bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Growth and Development of a Research Division in the Plastic Surgery Department of a Large Urban Academic Medical Center
Authors: James Andrew J. , Lineaweaver William C. , Yao Julia , Thayer Wesley , Perdikis Galen 
Published: September 2024

Introduction
Research is a critical component of academic medicine that may or may not be prioritized in centers with high clinical volumes. The benefits of research expansion go beyond notoriety and industry partnerships, expanding into resident training and preparation of the next generation of physician-scientists. Improving a division or department's research portfolio requires a commitment to reorganizing structure, personnel, resources, and a dedication to innovative funding models. To improve research productivity and quality, our group placed several initiatives into motion beginning in August 2017 that we have outlined and evaluated in the present study. Some of these initiatives included restructuring leadership, resourcing both bench and clinical outcomes research, providing initial funding directly from clinical profits and rewarding research fiscally.

Methods
Reviews of hiring records, publications, grant allocations, and interviews with key personnel were used to generate a road map of initiatives. Average impact factor was calculated by averaging journal impact factors for all publications from the department each year, excluding any publications with greater than 5 times the raw average, and creating a corrected average that more accurately represented the work. Student t tests were used to compare mean number of publications and impact factors from 2010 to 2017 to those from 2018 to 2022.

Results
Prior to restructuring (2010–2017), the department published an average of 9 articles annually, which increased to an average of 42 articles since that time (P < 0.01). Average impact increased from 0 in 2010 to 4.02 in 2022, with the number of publications in top 10 plastic surgery journals following a similar trajectory with 1 publication in 2010 and 31 in 2023. Following an initial $1 million investment to create an institutionally directed fund in 2018, the department leveraged its research to earn $3 million in endowments, $1.25 million in industry partnerships, $3.23 million in Department of Defense funding, and $1.65 million from a multi-institutional National Institutes of Health grant.

Conclusion
Deliberate prioritization of research initiatives as noted above has led to remarkable growth in academic output.
IMPACT OF ABCC8 AND TRPM4 GENETIC VARIATION IN CENTRAL NERVOUS SYSTEM DYSFUNCTION ASSOCIATED WITH PEDIATRIC SEPSIS
Authors: Kernan Kate F. , Adkins Ashley , Jha Ruchira M. , Kochanek Patrick M. , Carcillo Joseph A. , Berg Robert A. , Wessel David , Pollack Murray M. , Meert Kathleen , Hall Mark , Newth Christopher , Lin John C. , Doctor Allan , Cornell Tim , Harrison Rick E. , Zuppa Athena F. , Notterman Daniel A. , Aneja Rajesh K. 
Published: September 2024

ABSTRACT

Background: Sepsis-associated brain injury is associated with deterioration of mental status, persistent cognitive impairment, and morbidity. The SUR1/TRPM4 channel is a nonselective cation channel that is transcriptionally upregulated in the central nervous system with injury, allowing sodium influx, depolarization, cellular swelling, and secondary injury. We hypothesized that genetic variation in ABCC8 (SUR1 gene) and TRPM4 would associate with central nervous system dysfunction in severe pediatric sepsis. Methods: 326 children with severe sepsis underwent whole exome sequencing in an observational cohort. We compared children with and without central nervous system dysfunction (Glasgow Coma Scale <12) to assess for associations with clinical characteristics and pooled rare variants in ABCC8 and TRPM4. Sites of variation were mapped onto protein structure and assessed for phenotypic impact. Results: Pooled rare variants in either ABCC8 or TRPM4 associated with decreased odds of central nervous system dysfunction in severe pediatric sepsis (OR 0.14, 95% CI 0.003–0.87), P = 0.025). This association persisted following adjustment for race, organ failure, viral infection, and continuous renal replacement therapy (aOR 0.11, 95% CI 0.01–0.59, P = 0.038). Structural mapping showed that rare variants concentrated in the nucleotide-binding domains of ABCC8 and N-terminal melastatin homology region of TRPM4. Conclusion: This study suggests a role for the ABCC8/TRPM4 channel in central nervous system dysfunction in severe pediatric sepsis. Although exploratory, the lack of therapies to prevent or mitigate central nervous system dysfunction in pediatric sepsis warrants further studies to clarify the mechanism and confirm the potential protective effect of these rare ABCC8/TRPM4 variants.
Recurrence-Independent Progressive Inner-Retinal Thinning After Optic Neuritis: A Longitudinal Study
Authors: Moon Yeji , Gim Yujin , Park Kyung-Ah , Yang Hee Kyung , Kim Seong-Joon , Kim Sung-Min , Jung Jae Ho 
Published: September 2024

Background:
Longitudinal changes in the inner retina in patients with optic neuritis (ON) may be helpful in monitoring patients and determining maintenance treatment. The aim of this study was to investigate longitudinal changes in the inner retina after subsiding of acute demyelinating ON and to identify the factors associated with such changes.

Methods:
In this multicenter retrospective observational study, we reviewed the medical records of 77 patients with ON, including 23 with neuromyelitis optica spectrum disorder with aquaporin 4 (AQP4)-immunoglobulin G (IgG) (AQP4 group), 23 with myelin oligodendrocyte glycoprotein (MOG)-antibody-associated disease (MOG group), 18 with multiple sclerosis (MS group), and 13 with idiopathic ON (iON group). We measured the thickness of the peripapillary retinal nerve fiber layer (pRNFL) and the macular ganglion cell-inner plexiform layer (mGCIPL) using optical coherence tomography (OCT) at baseline and at follow-up examinations (mean follow-up duration, 29.6 ± 8.6 months; mean number of OCT, 4.2 ± 1.2) in the absence of ON recurrence.

Results:
The estimated rate of pRNFL thinning in the AQP4, MOG, MS, and iON groups was 0.66 (95% confidence interval, 0.35–0.97), 0.35 (0.04–0.66), 0.53 (0.16–0.90), and 0.25 (−0.18 to 0.68) μm/year, respectively, indicating that, in the iON group in contrast to the other groups, there was no significant decrease of pRNFL thickness. Among the AQP4, MOG, and MS groups, there was no significant difference in the rate of pRNFL thinning (P = 0.560). The rate of mGCIPL thinning in the AQP4 and MOG groups was 0.25 (0.04–0.46) μm/year and 0.38 (0.23–0.53) μm/year, respectively. Meanwhile, the rate of mGCIPL change in the MS and iON groups was 0.04 (−0.12 to 0.19) and 0.00 (−0.17 to 0.16) μm/year, respectively, which indicates that there was no significant mGCIPL thinning in the latter 2 groups. Between the AQP4 and MOG groups, meanwhile, the rate of mGCIPL change did not significantly differ (P = 0.295). Age older than 40 years was associated with significant progression of mGCIPL thinning (P = 0.005).

Conclusions:
We noted inner retina thinning progression independent of relapse activity in AQP4-ON, MOG-ON, and MS-ON. Because subclinical neuroaxonal damage continues to be incurred after an acute attack of ON subsides despite suppression of new attacks, long-term follow-up and neuroprotection should be considered to be integral to the treatment of patients with ON.
Interactions between neural representations of the social and spatial environment
Authors: Thompson James C. , Parkinson Carolyn 
Published: September 2024

Even in our highly interconnected modern world, geographic factors play an important role in human social connections. Similarly, social relationships influence how and where we travel, and how we think about our spatial world. Here, we review the growing body of neuroscience research that is revealing multiple interactions between social and spatial processes in both humans and non-human animals. We review research on the cognitive and neural representation of spatial and social information, and highlight recent findings suggesting that underlying mechanisms might be common to both. We discuss how spatial factors can influence social behaviour, and how social concepts modify representations of space. In so doing, this review elucidates not only how neural representations of social and spatial information interact but also similarities in how the brain represents and operates on analogous information about its social and spatial surroundings.
This article is part of the theme issue ‘The spatial–social interface: a theoretical and empirical integration’.
Anthropogenic impacts at the interface of animal spatial and social behaviour
Authors: Gaynor Kaitlyn M. , Abrahms Briana , Manlove Kezia R. , Oestreich William K. , Smith Justine A. 
Published: September 2024

Human disturbance is contributing to widespread, global changes in the distributions and densities of wild animals. These anthropogenic impacts on wildlife arise from multiple bottom-up and top-down pathways, including habitat loss, resource provisioning, climate change, pollution, infrastructure development, hunting and our direct presence. Animal behaviour is an important mechanism linking these disturbances to population outcomes, although these behavioural pathways are often complex and can remain obscured when different aspects of behaviour are studied in isolation from one another. The spatial–social interface provides a lens for understanding how an animal’s spatial and social environments interact to determine its spatial and social phenotype (i.e. measurable characteristics of an individual), and how these phenotypes interact and feed back to reshape environments. Here, we review studies of animal behaviour at the spatial–social interface to understand and predict how human disturbance affects animal movement, distribution and intraspecific interactions, with consequences for the conservation of populations and ecosystems. By understanding the spatial–social mechanisms linking human disturbance to conservation outcomes, we can better design management interventions to mitigate undesired consequences of disturbance.
This article is part of the theme issue ‘The spatial–social interface: a theoretical and empirical integration’.
Temporally Corrected Dose Accumulation – Next Steps in the Biology of Reirradiation
Authors: Gopalakrishnan Vishhvaan , Feng Bezhou , Somasundaram Eashwar , Pelesko Julia , Stephans Kevin , Magnelli Anthony , Koyfman Shlomo , Videtic Gregory , Qi Peng , Yang Xiaofeng , Abbott Elliot M. , Piper Jonathan W. , Qiu Richard L.J. , Scott Jacob G. 
Published: September 2024

ABSTRACTIntroductionTreatments encompassing multiple courses of radiation are becoming increasingly common in the management of oligometastatic disease, offering opportunities to extend progression-free and overall survival. However, a major challenge in clinical practice is the lack of standardized methods to assess and mitigate toxicity risks associated with successive radiation treatments. Furthermore, normal tissue recovery post-radiation remains poorly characterized, and the absence of standardized documentation for radiotherapy history complicates large-scale research efforts. To address these limitations, we propose the development of a novel DICOM-compatible object for integration into patient medical records.Materials and MethodsWe generated software designs and bundle mathematics that demonstrate the utility of this DICOM object and how various dose forgiveness algorithms can be applied to the data. We include simple linear, exponential, logarithmic, and Gaussian recovery algorithms as well as complex non-linear algorithms based on the literature currently available.ResultsWe applied the tool to an anonymized patient dataset, demonstrating the mathematical analysis applied to the data found in the new DICOM object. Noting ease and efficacy, we demonstrated that, in contrast to the current practice of gathering and structuring information distributed across electronic medical records, ready access to prior radiation courses accomplished two goals. (1) Facilitate data collection and analysis by streamlining access to comprehensive radiotherapy history, enabling researchers to conduct large-scale studies, and ultimately improve our understanding of tissue recovery. (2) Enhance clinical decision-making by enabling clinicians or software tools to leverage this data to personalize treatment plans, support clinical decision making to minimize toxicity risks during re-irradiation. For the anonymized patient, our analysis demonstrates safer delivery of re-radiation plans when viewed in the lens of dose forgiveness.ConclusionsA novel DICOM object which keeps track of radiation treatments enables clinicians to factor tissue recovery and response into planning safer multiple radiation therapy courses and facilitates cross-institution research on re-irradiation and dose forgiveness.
Temporal Genomic Dynamics Shape Clinical Trajectory in Multiple Myeloma
Authors: Maura Francesco , Kaddoura Marcella , Poos Alexandra M. , Baughn Linda B. , Ziccheddu Bachisio , Bärtsch Marc-Andrea , Cirrincione Anthony , Maclachlan Kylee , Chojnacka Monika , Diamond Benjamin , Papadimitriou Marios , Blaney Patrick , John Lukas , Reichert Philipp , Huhn Stefanie , Gagler Dylan , Zhang Yanming , Dogan Ahmet , Lesokhin Alexander M , Davies Faith , Goldschmidt Hartmut , Fenk Roland , Weisel Katja C. , Mai Elias K. , Korde Neha , Morgan Gareth J , Rajkumar S. Vincent , Kumar Shaji , Usmani Saad , Landgren Ola , Raab Marc S. , Weinhold Niels 
Published: September 2024

ABSTRACTTo comprehensively unravel the temporal relationship between initiating and driver events and its impact on clinical outcomes, we analyzed 421 whole-genome sequencing profiles from 382 patients. Using clock-like mutational signatures, we estimated a time lag of 2-4 decades between initiating events and diagnosis. In patients with hyperdiploidy, we demonstrate that trisomies of odd-numbered chromosomes can be acquired simultaneously with other chromosomal gains, such as 1q gain. We provide evidence that hyperdiploidy is acquired after canonical IGH translocation when both events are present. Finally, patients with early 1q gain had adverse outcomes similar to those with 1q amplification (>1 extra-copies), but faring worse than those with late 1q gain. This underscores that the prognostic impact of 1q gain/amp depends more on the timing of acquisition than on the number of extra copies gained. Overall, this study contributes to a better understanding of the life history of MM and may have prognostic implications.
Benchmarking Recent Computational Tools for DNA-binding Protein Identification
Authors: Luo Xizi , Yi Chi Amadeus Song , Lin Andre Huikai , Ong Tze Jet , Wong Limsoon , Rahman Chowdhury Rafeed 
Published: September 2024

AbstractIdentification of DNA-binding proteins (DBPs) is a crucial task in genome annotation, as it aids in understanding gene regulation, DNA replication, transcriptional control and various cellular processes. In this paper, we conduct an unbiased benchmarking of eleven state-of-the-art computational tools as well as traditional tools such as ScanProsite, BLAST, and HMMER for identifying DBPs. We highlight the data leakage issue in conventional datasets leading to inflated performance. We introduce new evaluation datasets to support further development. Through a comprehensive evaluation pipeline, we identify potential limitations in models, feature extraction techniques and training methods; and recommend solutions regarding these issues. We show that combining the predictions of the two best computational tools with BLAST based prediction significantly enhances DBP identification capability. We provide this consensus method as user-friendly software. The datasets and software are available at:https://github.com/Rafeed-bot/DNA_BP_Benchmarking.1.Key PointsWe designed a comprehensive evaluation pipeline which systematically evaluates eleven recent machine learning (ML) based DBP identification tools.We analyzed the test prediction mistakes made by top-performing tools identifying their potential limitations in terms of model architecture, feature extraction and class balancing.We showed that although the best of these tools do not convincingly outperform BLAST, they still provide substantial value when integrated together with BLAST into a simple majority-voting ensemble.We provide recommendations on more robust development & evaluation and better usability of future tools.We provide the two best-performing ML-based tools, BLAST and the ensemble method as user-friendly software, as well as our proposed datasets, publicly available via GitHub.
Not Too Late to Intervene? A Meta-analysis of 13 Studies Evaluating the Association of Endovascular Therapy with Clinical Outcomes in Stroke Patients Presenting Beyond 24 Hours
Authors: Doheim Mohamed F , Hagrass Abdulrahman Ibrahim 
Published: September 2024

AbstractBackgroundAssociation of endovascular therapy (EVT) with clinical outcomes beyond 24 hours remains unclear. We conducted a meta-analysis to answer this question.MethodsWe searched for eligible studies in PubMed from inception until June 2023. The outcomes included functional independence, as assessed with 90-day modified Rankin Scale (mRS) scores (0-2), thrombolysis in cerebral infarction (TICI) scores (2b-3 or 3), symptomatic intracranial hemorrhage (sICH), and 90-day mortality. Risk ratio (RR) and 95% confidence interval (CI) were pooled.ResultsWe finally included 13 studies in our meta-analysis (number of patients treated with EVT beyond 24 h=866). For single arm analysis, the pooled estimates of functional independence (mRS 0-2), sICH, and mortality were 0.342 (95% CI = 0.275 -0.410, P < 0.001), 0.062 (95% CI = 0.045 -0.078, P < 0.001), and 0.232 (95% CI = 0.164 -0.301, P < 0.001); respectively with successful reperfusion (TICI 2b-3) of 0.837 (95% CI = 0.812 -0.861, P < 0.001). Comparing EVT with medical management, the pooled analysis showed that EVT had a statistically significant advantage over medical management (RR = 2.62, 95% CI [1.38, 4.96], P = 0.003). However, our analysis showed a higher incidence of sICH in EVT group (RR = 3.58, 95% CI [1.53, 8.37], P = 0.003). When we pooled studies comparing EVT beyond 24 h with EVT within 6–24 h, the findings showed no statistically significant difference for functional independence, sICH, and 90-d Mortality.ConclusionEVT is associated with better clinical outcomes than medical management beyond 24 hours. These results are iconoclastic enhancing a new paradigm in which a contemporary restriction to specific time window to treat patients rather than their own clinical and imaging characteristics seems to be anecdotal. Prospective studies are needed to confirm the best eligible patients for EVT in this newly proposed window extension.
Fc-dependent protective efficacy of non-inhibitory antibodies targeting influenza A virus neuraminidase is limited by epitope availability
Authors: Pascha Mirte N. , Ballegeer Marlies , van Haperen Rien , Kooij Annick C. , van Miltenburg Danique M. , Smits Anthony A. , Schipper Jelle G. , Cui Hongrui , Albulescu Irina C. , Bosch Berend Jan , Grosveld Frank , van Kuppeveld Frank J.M. , Saelens Xavier , Drabek Dubravka , de Haan Cornelis A.M. 
Published: September 2024

AbstractAntibodies targeting hemagglutinin and neuraminidase (NA) are key components of the adaptive immune response against influenza A virus (IAV). However, antigenic drift allows the virus to escape inhibition by such antibodies. In this study, we aimed to isolate antibodies with cross-subtype reactivity against human H1N1 and H3N2 IAVs from transgenic mice bearing genes encoding the human immunoglobulin variable regions. We immunized these mice with recombinant N1 and N2 NA proteins, presenting them either as unconjugated soluble proteins or conjugated to self-assembling protein nanoparticles. This approach yielded a panel of NA-specific monoclonal antibodies (mAbs) with various levels of intra-and inter-subtype reactivity for N1 and N2 NA. Three of these mAbs, which collectively recognize two distinct epitopes, were cross-reactive against N1 and N2 NAs in ELISA, but did not inhibit NA enzymatic activity. Two of these mAbs, 21H8 and 45D9, were selected for further characterization. These recognized different epitopes and induced Fc-mediated effector functions to varying extents. Prophylactic administration of 21H8, but not 45D9, protected mice against challenge with H1N1 IAV, while neither mAb protected against a H3N2 challenge. The observed protective efficacy correlated with the mAbs’ capacity, or lack thereof, to bind membrane-associated full-length NA. The introduction of Fc silencing mutations in mAb 21H8 resulted in an inability to activate NK cells or mediate phagocytosisin vitroand significantly reduced protectionin vivo, indicating that the protective efficacy of mAb 21H8 is Fc-dependent. However, mAb 21H8 expressed with reduced core fucosylation of its Fc N-glycan, which specifically enhanced NK cell activationin vitro, failed to improve protection against H1N1 challengein vivo. Future work is needed to decipher in more detail the mechanism of Fc-mediated protection against influenza via NA-specific antibodies and to identify the optimal strategies for their enhancement.
Learning to see
R
-parity violating scalar top decays
Authors: Bickendorf Gerrit , Drees Manuel 
Published: September 2024

With this article, we introduce recent, improved machine learning methods from computer vision to the problem of event classification in particle physics. Supersymmetric scalar top decays to top quarks and weak-scale bino-like neutralinos, where the neutralinos decay via the UDD operator to three quarks, are difficult to search for and therefore weakly constrained. The jet substructure of the boosted decay products can be used to differentiate signal from background events. We apply the transformer-based computer vision models otet and axi to images built from jet constituents and compare the classification performance to a more classical convolutional neural network (CNN). We find that results from computer vision translate well to physics applications, and both transformer-based models perform better than the CNN. By replacing the CNN with axi, we find an improvement of S/B by a factor of almost 2 for some neutralino masses. We show that combining this classifier with additional features results in a strong separation of background and signal. We also find that replacing a CNN with a axi model in a simple mock analysis can push the 95% C.L. exclusion limit of stop masses by about 100 and 60 GeV for neutralino masses of 100 and 500 GeV.

Published by the American Physical Society
2024
Physical properties and electronic structure of the two-gap superconductor
V2Ga5
Authors: Cheng P.-Y. , Oudah Mohamed , Hung T.-L. , Hsu C.-E. , Chang C.-C. , Haung J.-Y. , Liu T.-C. , Cheng C.-M. , Ou M.-N. , Chen W.-T. , Deng L. Z. , Lee C.-C. , Chen Y.-Y. , Kuo C.-N. , Lue C.-S. , Machts Janna , Kojima Kenji M. , Hallas Alannah M. , Huang C.-L. 
Published: September 2024

We present a thorough investigation of the physical properties and superconductivity of the binary intermetallic V2Ga5. Electrical resistivity and specific heat measurements show that V2Ga5 enters its superconducting state below Tsc= 3.5 K, with a critical field of Hc2,⊥c(Hc2,||c)=6.5(4.1) kOe. With H⊥c, the peak effect was observed in resistivity measurements, indicating the ultrahigh quality of the single crystal studied. The resistivity measurements under high pressure reveal that the Tsc is suppressed linearly with pressure and reaches absolute zero around 20 GPa. Specific heat and muon spin relaxation measurements indicate that the two-gap s-wave model best describes the superconductivity of V2Ga5. The bands near the Fermi level around the Z and Γ points are observed and analyzed by the angle-resolved photoemission spectroscopy measurements and first-principles band structure calculations. We therefore conclude that V2Ga5 is a phonon-mediated two-gap s-wave superconductor.

Published by the American Physical Society
2024