bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics
Authors: Truong Thy , Johnston S. Madisyn , Webber Kei , Boekweg Hannah , Lindgren Caleb M , Liang Yiran , Nydeggar Alissia , Xie Xiaofeng , Payne Samuel H. , Kelly Ryan T. 
Published: October 2022

AbstractThe sensitivity of single-cell proteomics (SCP) has increased dramatically in recent years due to advances in experimental design, sample preparation, separations and mass spectrometry instrumentation. Further increasing the sensitivity of SCP methods and instrumentation will enable the study of proteins within single cells that are expressed at copy numbers too small to be measured by current methods. Here we combine efficient nanoPOTS sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in fast label-free analyses. WWA is based on data-dependent acquisition (DDA) but employs larger precursor isolation windows to intentionally co-isolate and co-fragment additional precursors along with the selected precursor. The resulting chimeric MS2 spectra are then resolved using the CHIMERYS search engine within Proteome Discoverer 3.0. Compared to standard DDA workflows, WWA employing isolation windows of 8-12 Th increases peptide and proteome coverage by ~28% and ~39%, respectively. For a 40-min LC gradient operated at ~15 nL/min, we identified an average of 2,150 proteins per single-cell-sized aliquots of protein digest directly from MS2 spectra, which increased to an average of 3,524 proteins including proteins identified with MS1-level feature matching. Reducing the active gradient to 20 min resulted in a modest 10% decrease in proteome coverage. We also compared the performance of WWA with DIA. DIA underperformed WWA in terms of proteome coverage, especially with faster separations. Average proteome coverage for single HeLa and K562 cells was respectively 1,758 and 1,642 based on MS2 identifications with 1% false discovery rate and 3042 and 2891 with MS1 feature matching. As such, WWA combined with efficient sample preparation and rapid separations extends the depths of the proteome that can be studied at the single-cell level.
Long-term, super-resolution HIDE imaging of the inner mitochondrial membrane in live cells with a cell-permeant lipid probe
Authors: Zheng Shuai , Dadina Neville , Mozumdar Deepto , Lesiak Lauren , Martinez Kayli , Miller Evan W. , Schepartz Alanna 
Published: October 2022

AbstractThe densely packed inner mitochondrial membrane (IMM) is vital for bioenergy generation and its dynamics control mitochondrial health and cellular homeostasis. IMM structure is complex, however, and imaging its dynamics with high temporal and spatial resolution is complicated by the photosensitivity of IMM-resident enzymes. Here we describe the cell-permeant, lipid-like acridine orange derivative MAO-N3and use it to assemble high-density, environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells. MAO-N3pairs with multiple SPAAC-reactive fluorophores to support HIDE imagingviaconfocal, Structured Illumination, Single Molecule Localization, and Stimulated Emission Depletion microscopy, all with significantly improved resistance against photobleaching. The HIDE probes generated using MAO-N3require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes, even under conditions that amplify the effects of mitochondrial toxins, and visualize the IMM for up to 12.5 hours with unprecedented spatial and temporal resolution.
Does the presence of three or more female directors associate with corporate recognition?
Authors: Neuberger Madeline N. , Bernardi Richard A. , Bosco Susan M. , Landry Erynne E. 
Published: October 2022

Purpose
The purpose of this study is to extend Landry et al.’s (2016) work and examines the possible association between corporations having three or more female directors and these companies being features on corporate recognition lists.

Design/methodology/approach
This study examines a sample of 335 corporations ranked as Fortune 500 corporations in the period 2013–2019. The authors test for the association between the percent of corporations that had three or more female directors and the percent of these corporations on external recognition lists.

Findings
The data indicate that the percent of corporations with three or more female directors more than doubled between 2013 and 2019; this change was accompanied by an increase in the percent of presence of these companies in corporate recognition lists. The percent of corporations that had three or more female directors was significantly associated with the percent of these corporations on external recognition lists.

Research limitations/implications
The first is the sample selection process; this study used only publicly traded corporations that were included in the Fortune 500 between 2013 through 2019. The second limitation is that this study did not include data on board members considered minorities.

Practical implications
The findings imply that there is a strong link between gender diversity on boards and being featured on corporate recognition lists, which means that firms who care about corporate social responsibility-related works, and more instrumentally, care about being on such lists should reconsider the gender balance on their boards.

Originality/value
This study extends this work for a time period in which the number of corporations with three or more female directors has significantly increased.
Two-step flash sintering of (Mg1/3Ta2/3)0.01Ti0.99O2 giant dielectric ceramics
Authors: Wang Zhentao , Peng Pai , Zhong Sujuan , Cheng Yafang , Xu Dong 
Published: October 2022

Purpose
The purpose of this paper on the one hand is to reduce the sintering temperature, shorten the sintering time and improve the electrical properties of the sample through the two-step flash sintering method and on the other hand is to study the effect of electric field on the phase structure, microstructure and electrical properties of the flash sintering sample.

Design/methodology/approach
In this paper, (Mg1/3Ta2/3)0.01Ti0.99O2 giant dielectric ceramics were prepared by conventional sintering and two-step flash sintering, respectively. Further, the effect of electric field (600–750 V/cm) on the electrical properties of (Mg1/3Ta2/3)0.01Ti0.99O2 giant dielectric ceramics was studied.

Findings
The results show that compared with the conventional sintering, the sintering temperature of the two-step flash sintering can be reduced by 200°C and the sintering time can be shortened by 12 times. All sintered samples were single rutile TiO2 structure. Compared with conventional sintering, two-step flash sintering samples have finer grain size. The two-step flash sintered sample has similar dielectric properties to the conventional sintered sample. The dielectric constant of flash sintered samples decreases with the increase of electric field. When the electric field is 700 V/cm, the ceramic sample has the optimal dielectric properties, where the dielectric constant is approximately 5.5 × 103 and the dielectric loss is about 0.18 at 1 kHz. Impedance spectroscopy analysis shows that the excellent dielectric properties are attributed to the internal barrier layer capacitance model.

Originality/value
This paper not only provides a new method for the preparation of co-doped TiO2 giant dielectric ceramics but also has great potential in greatly improving efficiency and saving energy.
Demonstration of bacterium‐free very rapid reverse genetics system using mumps virus
Authors: Bae Chaewon , Katoh Hiroshi , Wakata Aika , Sakata Masafumi , Kato Fumihiro , Takeda Makoto 
Published: October 2022

AbstractThe reverse genetics system is a very powerful tool for analyzing the molecular mechanisms of viral propagation and pathogenesis. However, full‐length genome plasmid construction is highly time‐consuming and laborious, and undesired mutations may be introduced by Escherichia coli. This study shows a very rapid E. coli‐free method of full‐genome construction using the mumps virus as an example. This method was able to reduce dramatically the time for full‐genome construction, which was used very efficiently for virus rescue, from several days or more to ~2 days, with a similar accuracy and yield to the conventional method using E. coli/plasmid.
Smoking enhances the expression of angiotensin‐converting enzyme 2 involved in the efficiency of severe acute respiratory syndrome coronavirus 2 infection
Authors: Suzuki Rigel , Ono Yuki , Noshita Koji , Kim Kwang Su , Ito Hayato , Morioka Yuhei , Tamura Tomokazu , Okuzaki Daisuke , Tagawa Tetsuzo , Takenaka Tomoyoshi , Yoshizumi Tomoharu , Shimamura Teppei , Iwami Shingo , Fukuhara Takasuke 
Published: October 2022

AbstractSmoking is one of the risk factors most closely related to the severity of coronavirus disease 2019 (COVID‐19). However, the relationship between smoking history and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infectivity is unknown. In this study, we evaluated the ACE2 expression level in the lungs of current smokers, ex‐smokers, and nonsmokers. The ACE2 expression level of ex‐smokers who smoked cigarettes until recently (cessation period shorter than 6 months) was higher than that of nonsmokers and ex‐smokers with a long history of nonsmoking (cessation period longer than 6 months). We also showed that the efficiency of SARS‐CoV‐2 infection was enhanced in a manner dependent on the angiotensin‐converting enzyme 2 (ACE2) expression level. Using RNA‐seq analysis on the lungs of smokers, we identified that the expression of inflammatory signaling genes was correlated with ACE2 expression. Notably, with increasing duration of smoking cessation among ex‐smokers, not only ACE2 expression level but also the expression levels of inflammatory signaling genes decreased. These results indicated that smoking enhances the expression levels of ACE2 and inflammatory signaling genes. Our data suggest that the efficiency of SARS‐CoV‐2 infection is enhanced by smoking‐mediated upregulation of ACE2 expression level.
Assessing the value of monitoring to biological inference and expected management performance for a European goose population
Authors: Johnson Fred A. , Madsen Jesper , Clausen Kevin K. , Frederiksen Morten , Jensen Gitte H. 
Published: October 2022

AbstractInformed conservation and management of wildlife require sufficient monitoring to understand population dynamics and to direct conservation actions. Because resources available for monitoring are limited, conservation practitioners must strive to make monitoring as cost‐effective as possible.Our focus was on assessing the value of monitoring to the adaptive harvest management (AHM) programme for pink‐footed geeseAnser brachyrhynchus. We conducted a retrospective analysis to assess the costs and benefits of a capture–mark–resight (CMR) programme, a productivity survey and biannual population censuses. Using all available data, we fit an integrated population model (IPM) and assumed that inference derived from it represented the benchmark against which reduced monitoring was to be judged. We then fit IPMs to reduced sets of monitoring data and compared their estimates of demographic parameters and expected management performance against the benchmark IPM.Costs and the precision and accuracy of key demographic parameters decreased with the elimination of monitoring data. Eliminating the CMR programme, while maintaining other monitoring instruments, resulted in the greatest cost savings, usually with small effects on inferential reliability. Productivity surveys were also expensive and some reduction in survey effort may be warranted. The biannual censuses were inexpensive and generally increased inferential reliability.The expected performance of AHM strategies was surprisingly robust to a loss of monitoring data. We attribute this result to explicit consideration of parametric uncertainty in harvest‐strategy optimization and the fact that a broad range of population sizes is acceptable to stakeholders.Synthesis and applications. Our study suggests that existing or potential monitoring instruments for wildlife populations should be scrutinized as to their cost‐effectiveness for improving biological inference and management performance. Using Svalbard pink‐footed geese as a case study, we show that the loss of some existing monitoring instruments may not be as adverse as commonly assumed if data are jointly analysed in an IPM. Finally, regardless of the monitoring data available, we suggest that conservation strategies that explicitly account for uncertainty in demography are more likely to be successful than those that do not.
Endogenous timing, strategic tariff game and bilateral trade in vertical oligopoly
Authors: Chen Tai‐Liang , Kuang Ying 
Published: October 2022

AbstractThis paper builds an observable delay game in endogenous timing to study the possible occurrence of trade wars in a vertical, bilateral trade model. It examines the effects of production cost differences and order of moves on optimal tariffs, market equilibria, dumping margin and social welfare in both fixed timing and endogenous timing games. In a fixed timing game, it shows that price dumping in the intermediate good market arises from differences in country‐specific final good production costs. Different from Bernhofen (1995; Journal of International Economics), trade costs resulting from reciprocal tariffs in upstream markets can reverse the price dumping under certain conditions. In an endogenous timing game, this paper finds that the magnitude of cost differences significantly influences countries’ decisions on the order of moves in a strategic tariff‐making game. Both countries want to be the first movers under a small cost difference and consequently reach a simultaneous equilibrium result. This demonstrates that the second‐best equilibrium proceeds under certain conditions. Under a large cost difference, sequential policy‐making is the subgame perfect Nash equilibrium. If the cost difference is sufficiently large, both countries have an incentive to launch a trade war as a multiple equilibrium game.
The impact of topical NSAID treatment on selective laser trabeculoplasty efficacy
Authors: Dahlgren Tobias , Ayala Marcelo , Zetterberg Madeleine 
Published: October 2022

AbstractPurposeSelective laser trabeculoplasty (SLT) is a first‐line intervention for glaucoma, with the aim to reduce the intraocular pressure (IOP). Topical non‐steroidal anti‐inflammatory drugs (NSAIDs) are sometimes prescribed after SLT. However, it has been proposed that such treatment may either increase or reduce SLT efficacy. The purpose of this study was to investigate this further.MethodsThe study was a retrospective chart review, including 192 eyes of 192 patients, half of which received a course of NSAID eyedrops after SLT. Absolute and relative IOP reduction 3–12 weeks after SLT was compared. Furthermore, subgroup analyses, a multiple linear regression analysis, and a Kaplan–Meier survival analysis regarding time to treatment escalation were performed.ResultsThe mean absolute IOP reduction was 4.3 ± 3.4 mmHg in the NSAID group and 5.4 ± 4.1 mmHg in the control group (p = 0.049). Relative IOP reduction was 17.5% ± 13.0% and 21.8% ± 14.8% in the NSAID and control groups, respectively (p = 0.033). The same tendency of superior results in control eyes compared with NSAID eyes was seen in an extensive subgroup analysis. A multiple linear regression analysis confirmed NSAID treatment as a negative predictor of IOP reduction after adjustment for covariates (p = 0.023). Survival analysis showed a longer median time to treatment escalation in the control group, though not statistically significant.ConclusionTopical NSAID treatment was not associated with an increased SLT efficacy. On the contrary, the present study is the first to demonstrate that SLT effectiveness may even be reduced by NSAIDs.
Real‐world experience among patients with relapsed/refractory mantle cell lymphoma after Bruton tyrosine kinase inhibitor failure in Europe: The SCHOLAR‐2 retrospective chart review study
Authors: Hess Georg , Dreyling Martin , Oberic Lucie , Gine Eva , Zinzani Pier Luigi , Linton Kim , Vilmar Adam , Jerkeman Mats , Chen Jenny M. H. , Ohler Anke , Stilgenbauer Stephan , Thieblemont Catherine , Lambert Jonathan , Zilioli Vittorio Ruggero , Sancho Juan‐Manuel , Jiménez‐Ubieto Ana , Fischer Luca , Eyre Toby A. , Keeping Sam , Park Julie E. , Wu James J. , Siddiqi Rubina , Reitan John , Wade Sally , Salles Gilles 
Published: October 2022

SummaryMantle cell lymphoma (MCL) after relapse is associated with poor prognosis. No standard of care exists and available evidence for treatments is limited, particularly in patients who fail Bruton tyrosine kinase inhibitor (BTKi) therapy. This multicentre retrospective chart review study, SCHOLAR‐2, addresses this knowledge gap and reports on data collected from 240 patients with relapsed/refractory MCL in Europe who were treated with BTKi‐based therapy between July 2012 and July 2018, and had experienced disease progression while on BTKi therapy or discontinued BTKi therapy due to intolerance. The median overall survival (OS) from initiation of first BTKi therapy was 14.6 months (95% confidence interval [CI] 11.6–20.0) in the overall cohort, 5.5 months (95% CI 3.9–8.2) in 91 patients without post‐BTKi therapy, and 23.8 months (95% CI 18.9–30.1) in 149 patients who received post‐BTKi therapy (excluding chimeric antigen receptor T‐cell treatment). In the latter group, patients received a median of one (range, one to seven) line of post‐BTKi therapy, with lenalidomide‐containing regimens and bendamustine plus rituximab being the most frequently administered; the median OS from initiation of first post‐BTKi therapy was 9.7 months (95% CI 6.3–12.7). These results provide a benchmark for survival in patients with R/R MCL receiving salvage therapy after BTKi failure.
Thulium fibre laser vs holmium: yttrium‐aluminium‐garnet laser lithotripsy for urolithiasis: meta‐analysis of clinical studies
Authors: Chua Michael E. , Bobrowski Adam , Ahmad Ihtisham , Kim Jin Kyu , Silangcruz Jan Michael , Rickard Mandy , Lorenzo Armando , Lee Jason Y. 
Published: October 2022

ObjectiveTo compare and assess the clinical outcomes between thulium fibre laser (TFL) and holmium: yttrium‐aluminium‐garnet (Ho:YAG) laser endoscopic lithotripsy of urolithiasis through a meta‐analysis of comparative clinical studies.MethodsA systematic literature search was performed in May 2022, grey literature search in July 2022. Comparative clinical studies were evaluated according to Cochrane recommendations. Assessed outcomes include the stone‐free rate (SFR), complication rate, operative time (OT), laser utilisation time (LUT), ablation rate (stone volume/laser time), ablation efficiency (energy use/stone volume), total energy usage, degree of retropulsion, and hospital stay. Risk ratios (RRs) and standardised mean differences (SMDs) were extrapolated. Subgroup analyses, heterogeneity, publication bias, and Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) assessment were performed. International Prospective Register of Systematic Reviews (PROSPERO) registration: CRD42022300788.ResultsA total of 15 studies with 1698 cases were included in this review. The outcome of SFR showed no significant between‐group difference (RR 1.09, 95% confidence interval [CI] 0.99–1.20). However, subgroup analysis of TFL vs Ho:YAG with no pulse modulation showed a SFR favouring TFL (RR 1.11, 95% CI 1.01–1.23). The composite postoperative complication rate was comparable between the two intervention groups (RR 0.97, 95% CI 0.66–1.43). OT, LUT and ablation rate were significantly better for TFL than Ho:YAG (SMD −1.19, 95% CI −1.85 to −0.52; SMD −1.67, 95% CI −2.62 to −0.72; SMD 0.59, 95% CI 0.15–1.03; respectively). The degree of retropulsion was significantly lower for TFL than Ho:YAG without pulse modulation (SMD −1.23, 95% CI −1.74 to −0.71). Ablation efficiency, total energy usage, and hospital stay were all comparable. Based on GRADE criteria, the evidence certainty was determined to be very low.ConclusionOverall, there was no between‐group difference for the SFR. However, compared to Ho:YAG with no pulse modulation, TFL rendered a better SFR. Shorter OT and LUT, a lesser degree of retropulsion, and a better ablation rate were noted in favour of the TFL. There was no overall between‐group difference for composite postoperative complication rate, ablation efficiency, total energy usage, and hospital stay. Currently, the available clinical evidence was assessed to be of very low certainty.
Do chimpanzees reason logically?
Authors: Engelmann Jan M. , Haux Lou M. , Völter Christoph , Schleihauf Hanna , Call Josep , Rakoczy Hannes , Herrmann Esther 
Published: October 2022

AbstractPsychologists disagree about the development of logical concepts such as or and not. While some theorists argue that infants reason logically, others maintain that logical inference is contingent on linguistic abilities and emerges around age 4. In this Registered Report, we conducted five experiments on logical reasoning in chimpanzees. Subjects (N = 16; 10 females; M = 24 years) participated in the same setup that has been administered to children: the two‐, three‐, and four‐cup‐task. Chimpanzees performed above chance in the two‐cup‐, but not in the three‐cup‐task. Furthermore, chimpanzees selected the logically correct option more often in the test than the control condition of the four‐cup‐task. We discuss possible interpretations of these findings and conclude that our results are most consistent with non‐deductive accounts.
When phylogenetics met biogeography: Willi Hennig, Lars Brundin and the roots of phylogenetic and cladistic biogeography
Authors: Morrone Juan J. 
Published: October 2022

AbstractWilli Hennig's (Beitr. Ent. 1960, 10, 15)Die Dipteren‐Fauna von Neuseeland als systematisches und tiergeographisches Problemapplied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer toa posteriorimethods of cladistic biogeography is erroneous and should be avoided.