bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-quality genome of the early diverging tychoplanktonic diatom Paralia guyana
Authors: Jian Jianbo , Du Feichao , Wang Binhu , Fang Xiaodong , Larsen Thomas Ostenfeld , Li Yuhang , Sonnenschein Eva C. 
Published: October 2024

AbstractThe diatom Paralia guyana is a tychoplanktonic microalgal species that represents one of the early diverging diatoms. P. guyana can thrive in both planktonic and benthic habitats, making a significant contribution to the occurrence of red tide events. Although a dozen diatom genomes have been sequenced, the identity of the early diverging diatoms remains elusive. The understanding of the evolutionary clades and mechanisms of ecological adaptation in P. guyana is limited by the absence of a high-quality genome assembly. In this study, the first high-quality genome assembly for the early diverging diatom P. guyana was established using PacBio single molecular sequencing. The assembled genome has a size of 558.85 Mb, making it the largest diatom genome on record, with a contig N50 size of 26.06 Mb. A total of 27,121 protein-coding genes were predicted in the P. guyana genome, of which 22,904 predicted genes (84.45%) were functionally annotated. This data and analysis provide innovative genomic resources for tychoplanktonic microalgal species and shed light on the evolutionary origins of diatoms.
Genome guided, organ-specific transcriptome assembly of the European flounder (P. flesus) from the Baltic Sea
Authors: Pomianowski Konrad , Kulczykowska Ewa , Burzyński Artur 
Published: October 2024

AbstractAlthough the European flounder is frequently used in research and has economic importance, there is still lack of comprehensive transcriptome data for this species. In the present research we show RNA-Seq data from ten selected organs of P. flesus female inhabiting brackish waters of the Gulf of Gdańsk (southern Baltic Sea). High throughput Next Generation Sequencing technology NovaSeq 6000 was used to generate 500 M sequencing reads. These were mapped against European flounder reference genome and reads extracted from the mapping were assembled producing 61k reliable contigs. Gene ontology (GO) terms were assigned to the majority of annotated contigs/unigenes based on the results of PFAM, PANTHER, UniProt and InterPro protein databases searches. BUSCOs statistics for eukaryota, metazoa, vertebrata and actinopterygii databases showed that the reported transcriptome represents a high level of completeness. The data set can be successfully used as a tool in design of experiments from various research fields including biology, aquaculture and toxicology.
Community composition and seasonal dynamics of microplastic biota in the Eastern Mediterranean Sea
Authors: Davidov Keren , Marsay Katherine S. , Itzahri Sheli , Rubin-Blum Maxim , Sobral Paula , Kranzler Chana F. , Oren Matan 
Published: October 2024

AbstractMarine plastic pollution poses a growing environmental threat, with microplastics accumulating in the global oceans. This study profiles the seasonal dynamics and taxonomic composition of the plastisphere, the microplastic ecosystem, in the Eastern Mediterranean Sea. Using long-read 16 S and 18 S metabarcoding, we analyzed offshore microplastic and whole seawater samples across each season over a two-year period. The analysis revealed a higher richness of prokaryotic communities on microplastics compared to seawater, which was predominantly composed of Proteobacteria and Bacteroidota and exhibited notable seasonal variability. Benthic eukaryotes were enriched on microplastics compared to the surrounding seawater. Diatoms (Bacillariophyceae), in particular, showed significant enrichment within the microplastic eukaryotic community with primarily pennate diatoms of Amphora, Navicula, and Nitzschia genera, whereas the seawater included mostly centric diatoms. Seasonal fluctuations were less pronounced in the microplastic communities than in seawater, highlighting the relative stability of this new human-made ecosystem. These findings underscore the unique ecological niche of microplastic-associated communities in marine environments.
Characterization of white blood cell ratios in South American camelids presented at a veterinary teaching hospital
Authors: Wagener Matthias Gerhard , Kornblum Max , Ganter Martin , Kiene Frederik 
Published: October 2024

AbstractWhite blood cell (WBC) ratios are used as diagnostic markers for various inflammatory or tumor diseases as well as stress in a broad range of species. The aim of this work was to provide data on five WBC ratios (neutrophil-to-lymphocyte ratio [NLR], band neutrophil-to-lymphocyte ratio [BLR], band neutrophil-to-neutrophil-to-lymphocyte ratio [BNLR], band neutrophil-to-neutrophil ratio [BNR] and lymphocyte-to-monocyte ratio [LMR]) in South American camelids (SAC) and characterize their association with demographic and important diagnostic parameters. Medical records of 307 SAC (275 alpacas, 32 llamas) that were presented at a veterinary teaching hospital were evaluated retrospectively. WBC ratios were calculated based on hematologic results of the initial blood samples. The influence of species, sex, age, body condition score, WBC count, and anemia on those ratios was investigated using descriptive statistics and generalized linear models. NLR, BLR and LMR were found to be significantly influenced by age and WBC count. Associations of individual WBC ratios with species, nutritional status or an anemic condition could be detected. NLR was 4.32; 2.31–7.81 (median; IQR), BLR 0.24; 0.07–0.87, BNLR 3.66 × 10–3; 1.17 × 10–3 − 14.20 × 10–3, BNR 0.06; 0.02–0.15 and LMR was 7; 3.54–14.67. Our data might serve as a basis for further studies on WBC ratios in SAC. The animals in this study showed a variety of underlying diseases. It should hence be noted that these values are orientation values and provide a representative overview of conditions in a clinic, but are not suitable as reference values for healthy animals.
The effect of trusting contexts in social dilemmas with collective and individual solutions
Authors: Lo Iacono Sergio , Sonmez Burak , Fairbrother Malcolm 
Published: October 2024

AbstractTrust encourages members of communities to cooperate and provide public goods. However, the literature has yet to fully investigate how high and low trusting communities deal with collective action dilemmas with multiple solutions. The latter may raise the risk of coordination failure. Using a preregistered interactive experiment (N participants/groups = 371/70), we investigated people’s decisions when they have three possible choices in confronting a collective action dilemma: investing in an individual solution, investing in a collective solution, and free-riding. We manipulated the incentives for trusting and trustworthy interactions among community members, and, consistent with our expectations, we found that people in high-trust contexts invest more in collective solutions, compared to people in low-trust contexts. In the latter case, participants opted more for individual solutions, using resources less efficiently. However, we found no difference in the prevalence of free-riding in high- compared to low-trust contexts.
Fe-N catalyst derived from and supported on Lycopodium clavatum sporopollenin exine capsules for the oxygen reduction reaction
Authors: Malik Waqas , Tafoya Jorge Pavel Victoria , Doszczeczko Szymon , Sobrido Ana Belen Jorge , Boa Andrew N. , Volpe Roberto 
Published: October 2024

AbstractA carbon-supported electrocatalyst, featuring carbon nanotubes anchored on 3D porous graphitic carbon, was developed with the aim to perform in the operating conditions of alkaline fuel cells and metal air batteries. The catalyst was developed via two steps: first powders of Sporopollenin exine capsules used as a bio-based carbon support were activated via CO2 gasification to obtain a high specific area and porosity, second the derived porous carbons were impregnated by an iron salt and a nitrogen source, to be carbonised in Nitrogen at high temperature. The prepared catalyst demonstrated an efficient oxygen reduction reaction activity showing a half-wave potential of ~ 0.775 V vs. Reversible hydrogen electrode, comparable with that of commercial 20 wt% Pt/C in alkaline conditions, a good stability after accelerated degradation testing, retaining ~ 86% of the initial limiting current density, and a higher diffusion limited current density (6.3 vs. 5.1 mA cm− 2) than the commercial counterpart. Overall, we show the suitability of Sporopollenin exine capsule as support for electrocatalysis and a promising methodology to develop sustainable catalysts for the oxygen reduction reaction.
Physical pressure resistance of gastrointestinal anastomotic site via plate of polyglycolic acid promoting fibrosis
Authors: Tanda Hideki , Shibutani Masatsune , Natsuki Seiji , Kasashima Hiroaki , Fukuoka Tatsunari , Maeda Kiyoshi 
Published: October 2024

AbstractAnastomotic-leakage incidence has been reported to be reduced on using polyglycolic acid (PGA) sheets as reinforcing materials; however, there is insufficient evidence regarding the reinforcement mechanism. Therefore, we investigated effects of PGA sheets on gastrointestinal anastomoses in rats. In the first approach, five rats underwent laparotomy; the PGA sheet was pasted onto the normal cecal wall. After five days, the cecum was removed and histologically evaluated. In the second approach, ten rats were randomly divided into two groups of five animals each. The rats underwent laparotomy; the cecal wall was sutured after a full-thickness incision. In the PGA group, a PGA sheet was used to cover the suture area. After 5 days, the cecum was removed, and the physical pressure resistance was evaluated. We confirmed the growth of a fibrous capsule measuring 855 (648–1048) µm outside the cecal serosa in the first approach. The median pressure resistance in the second approach was 57.0 (45.0–90.0) and 90.0 (82.5–94.5) mmHg in Control and PGA groups, respectively. The pressure resistance was significantly higher in the PGA group (p = 0.046). In summary, the PGA sheet may form a barrier of fibrosis on the intestinal wall and provide reinforcement to prevent anastomotic leakage.
Evolution shapes and conserves genomic signatures in viruses
Authors: Holmudden Martin , Gustafsson Joel , Bertrand Yann J. K. , Schliep Alexander , Norberg Peter 
Published: October 2024

AbstractThe genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome 1, such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse.Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors.
Global loss of promoter–enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis
Authors: Zhu Yizhou , Lee Hayan , White Shannon , Weimer Annika K. , Monte Emma , Horning Aaron , Nevins Stephanie A. , Esplin Edward D. , Paul Kristina , Krieger Gat , Shipony Zohar , Chiu Roxanne , Laquindanum Rozelle , Karathanos Thomas V. , Chua Melissa W. Y. , Mills Meredith , Ladabaum Uri , Longacre Teri , Shen Jeanne , Jaimovich Ariel , Lipson Doron , Kundaje Anshul , Greenleaf William J. , Curtis Christina , Ford James M. , Snyder Michael P. 
Published: October 2024

Abstract
Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss of genome-wide cis-regulatory connectivity at early malignancy stages, correlating with nonlinear gene regulation effects. Genes with high promoter–enhancer (P–E) connectivity in unaffected mucosa were not linked to elevated baseline expression but tended to be upregulated in advanced stages. Inhibiting highly connected promoters preferentially represses gene expression in CRC cells compared to normal colonic epithelial cells. Our results suggest a two-phase model whereby neoplastic transformation reduces P–E connectivity from a redundant state to a rate-limiting one for transcriptional levels, highlighting the intricate interplay between 3D genome architecture and gene regulation during early CRC progression.
M-MAT Meta: Treatment of Self-Awareness and Language for Individuals With Severe Wernicke's Aphasia
Authors: Wadams Amanda , Mozeiko Jennifer 
Published: October 2024

Purpose:
In this study, we evaluated the feasibility and efficacy of language plus goal management training program for individuals with aphasia. The intervention targeted expressive language, while concurrently integrating tasks designed to improve executive function and error awareness.

Method:

A single-subject repeated-measures design was utilized to determine whether a combined treatment (Multi-Modal Aphasia Therapy PLUS Goal Management Training [M-MAT Meta]) would be efficacious for individuals with aphasia. This article reports on two participants with severe Wernicke's aphasia, who comprised one of the four dyads of the study. Treatment was administered in a small group setting (
N
= 2) for 2 hr per day, 3 days per week for 4 weeks. Individual video feedback sessions were conducted once a week. Analysis of outcomes included visual inspection and calculation of Tau-U effect sizes of probed treatment data as well as statistical analysis of standardized language and executive function assessments.

Results:
Visual inspection indicated improvements in naming and discourse skills, which were maintained at the 1-month follow-up. Both participants' standardized scores indicated a significant decrease in aphasia severity, which was maintained 1 month posttreatment. Error awareness improved for one of the two participants, but this improvement was not maintained. Participants demonstrated increased inhibition of unwanted responses and took longer on the planning and problem-solving time required to complete the assessment, indicating a decrease in impulsivity.

Conclusion:
The results of this preliminary study suggest that M-MAT Meta may be an effective way to increase self-awareness and communication in individuals with severe Wernicke's aphasia.
Multidimensional Individualized Stuttering Therapy Outcomes At 24 Months Post Clinic: An Embodiment and Awareness Perspective
Authors: Sønsterud Hilda , Costain Kirsten , Ward David 
Published: October 2024

Purpose:
Multidimensional Individualized Stuttering Therapy (MIST) is based on proactive collaborative work and shared decision making between client and clinician with the goal of identifying individual case-appropriate procedures and therapy elements in a manner that is meaningful and context-sensitive for each person. MIST combines value- and awareness-based elements from acceptance and commitment therapy (ACT) with stuttering and speech modification interventions. In keeping with the principles of ACT, we locate mindfulness as part of an embodied practice facilitated through a collaboration between the person who stutters and the speech-language therapist.

Method:
The aim of this study was to see whether the positive results of MIST recorded at 12 months post-therapy remained stable at 24 months post-therapy and to consider the role of embodiment and awareness within MIST. Fifteen of 18 adults already enrolled in a treatment study (2015/FO12451) took part in a single-group repeated-measures design. They completed measures of stuttering severity, impact of stuttering, unhelpful thoughts and beliefs about stuttering, general anxiety symptoms, and fear of negative evaluation.

Results:
There was a significant reduction of stuttering severity and negative impact of stuttering from pre-therapy to 24 months post-therapy. Unhelpful thoughts and beliefs about stuttering, symptoms of general anxiety, and fear of negative evaluation were reduced at 12 months post-therapy, and these values remained stable at 24 months post-therapy.

Conclusions:
MIST was associated with positive outcomes at 24 months post-therapy, suggesting a possible connection between the person-centered approach and longer-term benefit. Findings are discussed within the context of mindfulness and embodied adjustment, and shared client–clinician decision making. The absence of a control group is a limiting factor regarding certainty of interpretation. Future research is therefore needed on collaborative and individualized approaches to stuttering therapy that include embodiment and awareness perspectives.
Anterior–Posterior View Acquisition During Videofluoroscopy: A Survey Study Exploring Influential Factors on Speech-Language Pathologists' Practice Patterns
Authors: Jones-Rastelli R. Brynn , Tang Xi , Harel Daphna , Molfenter Sonja M. 
Published: October 2024

Purpose:
This study explored factors influencing speech-language pathologists' (SLPs') decision making surrounding anterior–posterior (AP) view inclusion practices during videofluoroscopic swallowing studies (VFSSs) in the United States.

Method:
SLPs completing VFSSs were recruited to complete an online anonymous survey. Questions represented six constructs of interest including: (a) clinician demographics, (b) practice patterns, (c) diagnostic perceptions, (d) professional influences, (e) training and education, and (f) logistical facilitators and barriers. Binary logistic regression was used to explore the relationship between construct items and likelihood of AP view inclusion.

Results:

A total of 136/213 (64%) of respondents reported obtaining an AP view routinely. Facilitators of AP view inclusion were post-acute work setting (
OR
= 3.40,
p
= .001); perception that department practices “probably” (
OR
= 5.65,
p
= .006) or “definitely” align (
OR
= 5.30,
p
= .006) with evidence-based practice; perception the AP view has “a lot” (
OR
= 4.17,
p
= .025) or “a great deal” (
OR
= 4.77,
p
= .028) of diagnostic value; perception that their department is “definitely” supportive (
OR
= 4.69,
p
= .040); “moderate” (
OR
= 4.75,
p
= .001) or “no” (
OR
= 7.51,
p
< .001) equipment limitations; and radiologist support greater than “extremely unsupportive or resistant” (“somewhat unsupportive” [
OR
= 5.74,
p
= .041], “neutral” [
OR
= 11.23,
p
= .002], “somewhat supportive” [
OR
= 13.92,
p
= .001], or “extremely supportive” [
OR
= 13.92,
p
= .001]). Barriers to AP view inclusion were geographic location in the southern U.S. census region (
OR
= 0.31,
p
= .007), being “significantly” influenced by coworker opinions (
OR
= 0.13,
p
= .018), and productivity tracking (
OR
= 0.21,
p
= .008).

Conclusion:
Environmental factors and organizational culture heavily influence AP view inclusion practices.
Artificial floating littoral zones: a promising nursery to support Pike (Esox lucius) in reservoirs
Authors: Salmon Quentin , Westrelin Samuel , Dublon Julien , Abadie Etienne , Baudoin Jean-Marc 
Published: October 2024

The use of water resources in reservoirs leads to artificial water level fluctuations sometimes with extreme amplitudes and frequencies. These artificial fluctuations homogenize littoral habitats and often make macrophytes disappear. Consequently, spawning and refuge-nursery habitats become scarce which is critical for phytophilous species such as Northern Pike (Esox lucius) whose populations decline. Quite recently, floating artificial structures have emerged as a mitigation solution. However, the design of these structures is relatively simplistic and only consists in a simple 2D-floating mat of vegetation. Their effectiveness to support fish populations, especially pike in regulated reservoir, by providing suitable habitats for spawning, refuge and nursery remains poorly documented. Here we conceived 3D artificial Floating Littoral Zones (FLOLIZ) that mimic a natural littoral zone to support both pike spawning and juvenile growth (helophytes, hydrophytes, specific shelter areas). To assess their effectiveness, three structures of 70 m2 area and 1 m deep were installed in September 2018 in a French reservoir subject to extreme water level fluctuations. Visual surveys carried out in spring and summer by snorkelling over 2019–2023 highlighted an annual recurrence of juvenile pike in FLOLIZ, but also a higher abundance than in control stations. The maximum number of individuals observed simultaneously on the same structure was 14. Even if it cannot be asserted that pike spawned in FLOLIZ, these results highlight that FLOLIZ can provide refuge and nursery habitats for juvenile fish in reservoirs with poor littoral habitats.
Intraoperative patellar tracking assessment during image-based robotic-assisted total knee arthroplasty: technical note and reliability study
Authors: Batailler Cécile , Greiner Salomé , Rekik Hanna-Lisa , Olivier Flora , Servien Elvire , Lustig Sébastien 
Published: October 2024

Introduction: Restoration of the anterior knee compartment is increasingly studied with the development of personalized surgery. However, evaluating the patellar tracking during the surgery is still subjective and at the surgeon’s discretion. This study aimed 1) to describe the assessment of the patellar tracking during robotic-assisted total knee arthroplasty (TKA), 2) to describe a new measurement technique for evaluating the evolution of this patellar tracking, and 3) to assess its reliability and repeatability. Method: This monocentric study assessed the evolution of patellar tracking for 20 robotic-assisted TKA. The sharp probe was used to perform patellar tracking in all the arcs of knee flexion before and after the bone cuts. The patella positioning was recorded every 10° of flexion between the full extension and 90° knee flexion and was assessed in the coronal and sagittal planes. For the measurements of the patellar tracking, we used a sagittal view and a coronal view of the knee on the MAKO software. From these two views, the difference between the patellar tracking before and after the bone cuts with the definitive implants was measured. Two independent reviewers performed the measurements to assess their reliability. To determine intraobserver variability, the first observer performed the measurements twice. Results: The mean age was 68.7 years old ± 5.2 [61; 75], the mean body mass index was 28.8 kg/m2 ± 4.2 [21.4; 36.2], the mean HKA angle was 176.3° ± 3.7° [174.1.4; 179.7]. The radiographic measurements showed very good to excellent intra-observer and inter-observer agreements (0.60 to 1.0). Conclusion: This new measurement technique assessed the evolution of patellar tracking after TKA with good inter and intra-observer reliability.