bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of the Close Collaboration With Parents Intervention on the Quality of Family-Centered Care in NICUs
Authors: Toivonen Mirka , Lehtonen Liisa , Ahlqvist-Björkroth Sari , Axelin Anna 
Published: October 2021

Background:
Systematic training for the neonatal staff to support parents' active involvement is lacking. There is little information about the effectiveness of educational interventions.

Purpose:
To evaluate the effects of an educational intervention to neonatal staff on the quality of family-centered care from the perspectives of parents and nurses.

Methods:
A quasi-experimental before and after study was carried out in 5 Finnish neonatal units in 2014-2018. Data were collected using the DigiFCC-tools with a 7-point Likert scale. Thirty-one fathers and 53 mothers were recruited before the intervention and 21 fathers and 61 mothers after the intervention. They answered 1 question every evening until their infants' discharge. Each nurse answered 1 corresponding question after every shift, during the same period before and after the intervention. Before the intervention 3239 responses and after the intervention 3092 responses were received from nurses.

Results:
The fathers' total score and the score indicating “Shared decision making” were higher after the intervention than before the intervention. The mothers' total score did not differ between the 2 time periods. The nurses' total score was higher after the intervention than before the intervention. Of the individual items, higher scores were found for “Active listening,” “Parents' trust in the nurse,” and “Emotional support.”

Implications for Practice:
Developing the staff's negotiating and active listening skills facilitates better support for parents during infants' intensive care.

Implications for Research:
Family-centered care interventions such as Close Collaboration with Parents should be studied in randomized controlled trials, also including child outcomes.
Mesenteric Excision and Exclusion for Ileocolic Crohn’s Disease: Feasibility and Safety of an Innovative, Combined Surgical Approach With Extended Mesenteric Excision and Kono-S Anastomosis
Authors: Holubar Stefan D. , Gunter Rebecca L. , Click Benjamin H. , Achkar Jean-Paul , Lightner Amy L. , Lipman Jeremy M. , Hull Tracy L. , Regueiro Miguel , Rieder Florian , Steele Scott R. 
Published: October 2021

INTRODUCTION:
Ileocolic resection for Crohn’s disease traditionally does not include a high ligation of the ileocolic pedicle, and most commonly is performed with a stapled side-to-side ileocolic anastomosis. The mesentery has recently been implicated in the pathophysiology of Crohn’s disease. Two techniques have been developed and are associated with reduced postoperative recurrence: the Kono-S anastomosis that excludes diseased mesentery and extended mesenteric excision that resects diseased mesentery. We aimed to assess the technical feasibility and safety of a novel combination of techniques: mesenteric excision and exclusion.

TECHNIQUES:
This initial report is a single-center descriptive study of consecutive adults who underwent mesenteric excision and exclusion for primary or recurrent ileocolic Crohn’s disease from September 2020 to June 2021. Medication exposure and endoscopic balloon dilation before surgery were recorded. Phenotype was classified using the Montreal Classification. Thirty-day outcomes were reported. A video of the mesenteric excision and exclusion including the Kono-S anastomosis is presented.

RESULTS:
Twenty-two patients with ileocolic Crohn’s disease underwent mesenteric excision and exclusion: 100% had strictures, 59% had fistulas, 81% were on biologics, and 27% had previous ileocolic resection(s). Seventy-two percent underwent laparoscopic procedures, a mesenteric defect was closed in 86%, omental flaps were fashioned in 77%, and 3 patients were diverted. Median operative time was 175 minutes. Median postoperative stay was 4 days. At 30 days, there were 2 readmissions for reintervention: 1 seton placement and 1 percutaneous drainage of a sterile collection. There were no cases of intra-abdominal sepsis or anastomotic leak.

CONCLUSIONS:
Mesenteric excision and exclusion represents an innovative, progressive, and promising approach that appears to be highly feasible and safe. Further study is warranted to determine if mesenteric excision and exclusion is associated with reduced postoperative recurrence of ileocolic Crohn’s disease.
Biomechanical comparisons of different diagonal screw designs in a novel embedded calcaneal slide plate
Authors: Wang Shun-Ping , Lai Wei-Yi , Lin Yi-Yin , Lin Tzu-Wei , Tsai Ming-Tzu , Yang Yi-Ping , Hsu Cheng-En , Chen Chao-Ping , Lee Cheng-Hung , Su Kuo-Chih 
Published: October 2021

Background:
Medial displacement calcaneal osteotomy (MDCO) is frequently used for the surgical correction of flatfoot. This study aims to investigate the biomechanical effect of the different diagonal screw design on a novel-designed embedded calcaneal plate for MDCO using finite element analysis (FEA), mechanical test and digital image correlation (DIC) measurement.

Methods:
Four groups according to the varied implanted plate were set as control group (Group 1), non-diagonal screw (Group 2), one-diagonal screw (Group 3), and two-diagonal screws groups (Group 4). For FEA, A 450 N load was applied to on the anterior process of the calcaneus from top to bottom. Observational indices included the stress on the cortical and cancellous bone of the calcaneus surrounding the implant, the plate itself as well as screws, and the displacement of the overall structure. In addition, this study also used in vitro biomechanics test to investigate the stiffness of the structure after implantation, and used DIC to observe the displacement of the calcaneus structure after external force.

Results:
Under a simulated load in FEA, there are significant overall instability and high stress concentration on the calcaneal surrounding host bone and the plate/screws system, respectively, in group 2 compared with other groups. Regard to the mechanical testing with DIC system, significant increased rotation stability, maximum force and stiffness with the addition of diagonal screws. In comparison to Group 2, the increase of 112% and 157% in maximum force as well as 104% and 176% in stiffness were found in Group 3 and 4, respectively.

Conclusion:
For reducing stress concentration and enhancing overall stability, more than one-diagonal screw design is recommended and two-diagonal screws design will be superior. This study provided biomechanical references for further calcaneal implants design to prevent clinical failure after MDCO.
SARS-CoV-2 Infection Among People Living With HIV Compared With People Without HIV: Survey Results From the MACS-WIHS Combined Cohort Study
Authors: D'Souza Gypsyamber , Tong Weiqun , Gustafson Deborah , Alcaide Maria L. , Lahiri Cecile D. , Sharma Anjali , French Audrey L. , Palella Frank J. , Kempf Mirjam-Colette , Mimiaga Matthew J. , Ramirez Catalina , Kassaye Seble , Rinaldo Charles R. , Brown Todd T. , Tien Phyllis C. , Adimora Adaora A. 
Published: October 2021

Background:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) symptoms among people living with HIV (PLWH) are not well described.

Setting:
Longitudinal survey within the MACS/WIHS Combined Cohort Study (MWCCS) of PLWH compared with similar HIV-seronegative (SN) individuals.

Methods:
Telephone-administered survey of MWCCS participants at 13 clinical research sites across the United States addressing COVID-19 symptoms, SARS-CoV-2 testing, and pandemic impact on social distancing and antiretroviral therapy (ART) use. Primary data collection occurred during May (wave 1), June–July (wave 2), and August–September, 2020 (wave 3).

Results:
One-third of MWCCS participants were tested for SARS-CoV-2 infection; 10% was tested ≥2 times. Similar proportions of PLWH and SN participants were tested, but SARS-CoV-2 positivity was higher among PLWH than among SN individuals (9.4% vs 4.8%, P = 0.003). Odds of SARS-CoV-2 positivity remained higher among PLWH after adjusting for age, sex, race/ethnicity, and study site (adjusted odds ratio = 2.0, 95% confidence interval = 1.2 to 3.2). SARS-CoV-2 positivity was not associated with CD4 cell counts among PLWH. Among SARS-CoV-2 positive participants, 9% had no symptoms, 7% had 1–2 mild symptoms, and 84% had ≥3 symptoms. Most of the (98%) participants reported physical distancing during all survey waves; self-reported ART adherence among PLWH was not adversely affected during the pandemic compared with the previous year (similar adherence in 89% of participants, improved in 9% of participants, and decreased in 2% of participants).

Conclusions:
Despite similar SARS-CoV-2 testing and physical distancing profiles by HIV serostatus among MWCCS participants, PLWH who reported SARS-CoV-2 testing were more likely to have a positive test result. Additional studies are needed to determine whether and why PLWH are at increased risk of SARS-CoV-2 infection.
225Ac-Prostate-Specific Membrane Antigen Therapy for Castration-Resistant Prostate Cancer
Authors: Sanli Yasemin , Kuyumcu Serkan , Simsek Duygu Has , Büyükkaya Fikret , Civan Caner , Isik Emine Goknur , Ozkan Zeynep Gozde , Basaran Mert , Sanli Oner 
Published: October 2021

Purpose
Prostate-specific membrane antigen (PSMA)–targeted therapies are among the current promising treatments. We present our preliminary results on the use of 225Ac-PSMA therapy in patients with metastatic castration-resistant prostate cancer as a single center.

Methods
Twelve advanced stage metastatic castration-resistant prostate cancer patients who received 225Ac-PSMA therapy were recruited in this retrospective study. Patients were treated with 225Ac-PSMA therapy every 8 weeks, and prostate-specific antigen (PSA) response was analyzed. Meanwhile, overall survival (OS) and progression-free survival (PFS) were estimated. Hematological and nonhematological adverse effects were recorded before and at 8 weeks after the last treatment cycle.

Results
In total, 25 cycles of 225Ac-PSMA were administered to 12 patients. The pretreatment median PSA level was 129 ng/mL. After the first cycle of therapy, any PSA response was observed in 9 of 12 patients, whereas 6 of them had biochemical response of >50%. Four of 12 patients reached the best PSA response after the first treatment cycle, whereas 3 patients after the second and 2 patients after the third cycle. The median PFS and OS were 4 and 10 months, respectively. For patients with any PSA response after the first cycle, OS was found to be higher despite without any statistical significance (10 vs 4 months; P = 0.301) when compared with the nonresponsive group. No significant difference was encountered in terms of adverse effect in the pretreatment and posttreatment era.

Conclusions
Our preliminary results are encouraging, especially patients who had PSA response after the first cycle of 225Ac-PSMA therapy.
Carpenter Bee Thorax Vibration and Force Generation Inform Pollen Release Mechanisms During Floral Buzzing
Authors: Jankauski Mark , Casey Cailin , Heveran Chelsea , Busby M. Kathryn , Buchmann Stephen 
Published: October 2021

AbstractApproximately 10% of flowering plant species conceal their pollen within tube-like poricidal anthers. Bees extract pollen from poricidal anthers via floral buzzing, a behavior during which they apply cyclic forces by biting the anther and rapidly contracting their flight muscles. The success of pollen extraction during floral buzzing relies on the direction and magnitude of the forces applied by the bees, yet these forces and forcing directions have not been previously quantified. In this work, we developed an experiment to simultaneously measure the directional forces and thorax kinematics produced by carpenter bees (Xylocopa californica) during defensive buzzing, a behavior regulated by similar physiological mechanisms as floral buzzing. We found that the buzzing frequencies averaged about 130 Hz and were highly variable within individuals. Force amplitudes were on average 170 mN, but at times reached nearly 500 mN. These forces were 30 – 80 times greater than the weight of the bees tested. The two largest forces occurred within a plane formed by the bees’ flight muscles. Force amplitudes were moderately correlated with thorax displacement, velocity and acceleration amplitudes but only weakly correlated with buzzing frequency. Linear models developed through this work provide a mechanism to estimate forces produced during non-flight behaviors based on thorax kinematic measurements in carpenter bees. Based on the buzzing frequencies, individual bee’s capacity to vary buzz frequency and predominant forcing directions, we hypothesize that carpenter bees leverage vibration amplification to increase the deformation of poricidal anthers, and hence the amount of pollen ejected.
A Genetic Platform for Functionally Profiling Odorant Receptors Ex Vivo Using Olfactory Cilia
Authors: Omura Masayo , Takabatake Yukie , Lempert Eugene , Benjamin-Hong Sigi , D’Hulst Charlotte , Feinstein Paul 
Published: October 2021

AbstractThe molecular basis for odor perception in humans remains an enigma as odorant receptors (ORs) are notoriously difficult to study outside of their native environment. Efforts toward OR expression and functional profiling have been met with limited success due to poor efficiency of in vitro cell surface expression. Olfactory cilia are known to contain all components of the olfactory signal transduction machinery and can be placed into an ex vivo well-plate assay to rapidly measure robust, reproducible odor-specific responses. We now describe the isolation of cilia from mouse nose bioreactors for two human ORs, OR1A1 and OR5AN1, and reveal 10-100 fold more sensitivity compared to previously reported assays. A single animal can produce up to 4,000 384-well assay wells, and isolated olfactory cilia can be stored frozen and thus preserved. This pipeline offers a sensitive, highly scalable ex vivo odor screening platform that opens the door for decoding human olfaction.One Sentence Summaryolfactory-cilia based odor screening platform.
Different methods for niche and fitness differences computation offer contrasting explanations of species coexistence
Authors: Spaak Jurg W. , Ke Po-Ju , Letten Andrew D. , De Laender Frederik 
Published: October 2021

AbstractIn modern coexistence theory, species coexistence can either arise via stabilizing mechanisms that increase niche differences or equalizing mechanisms that reduce fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. Several methods for quantifying niche and fitness differences exist, but it remains unknown to what extent these methods agree on the reasons why species coexist. Here, we apply four common methods to quantify niche and fitness differences to one simulated and two empirical data sets. We ask if different methods result in different insights into what drives species coexistence. We find that different methods disagree on the effects of resource supply rates (simulated data), and of plant traits or phylogenetic distance (empirical data), on niche and fitness differences. More specifically, these methods often do not agree better than expected by chance. We argue for (1) a better understanding of what connects and sets apart different methods, and (2) the simultaneous application of multiple methods to enhance a more complete insight into why species coexist.
Beyond the reach of homology: successive computational filters find yeast pheromone genes
Authors: Srikant Sriram , Gaudet Rachelle , Murray Andrew W. 
Published: October 2021

AbstractThe mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are fewer than 100 amino acids long, contain a proteolytic processing motif upstream of the potential mature pheromone sequence, and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 fungal genomes, we identified strong candidate pheromone genes in 238 genomes, covering 13 clades that are separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
MotifBoost: k-mer based data-efficient immune repertoire classification method
Authors: Katayama Yotaro , Kobayashi Tetsuya J. 
Published: October 2021

ABSTRACTThe repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing. In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that the their performances are impaired catastrophically below critical sample sizes. To overcome this, we propose MotifBoost, which exploits the information of short motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of motifs as representation features of repertoires. Finally, by comparing predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.
Single-cell RNA-seq analysis reveals aberrant CSF1 expression in disease-causing synovial fibroblasts of pigmented villonodular synovitis
Authors: Tang Yiyong , Ma Mengjun , Mi Rujia , Liu Wenzhou , Hou Jingyi , Feng Yanjie , Zhang Meijun , Yu Menglei , Li Fangqi , Song Yihui , Lu Yixuan , Yan Yan , Yang Rui 
Published: October 2021

AbstractObjectivesAlthough the role of the CSF1/CSF1R axis in pigmented villonodular synovitis (PVNS) has been confirmed, the cells that express CSF1 and CSF1R and the underlying mechanism remain unclear. Single-cell RNA sequencing (scRNA-seq) of PVNS obtained through biopsies depicted the cellular diversity of PVNS, revealed specific CSF1/CSF1R-expressing cells and further identified novel gene expression that is associated with the development of PVNS.MethodsscRNA-seq was performed on tissues obtained from the 6 biopsies of 3 patients with PVNS. Flow cytometry, immunofluorescence and western blot validated the transcriptional results, while co-culture systems revealed the cross talk between fibroblasts and macrophages.Results8 subsets of fibroblasts and 5 subsets of macrophages were identified from the synovium of patients with PVNS and were found to be related to distinct signaling pathways. The cellular components of localized and diffuse PVNS are overall similar. Moreover, the synovium and nodule of PVNS share similar composition. The specific cells expressing CSF1/CSF1R were also identified. Other than that, unique CXCL12+CSF1+ fibroblasts were revealed to attract macrophages as disease-causing synovial fibroblasts, leading to the formation of masses in PVNS.ConclusionsPVNS consists of macrophages, fibroblasts, T cells, endothelial cells and mast cells. Among them, the CSF1-expressing fibroblasts appeared to be tumor-like cells that attract macrophages, subsequently forming tumor-like mass in PVNS. This paves the path for novel treatments of PVNS by targeting CXCL12+CSF1+ fibroblasts and the CXCL12-CXCR4 axis.
Genome graphs detect human polymorphisms in active epigenomic state during influenza infection
Authors: Groza Cristian , Chen Xun , Pacis Alain , Simon Marie-Michelle , Pramatarova Albena , Aracena Katherine A. , Pastinen Tomi , Barreiro Luis B. , Bourque Guillaume 
Published: October 2021

AbstractGenetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. Given the contributions of mobile elements to the evolution of primate innate immunity, we tested this in monocyte-derived macrophages obtained from 35 individuals before and afterInfluenzavirus infection. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression ofTRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
Loss of the GARP but not EARP protein complex drives Golgi sterol overload during dendrite remodeling
Authors: O’Brien Caitlin , Younger Susan H. , Jan Lily Yeh , Jan Yuh Nung 
Published: October 2021

AbstractMembrane trafficking is essential for sculpting neuronal morphology. The GARP and EARP complexes are conserved tethers that regulate vesicle trafficking in the secretory and endolysosomal pathways, respectively. Both complexes contain the Vps51, Vps52, and Vps53 proteins, and a complex-specific protein: Vps54 in GARP and Vps50 in EARP. In Drosophila, we find that both complexes are required for dendrite morphogenesis during developmental remodeling of multidendritic class IV da (c4da) neurons. Having found that sterol accumulates at the trans-Golgi network (TGN) in Vps54KO/KO neurons, we investigated genes that regulate sterols and related lipids at the TGN. Overexpression of oxysterol binding protein (Osbp) or knockdown of the PI4K four wheel drive (fwd) exacerbates the Vps54KO/KO phenotype, whereas eliminating one allele of Osbp rescues it, suggesting that excess sterol accumulation at the TGN is, in part, responsible for inhibiting dendrite regrowth. These findings distinguish the GARP and EARP complexes in neurodevelopment and implicate vesicle trafficking and lipid transfer pathways in dendrite morphogenesis.