populations (Cardiidae:Tridacna) from 11 years of monitoring at Koh Tao, Thailand
Authors: Mehrotra Rahul , Allchurch Alyssa , Monchanin Coline , Scott Chad M 
Published: November 2021

ABSTRACTGiant clams (Tridacninae) are an ecologically important species in coral reef habitats across the Indo-Pacific. Numerous examples of giant clam population declines of varying degrees of severity have been documented since the 1970s. These have been attributed to several reasons, such as overexploitation in regional fisheries and ornamental trades, extreme weather events and anomalous marine warming events leading to bleaching. In Thailand, this has led to extensive conservation efforts, such as legal protections and population restocking. Despite these strong measures, to date no long-term studies have been conducted on giant clam populations in Thai waters. We provide results from 11 years (2009–2019) of giant clam population monitoring, at Koh Tao, an island with a well-documented history of coral reef-associated stressors as well as conservation efforts. Surveys were conducted across two depth ranges at 18 reef sites around the island, revealing contrasting trends. Our findings indicate a significant population decline of Tridacna crocea from coral reefs in the 6–8 m depth range, from 1.41 (±0.47) individuals/100 m2 in 2010 to 0.59 (±0.17) individuals/100 m2 in 2019, with, however, no significant change in T. squamosa populations at this depth range. Data from the 3–5 m depth range indicate no significant change in the T. crocea population over the years, but a population increase of T. squamosa from 0.78 (±0.18) individuals/100 m2 in 2009 to 2.07 (±0.38) individuals/100 m2 in 2019. Abundance estimates from these sites indicate extensive heterogeneity in giant clam populations around the island, and highlight the importance of sufficient spatial resolution in identifying population trends.
Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions
Authors: Zardoni Luca , Nardini Eleonora , Brambati Alessandra , Lucca Chiara , Choudhary Ramveer , Loperfido Federica , Sabbioneda Simone , Liberi Giordano 
Published: November 2021

Abstract
Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.
An update on the use of tolvaptan for autosomal dominant polycystic kidney disease: consensus statement on behalf of the ERA Working Group on Inherited Kidney Disorders, the European Rare Kidney Disease Reference Network and Polycystic Kidney Disease International
Authors: Müller Roman-Ulrich , Messchendorp A Lianne , Birn Henrik , Capasso Giovambattista , Cornec-Le Gall Emilie , Devuyst Olivier , van Eerde Albertien , Guirchoun Patrick , Harris Tess , Hoorn Ewout J , Knoers Nine V A M , Korst Uwe , Mekahli Djalila , Le Meur Yannick , Nijenhuis Tom , Ong Albert C M , Sayer John A , Schaefer Franz , Servais Aude , Tesar Vladimir , Torra Roser , Walsh Stephen B , Gansevoort Ron T 
Published: November 2021

ABSTRACTApproval of the vasopressin V2 receptor antagonist tolvaptan—based on the landmark TEMPO 3:4 trial—marked a transformation in the management of autosomal dominant polycystic kidney disease (ADPKD). This development has advanced patient care in ADPKD from general measures to prevent progression of chronic kidney disease to targeting disease-specific mechanisms. However, considering the long-term nature of this treatment, as well as potential side effects, evidence-based approaches to initiate treatment only in patients with rapidly progressing disease are crucial. In 2016, the position statement issued by the European Renal Association (ERA) was the first society-based recommendation on the use of tolvaptan and has served as a widely used decision-making tool for nephrologists. Since then, considerable practical experience regarding the use of tolvaptan in ADPKD has accumulated. More importantly, additional data from REPRISE, a second randomized clinical trial (RCT) examining the use of tolvaptan in later-stage disease, have added important evidence to the field, as have post hoc studies of these RCTs. To incorporate this new knowledge, we provide an updated algorithm to guide patient selection for treatment with tolvaptan and add practical advice for its use.
Metabarcoding of stomach contents and fecal samples provide similar insights about Seaside Sparrow diet
Authors: Snider Allison M , Bonisoli-Alquati Andrea , Pérez-Umphrey Anna A , Stouffer Philip C , Taylor Sabrina S 
Published: November 2021

Abstract
DNA metabarcoding is a popular tool for animal diet studies to address a variety of research topics across disciplines and taxa. Despite its widespread use, there has been relatively little focus on how digestion influences prey DNA detection and the description of a predator’s diet. Fecal samples are a compelling source of dietary DNA because they are collected non-invasively. However, these samples may provide incomplete or inaccurate descriptions of diet because of differential digestion and DNA degradation across prey taxa during gut passage. This is especially pertinent for avian diet studies, which have widely adopted the use of fecal samples as a proxy for overall diet. To explore how digestion affects the recovery and detection of prey DNA in passerines, we used DNA metabarcoding to compare the recovery of prey DNA from paired stomach contents and fecal samples in Seaside Sparrows (Ammospiza maritima). Stomach contents produced ~2.5 times greater DNA concentrations than fecal samples and—while this difference in DNA concentration was not statistically significant—stomach contents produced significantly more read identifications than fecal samples. However, these differences did not influence the description of diet, as similar measures of richness and diversity were found in both sample types. The relative read abundance of common prey families remained consistent between sample types, suggesting that while less DNA may survive digestion, the proportions of prey remain largely unaffected. We found no difference in the description of diet based on sample type at the population level, but our results show that comparing stomach and fecal samples from the same individual can reveal distinct foraging bouts. With no clear benefit to using stomach contents, we conclude that fecal samples are the preferred sample type for avian metabarcoding diet studies, unless research goals necessitate otherwise.
Public attitude towards militant protest in Hong Kong: An investigation based on the elaborated social identity model
Authors: Zhu Alex Yue Feng , Chou Kee Lee 
Published: November 2021

Abstract
Group-based norms regarding political participation are not static; they are malleable attributes affected by police–protest dynamics in the social movement context. This study used a comprehensive and authoritative sampling framework to collect the views of Hong Kong residents at the end of the anti-extradition bill movement (n = 1,000; 53.6% female; mean age = 46.4, range 18–86) and evaluated them using the Elaborated Social Identity Model. The results revealed a full mediational pathway from police action perceived as indiscriminate that facilitated the public’s identification with the militant protesters and bolstered public support for the militant protest. Our findings provide an in-depth understanding of why the public supported violent protest and criminal vandalism in the movement by adopting the interactive arena between police and protesters as the entry point and the development of shared identity as the process. Our findings highlight crowd management as a complex issue in relational dynamics rather than a purely logistical challenge.
Biographical representation, from narrative to list: The evolution of curricula vitae in the humanities, 1950 to 2010
Authors: Hamann Julian , Kaltenbrunner Wolfgang 
Published: November 2021

AbstractCurricula vitae (CVs) are a crucial device for the evaluation of academic personae and biographies. They play a key role in the competitive assessments that underpin the reproduction of the academic workforce. Drawing on 80 CVs which have been part of candidates’ applications for vacant professorships, our article provides a longitudinal study of the development of CVs used by German scholars in professorial appointment procedures in the disciplines of German studies and history between 1950 and the late 2010s. The analysis reveals the evolution of CVs by tracing their various morphological shifts. We distinguish four formats throughout the period of study: CVs initially had a (1) narrative format that develops into an (2) intermediary segmented form before CVs take on a (3) list form in which biographical information congeals into distinct categories. In the 2010s, the list form develops into a (4) hyper-differentiated list form in which coherent biographical representations are finally dissolved into almost eclectic accumulations of finely grained performance categories. Against the backdrop of this finding, the contribution concludes with three general observations: First, the evolution of CVs reflects changes in the institutional environment, not least the increased competitive pressures in academic careers. Second, the evolution of biographical representations also conveys a transformation of the academic persona throughout which boundaries between personal and professional biographies are established. Third, we propose a reactivity of current list form CVs through which academics are disciplined to live up to the categories that wait to be realized in their CVs.
During development of rheumatoid arthritis, intermetatarsal bursitis may occur before clinical joint swelling: a large imaging study in patients with clinically suspect arthralgia
Authors: van Dijk Bastiaan T , Wouters Fenne , van Mulligen Elise , Reijnierse Monique , van der Helm-van Mil Annette H M 
Published: November 2021

Abstract

Objectives
Intermetatarsal bursitis (IMB) represents juxta-articular synovial inflammation of the intermetatarsal bursae. Recent MRI studies identified IMB as feature of early RA, but whether IMB already occurs in the pre-arthritic phase is unknown. We performed a large MRI study in clinically suspect arthralgia (CSA) to assess the occurrence and prognostic value of IMB.

Methods
A total of 577 consecutive CSA patients underwent contrast-enhanced MRI of the forefoot, metacarpophalangeal joints and wrist. MRIs were evaluated for subclinical synovitis/tenosynovitis/osteitis in line with the RA MRI scoring system (summed as RAMRIS inflammation) and for IMB. IMB was considered present if uncommon in the general population at the same location (i.e. size scored above the 95th percentile in age-matched symptom-free controls). The relation of IMB with other MRI-detected subclinical inflammation (synovitis/tenosynovitis/osteitis) was studied. Cox-regression assessed the association with clinical arthritis development during median 25 months follow-up. ACPA stratification was performed.

Results
At presentation with CSA, 23% had IMB. IMB was more frequent in ACPA-positive than ACPA-negative CSA (47% vs 19%, P &lt; 0.001). Patients with IMB were more likely to also have subclinical synovitis [OR 3.4 (95% CI 1.8, 6.5)] and tenosynovitis [5.9(2.8, 12.6)]. IMB conferred higher risk of developing arthritis [HR 1.6(1.0–2.7) adjusted for other subclinical inflammation]. IMB-presence predicted arthritis development in ACPA-positive CSA [adjusted HR 2.2(1.0–4.7)], but not in ACPA-negative CSA-patients [0.8(0.4–1.7)].

Conclusion
Approximately a quarter of CSA patients have IMB, which is frequently accompanied by subclinical synovitis and tenosynovitis. IMB precedes development of clinical arthritis, particularly in ACPA-positive CSA. These results reinforce the notion that juxta-articular synovial inflammation is involved in the earliest phases of RA development.
Labor Taxation and the Uneven Growth of Wage Inequality
Authors: Thompson Daniel 
Published: November 2021

Abstract
Wage inequality has risen in some rich countries but not others, and where it has risen, the divergence has been mainly between middle and high earners. I argue that taxation is an important factor driving this uneven growth of pretax wage inequality. In some countries, marginal tax rates on upper-middle incomes are high and stable, reducing the income that workers receive relative to the costs borne by employers. In others, marginal taxes on upper-middle incomes have been reduced, in some instances considerably, which incentivizes pretax income growth. I show that marginal tax rates are strongly correlated with pretax 90/10 and 90/50 wage ratios. The results are robust to alternative estimators that control for unobserved heterogeneity and other statistical issues. The findings suggest that, in an era of liberalized wage bargaining and decreased economic coordination, taxation may have taken on a greater role as an inequality-reducing institution.
Therapeutic Drug Monitoring of Antibiotics in the Elderly: A Narrative Review
Authors: Cattaneo Dario , Falcone Marco , Gervasoni Cristina , Marriott Deborah J. E. 
Published: November 2021

Background:
Antibiotic dosing adaptation in elderly patients is frequently complicated by age-related changes affecting the processes of drug absorption, distribution, metabolism, and/or elimination. These events eventually result in treatment failure and/or development of drug-related toxicity. Therapeutic drug monitoring (TDM) can prevent suboptimal antibiotic exposure in adult patients regardless of age. However, little data are available concerning the specific role of TDM in the elderly patients.

Methods:
This review is based on a PubMed search of the literature published in the English language. The search involved TDM studies of antibiotics in the elderly patients performed between 1990 and 2021. Additional studies were identified from the reference lists of the retrieved articles. Studies dealing with population pharmacokinetic modeling were not considered.

Results:
Only a few studies, mainly retrospective and with observational design, have specifically dealt with appropriate antibiotic dosing in the elderly patients based on TDM. Nevertheless, some clinical situations in which the selection of optimal antibiotic dosing in the elderly patients was successfully guided by TDM were identified.

Conclusions:
Elderly patients are at an increased risk of bacterial infections and inadequate drug dosing compared with younger patients. Therefore, the availability of TDM services can improve the appropriateness of antibiotic prescriptions in this population.
Association between vasomotor symptoms and sarcopenia assessed by L3 skeletal muscle index among Korean menopausal women
Authors: Ryu Ki-Jin , Kim Hyun Kyun , Lee Yeon Ju , Park Hyuntae , Kim Tak 
Published: November 2021

Abstract

Objective:
To evaluate the association between vasomotor symptoms (VMS), skeletal muscle index (SMI), and sarcopenia in menopausal women.

Methods:
This cross-sectional study included 295 Korean menopausal women 40 to 65 years old who underwent abdominal computed tomography during routine health checkups between January 2014 and May 2016. The cross-sectional areas of adipose and skeletal muscles were measured at the L3 level using computed tomography. The SMI is defined as the sum of the skeletal muscle area (cm2)/height2 (m2). Sarcopenia was identified by an SMI of <34.9 cm2/m2. VMS were assessed using the Menopause Rating Scale.

Results:
The mean age of the participants was 54.93 ± 6.20 years. VMS were reported in 160 women (54.2%). Sarcopenia was more prevalent in women without VMS (18.5%) than in those with (6.9%). Multivariate logistic regression showed that the prevalence of sarcopenia was inversely associated with the prevalence of VMS (odds ratio, 0.32; 95% CI, 0.15-0.67). Moreover, the paraspinal muscle index was positively associated with the prevalence of VMS (odds ratio, 1.06; 95% CI, 1.01-1.11) after adjusting for age, body mass index, waist circumference, adipose tissue area, history of hormone therapy, systolic and diastolic blood pressures, total cholesterol, insulin resistance, alcohol intake, and exercise.

Conclusions:
VMS are less common in women with sarcopenia than in those without and are positively associated with paraspinal muscle mass in Korean menopausal women. Further longitudinal studies are required to investigate the causal relationships and underlying mechanisms.
Nutritional and dietary interventions to prolong renal allograft survival after kidney transplantation
Authors: Tantisattamo Ekamol , Kalantar-Zadeh Kamyar , Molnar Miklos Z. 
Published: November 2021

Purpose of review
Diet plays an important role in slowing progression of chronic kidney disease in native and transplanted kidneys. There is limited evidence on the association on dietary intake with renal allograft function. Mechanisms of major nutrients and dietary patterns with focusing on a plant-based diet related to kidney transplant health and longevity are reviewed.

Recent findings
High dietary protein intake may adversely affect renal allograft. Low protein plant-focused diets such as Dietary Approaches to Stop Hypertension, plant-dominant low-protein diet and Mediterranean diets appear associated with favorable outcomes in slowing renal allograft function decline. The mechanism may be related to a change in renal hemodynamic by decreasing glomerular hyperfiltration from low dietary protein intake and plant-based ingredients. Recent observational studies of association between dietary protein intake and kidney allograft outcomes are conflicting. Although strong evidence is still lacking, a low protein diet of 0.6–0.8 g/kg/day with at least 50% of the protein source from plant-based components in kidney transplant recipients with stable kidney allograft function should be considered as the dietary target.

Summary
Dietary intervention with low-protein plant-focused meals may improve outcomes in kidney transplant recipients, but the evidence remains limited and further studies are warranted.