bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nano‐Strainer: A workflow for the identification of single‐copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
Authors: Scheunert Agnes , Lautenschlager Ulrich , Ott Tankred , Oberprieler Christoph 
Published: July 2023

AbstractIn modern plant systematics, target enrichment enables simultaneous analysis of hundreds of genes. However, when dealing with reticulate or polyploidization histories, few markers may suffice, but often are required to be single‐copy, a condition that is not necessarily met with commercial capture kits. Also, large genome sizes can render target capture ineffective, so that amplicon sequencing would be preferable; however, knowledge about suitable loci is often missing. Here, we present a comprehensive workflow for the identification of putative single‐copy nuclear markers in a genus of interest, by mining a small dataset from target capture using a few representative taxa. The proposed pipeline assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre‐defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top‐scoring loci are considered putatively single‐ or low copy. The approach can be applied to any probe set. As it relies on long reads, the present contribution also provides template workflows for processing Nanopore‐based target capture data. Obtained markers are further tested and then entered into amplicon sequencing. For the detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, we also employ the long‐read assembly tool Canu. In diploid representatives of the young Compositae genus Leucanthemum, characterized by high levels of polyploidy, our approach resulted in successful amplification of 13 loci. Modifications to remove traces of paralogy were made in seven of these. A species tree from the markers correctly reproduced main relationships in the genus, however, at low resolution. The presented workflow has the potential to valuably support phylogenetic research, for example in polyploid plant groups.
Habitat fragmentation drives divergent survival strategies of a cold‐water fish in a warm landscape
Authors: Hahlbeck Nick , Anlauf‐Dunn Kara J. , Piotrowski Stanley J. , Ortega Jordan D. , Tinniswood William R. , Eliason Erika J. , O'Malley Kathleen G. , Sloat Matthew R. , Wyatt Matthew A. , Hereford Mark E. , Ramirez Ben S. , Armstrong Jonathan B. 
Published: July 2023

AbstractClimate change is a global phenomenon, but natural selection occurs within landscapes. Many global analyses predict how climate change will shape behavior and physiology, but few incorporate information from the landscape scales at which animals actually respond to selective pressure. We compared cold‐water fish (redband trout Oncorhynchus mykiss newberrii) from neighboring habitats in a naturally warm, recently fragmented basin to understand how different responses to warming may arise from landscape constraints. Trout in warm, hydrologically connected Upper Klamath Lake fled summer temperatures and sought refuge in cool tributaries, while trout in an equally warm but fragmented reach of the Klamath River endured summer conditions. Trout in the river were more physiologically tolerant of high temperatures than trout in the lake across multiple metrics, including capacity for aerobic activity, recovery from exertion, and loss of equilibrium. Two independent metrics of energetic condition indicated that the behavioral strategy of trout in the lake came at a substantial energetic cost, while the physiological strategy of trout in the river was able to mitigate most energetic consequences of high temperatures. No clear genetic basis for increased tolerance was found in trout from the river, which may suggest tolerance was derived from plasticity, although our analysis could not rule out genetic adaptation. Our results show that landscape processes such as fragmentation can cause different climate survival strategies to emerge in neighboring populations. Connecting the mechanisms that favor similar survival strategies among related organisms at broad scales with mechanisms that drive landscape‐scale variability within taxa should be a major goal for future predictions of biological responses to climate change.
Quantitative Assessment of Ribociclib Exposure–Response Relationship to Justify Dose Regimen in Patients with Advanced Breast Cancer
Authors: Ji Yan , Darstein Christelle , Yang Shu , Quinlan Michelle , Chakravartty Arunava , Zarate Juan Pablo , Chakraborty Abhijit , Ho Yu‐Yun 
Published: July 2023

AbstractRibociclib in combination with endocrine therapy (ET) is a globally approved treatment option for patients with hormone receptor‐positive (HR+)/human epidermal growth factor receptor 2‐negative (HER2−) advanced breast cancer (ABC) and has demonstrated significantly improved overall survival (OS) in 3 phase 3 clinical trials. To justify the dose regimen and dose modification scheme for patients with ABC, the pharmacokinetic (PK), safety, and efficacy data of ribociclib were analyzed. The data of several phase 1‐3 clinical studies were pooled and analyzed to characterize the relationship between exposure (dose or PK) and efficacy (progression‐free survival (PFS), time to response, and OS) or safety (neutropenia and QT interval prolongation). The exposure–efficacy analysis showed no apparent relationship between ribociclib exposure and efficacy (PFS and OS), and efficacy analysis by dose reduction showed that patients with ABC continued to benefit from the treatment following dose reduction, supporting the starting dose of 600 mg as well as dose reductions to 400 and 200 mg. The exposure–safety analysis showed that neutropenia and QT prolongation are related to ribociclib exposure that can be effectively managed by individualized dose modification (dose reduction/interruption). Collective evidence from the exposure–response analyses for efficacy and safety support the use of ribociclib in combination with ET partners at the starting dose of 600 mg, and also the effectiveness of individualized dose reductions in managing safety, while maintaining efficacy, in patients with HR+/HER2− ABC. This analysis illustrates the utility of quantitative assessment in justifying dose selection and dose modification for oncology medicines.
Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency
Authors: Bisello Giovanni , Ribeiro Rui P. , Perduca Massimiliano , Belviso Benny Danilo , Polverino de' Laureto Patrizia , Giorgetti Alejandro , Caliandro Rocco , Bertoldi Mariarita 
Published: July 2023

AbstractHuman aromatic amino acid decarboxylase (AADC) is a pyridoxal 5′‐phosphate‐dependent enzyme responsible for the biosynthesis of dopamine and serotonin, essential neurotransmitters involved in motor and cognitive abilities. Mutations in its gene lead to AADC deficiency, a monogenic rare neurometabolic childhood parkinsonism characterized by severe motor and neurodevelopmental symptoms. Here, for the first time, we solved the crystal structure of human holoAADC in the internal aldimine (1.9 Å) and in the external aldimine (2.4 Å) of the substrate analog L‐Dopa methylester. In this intermediate, the highly flexible AADC catalytic loop (CL) is captured in a closed state contacting all protein domains. In addition, each active site, composed by residues of both subunits, is connected to the other through weak interactions and a central cavity. By combining crystallographic analyses with all‐atom and coarse‐grained molecular dynamics simulations, SAXS investigations and limited proteolysis experiments, we realized that the functionally obligate homodimeric AADC enzyme in solution is an elongated, asymmetric molecule, where the fluctuations of the CL are coupled to flexibility at the edge between the N‐terminal and C‐terminal domains. The structural integrity of this peripheral protein region is essential to catalysis, as assessed by both artificial and 37 AADC deficiency pathogenic variants leading to the interpretation that structural dynamics in protein regions far from the active site is essential for CL flexibility and the acquirement of a correct catalytically competent structure. This could represent the molecular basis for pathogenicity prediction in AADC deficiency.
Momentum‐innovation recursive least squares identification algorithm for a servo turntable system based on the output error model
Authors: Liu Zhiwen , Cheng Tianji , Han Chongyang , Liu Enhai , Wang Ranjun 
Published: July 2023

AbstractIn this article, the parameter identification problem of the output error model is investigated under the application requirement of online parameter identification of a two‐degree‐of‐freedom servo turntable system. To eliminate the influence of colored noise in the observed output signal of the output error model on the algorithm identification accuracy, the momentum factor is introduced into the innovation term of the recursive least squares algorithm, and the momentum‐innovation recursive least squares (MI‐RLS) algorithm is proposed. Further, to improve the convergence speed and identification accuracy of the algorithm while avoiding increasing the algorithm complexity significantly, a reframed multi‐innovation strategy is introduced, and a momentum reframed multi‐innovation least squares (MR‐MILS) algorithm is developed. After analyzing the complexity of the proposed algorithms, the convergence performances of the two algorithms are verified using the theory of martingale convergence, and the results show that the reframed multi‐innovation strategy can accelerate the convergence speed of the MR‐MILS algorithm. The effectiveness of the proposed identification approach is demonstrated via simulation results.
Gesundheit wohnungsloser Menschen während der COVID-19-Pandemie
Authors: van Rüth Victoria , Hajek André , Heinrich Fabian , Ondruschka Benjamin , Püschel Klaus , Bertram Franziska 
Published: July 2023

ZusammenfassungDie Lebenssituation und die Gesundheit wohnungsloser Menschen unterscheiden sich in vielerlei Hinsicht von denen der Allgemeinbevölkerung. Die Vermutung liegt nahe, dass es sich bei wohnungslosen Menschen um eine besonders vulnerable Personengruppe während der Coronavirus-Disease-2019(COVID-19)-Pandemie handelt. In dieser narrativen Übersichtsarbeit soll die aktuelle Literatur zur Gesundheit und Versorgung von wohnungslosen Menschen während der COVID-19-Pandemie zusammengefasst werden. Recherchiert wurde zwischen Dezember 2022 und Februar 2023. Neben der aktuellen nationalen und internationalen Literatur sollen insbesondere die Ergebnisse des „National survey on psychiatric and somatic health of homeless individuals“ (NAPSHI-Studie) synoptisch dargestellt werden; diese untersucht psychische und somatische Erkrankungen sowie die Versorgung wohnungsloser Menschen in Deutschland.Wohnungslose Menschen sind häufig psychisch und somatisch erkrankt und haben einen eingeschränkten Zugang zum medizinischen Regelsystem. Versorgungseinrichtungen mit Gruppenräumen und Schlafsälen stellen ein Risiko für ein Ausbruchsgeschehen in der COVID-19-Pandemie dar. Wie vermutet, zeigten sich im Verlauf der Pandemie bei wohnungslosen Menschen häufiger als in der Allgemeinbevölkerung Hinweise für Severe Acute Respiratory Syndrome Coronavirus Type 2(SARS-CoV‑2)-Infektionen, viele davon schienen allerdings asymptomatisch zu verlaufen. Eine hohe Rate an unwissentlich infizierten wohnungslosen Menschen könnte zur Verbreitung der Viruserkrankung beigetragen haben. Trotzdem war ein unkontrolliertes COVID-19-Ausbruchsgeschehen, vor dem einige Wissenschaftler:innen zu Beginn der Pandemie warnten, nicht zu beobachten.
Descriptive Characterization of High-Frequency Distortion Product Otoacoustic Emission Source Components in Children
Authors: Dreisbach Laura , Konrad-Martin Dawn , Gagner Christine , Reavis Kelly M. , Jacobs Peter G. 
Published: July 2023

Purpose:

Distortion product otoacoustic emissions (DPOAEs) provide an objective assessment of cochlear function and are used for serial ototoxicity monitoring in pediatric cancer patients. DPOAEs are modeled as having distortion (near
f
2
) and reflection (near 2
f
1
-
f
2
) component sources, and developmental changes are observed in these components' relative strengths in infants compared with adults. However, little is known about source component strengths in childhood or at extended high frequencies (EHFs; > 8 kHz). Thus, the purpose of this study was to describe the effects of age and stimulus frequency on DPOAE components in children.

Method:

DPOAEs were collected with varied frequency ratios (
f
2
/
f
1
= 1.1–1.25) for a wide range of frequencies (2–16 kHz) in 39 younger (3–6 years) and 41 older (10–12 years) children with constant levels (L
1
/L
2
) of 65/50 dB SPL. A depth-compensated simulator sound pressure level method of calibration was employed. A time waveform representation of the results across various ratios was created to estimate peak pressures and latencies of each DPOAE component.

Results:
Estimated peak pressures of DPOAE components revealed the greatest differences in DPOAE sources between children occurring at the highest frequencies tested, where the peak pressure of both components was largest for younger compared with older children. Latency differences between the children were only noted at higher frequencies for the distortion component.

Conclusions:
These results suggest that DPOAE levels decrease with age and reflection emissions are vulnerable to cochlear change. This work guides optimization of protocols for pediatric ototoxicity monitoring, whereby including EHF otoacoustic emissions is clearly warranted and choosing to isolate DPOAE sources may prove beneficial.

Supplemental Material:

https://doi.org/10.23641/asha.23669214
Ventilation Mechanics
Authors: Farré Ramon , Navajas Daniel 
Published: July 2023

AbstractA fundamental task of the respiratory system is to operate as a mechanical gas pump ensuring that fresh air gets in close contact with the blood circulating through the lung capillaries to achieve O2 and CO2 exchange. To ventilate the lungs, the respiratory muscles provide the pressure required to overcome the viscoelastic mechanical load of the respiratory system. From a mechanical viewpoint, the most relevant respiratory system properties are the resistance of the airways (R
aw), and the compliance of the lung tissue (C
L) and chest wall (C
CW). Both airflow and lung volume changes in spontaneous breathing and mechanical ventilation are determined by applying the fundamental mechanical laws to the relationships between the pressures inside the respiratory system (at the airway opening, alveolar, pleural, and muscular) and R
aw, C
L, and C
CW. These relationships also are the basis of the different methods available to measure respiratory mechanics during spontaneous and artificial ventilation. Whereas a simple mechanical model (R
aw, C
L, and C
CW) describes the basic understanding of ventilation mechanics, more complex concepts (nonlinearity, inhomogeneous ventilation, or viscoelasticity) should be employed to better describe and measure ventilation mechanics in patients.
Ethical considerations regarding penis transplantation surgery in transgender men—an empirical ethics study
Authors: de Haseth Kristin B , Gehrels Anne M , Widdershoven Guy , Bouman Mark-Bram , van de Grift Tim C 
Published: July 2023

Abstract

Background
The ongoing quest to surgically create the (nearly) ideal neophallus in transgender men has led to the continuous development of transgender medicine and the proposed introduction of penis transplantation. However, both technical and ethical issues arise when developing this treatment.

Aim
We sought to extract ethical considerations among different stakeholder groups regarding penile transplantation surgery in transgender men and to define preliminary clinical recommendations.

Methods
Three semistructured focus groups, consisting of different stakeholders, were organized to participate in discussions of ethical considerations retrieved from the ethics literature of transplantation and transgender medicine. Analysis of the results was performed according to empirical ethics.

Outcomes
Study outcomes were the identification of qualitative themes describing ethical considerations pertaining to penile transplantation in transgender men.

Results
Nineteen people participated in this qualitative study. The main domains that emerged included arguments in favor of and arguments against penile transplantation. Although the participants expressed positive attitudes toward developing this care, with acknowledgement of the current limitations stakeholders of all groups were reluctant to endorse the introduction of penile transplantation for transgender men at this point.

Clinical Implications
Under the present circumstances, all groups expressed both a wide variety of ethical considerations as well as a tendency to prefer developing alternative treatment options or improving the results of currently available treatments in relation to penile transplantation for transgender men.

Strengths and Limitations
This study was the first (empirical) study to focus on this topic and included a diversity of stakeholder perspectives. Limitations included the hypothetical nature of the discussion as well as the clinical setting in which the topic has been studied.

Conclusion
Introducing penile transplantation for transgender men, under the current circumstances, comes with a wide range of ethical considerations, which deal with personal identity, autonomy, medical risks, risk for transgender support and donor willingness, and issues regarding equality. Despite the present hesitancy to use penile transplantation, should the technical side of this treatment option develop, further research in the ethical field of penile transplantation for transgender men is recommended.
Watch-and-wait approach for inactive echinococcal cysts: scoping review update since the issue of the WHO-IWGE Expert Consensus and current perspectives
Authors: Brunetti Enrico , Tamarozzi Francesca 
Published: July 2023

Purpose of review
This work aims to provide an update of knowledge on the evolution of inactive cystic echinococcosis (CE) cysts (CE4-CE5) managed by ‘watch-and-wait’, by means of a scoping review of the literature published after the publication of the WHO-IWGE (Informal Working Group on Echinococcosis) Expert Consensus document in 2010.

Recent findings
A total of 31 articles were included. Population ultrasound-based studies showed that spontaneously inactivated CE cysts represent 50.2% (95% confidence interval 38.7–61.8) of all detected untreated CE cysts, and that the prevalence of CE4-CE5 cysts tends to increase with age. Four longitudinal population-based studies showed that CE cysts naturally tend to evolve towards inactivation and that spontaneously inactivated cysts reactivate in a minority of cases. This was confirmed by four hospital-based studies, showing that spontaneously inactivated cysts reactivate rarely, while rate of reactivation is higher if inactivity was obtained posttreatment. It was not possible to drive conclusions on any difference in the clinical course of infection in immunocompromised or pregnant patients.

Summary
CE cysts tend to evolve spontaneously to inactivation over time. The published literature supports the safety of the watch-and-wait approach for inactive cysts, sparing treatment to a substantial proportion of asymptomatic patients. A regular follow-up with ultrasound of all inactive cysts is required to detect reactivations.
Neurodevelopmental outcomes in congenital and perinatal infections
Authors: Fortin Olivier , Mulkey Sarah B. 
Published: July 2023

Purpose of review
Congenital infections are a major cause of childhood multidomain neurodevelopmental disabilities. They contribute to a range of structural brain abnormalities that can cause severe neurodevelopmental impairment, cerebral palsy, epilepsy, and neurosensory impairments. New congenital infections and global viral pandemics have emerged, with some affecting the developing brain and causing neurodevelopmental concerns. This review aims to provide current understanding of fetal infections and their impact on neurodevelopment.

Recent findings
There are a growing list of congenital infections causing neurodevelopmental issues, including cytomegalovirus, Zika virus, syphilis, rubella, lymphocytic choriomeningitis virus, and toxoplasmosis. Fetal exposure to maternal SARS-CoV-2 may also pose risk to the developing brain and impact neurodevelopmental outcomes, although studies have conflicting results. As Zika virus was a recently identified congenital infection, there are several new reports on child neurodevelopment in the Caribbean and Central and South America. For many congenital infections, children with in-utero exposure, even if asymptomatic at birth, may have neurodevelopmental concerns manifest over time.

Summary
Congenital infections should be considered in the differential diagnosis of a child with neurodevelopmental impairments. Detailed pregnancy history, exposure risk, and testing should guide diagnosis and multidisciplinary evaluation. Children with congenital infections should have long-term follow-up to assess for neurodevelopmental delays and other neurosensory impairments. Children with confirmed delays or high-risk should be referred for rehabilitation therapies.
Selective attention to audiovisual speech routes activity through recurrent feedback-feedforward loops between different nodes of the speech network
Authors: Wikman Patrik , Salmela Viljami , Sjöblom Eetu , Leminen Miika , Laine Matti , Alho Kimmo 
Published: July 2023

AbstractSelective attention related top-down modulation plays a significant role in separating relevant speech from irrelevant background speech when vocal attributes separating concurrent speakers are small and continuously evolving. Electrophysiological studies have shown that such top-down modulation enhances neural tracking of attended speech. Yet, the specific cortical regions involved remain unclear due to the limited spatial resolution of most electrophysiological techniques. To overcome such limitations, we collected both EEG (high temporal resolution) and fMRI (high spatial resolution), while human participants selectively attended to speakers in audiovisual scenes containing overlapping cocktail party speech. To utilize the advantages of the respective techniques, we analysed neural tracking of speech using the EEG data and performed representational dissimilarity-based EEG-fMRI fusion. We observed that attention enhanced neural tracking and modulated EEG correlates throughout the latencies studied. Further, attention related enhancement of neural tracking fluctuated in predictable temporal profiles. We discuss how such temporal dynamics could arise from a combination of interactions between attention and prediction as well as plastic properties of the auditory cortex. EEG-fMRI fusion revealed attention related iterative feedforward-feedback loops between hierarchically organised nodes of the ventral auditory object related processing stream. Our findings support models where attention facilitates dynamic neural changes in the auditory cortex, ultimately aiding discrimination of relevant sounds from irrelevant ones while conserving neural resources.