bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of a custom Photogrammetry for Anatomical CarE (PHACE) system with other Low- Cost Facial Scanning Devices
Authors: To Josiah K. , Vu Anderson N. , Ediriwickrema Lilangi S. , Browne Andrew W. 
Published: April 2023

AbstractPurposeTo compare a custom Photogrammetry for Anatomical CarE (PHACE) system with other cost-effective 3-dimensional (3D) facial scanning systems to objectively characterize morphology and volume of periorbital and adnexal anatomy.MethodsThe imaging systems evaluated include the low-cost custom PHACE system and commercial software product for the iPhone called Scandy Pro (iScandy) application (Scandy, USA), and the mid-priced Einscan Pro 2X (Shining3D Technologies, China) device and Array of Reconstructed Cameras 7 (ARC7) facial scanner (Bellus3D, USA). Imaging was performed on a manikin facemask and humans with various Fitzpatrick scores. Scanner attributes were assessed using mesh density, reproducibility, surface deviation, and emulation of 3D printed phantom lesions affixed above the superciliary arch (brow line).ResultsThe Einscan served as a reference for lower cost imaging systems because it qualitatively and quantitatively renders facial morphology with the highest mesh density, reproducibility (0.13 ± 0.10 mm), and volume recapitulation (approximately 2% of 33.5 μL). Compared to the Einscan, the PHACE system (0.35 ± 0.03 mm, 0.33 ± 0.16 mm) demonstrated non-inferior mean accuracy and reproducibility root mean square (RMS) compared to the iScandy (0.42 ± 0.13 mm, 0.58 ± 0.09 mm), and significantly more expensive ARC7 (0.42 ± 0.03 mm, 0.26 ± 0.09 mm). Similarly, the PHACE system showed non-inferior volumetric modeling when rendering a 124 μL phantom lesion compared to the iScandy and more costly ARC7 (mean percent difference from the Einscan: 4.68 ± 3.73%, 9.09 ± 0.94%, and 21.99 ± 17.91% respectively).ConclusionsThe affordable PHACE system accurately measures periorbital soft tissue as well as other established mid-cost facial scanning systems. Additionally, the portability, affordability, and adaptability of PHACE can facilitate widespread adoption of 3D facial anthropometric technology as an objective measurement tool in ophthalmology.PrecisWe demonstrate a custom system for facial photogrammetry (Photogrammetry for Anatomical CarE -PHACE) to produce 3D renderings of facial volume and morphology which compares with more expensive alternative 3D scanning technologies.
Prevention of cyclical resurgences of COVID-19-like pandemics in the long term: What are the trade-offs?
Authors: Nakamoto Ichiro 
Published: April 2023

AbstractVaccines have facilitated the substantial reduction and containment of COVID-19 transmission in many countries by early 2023. However, the long-term interconnection between vaccines, traits of the pathogen, vaccination strategies, and cases averted/trade-offs of health outcomes is not well understood. Utilizing a compartment-calibrated model, I estimated the aversion/trade-offs effect on six major disease burdens (i.e., total/symptomatic/asymptomatic/hospitalized/ICU/death cases averted) over time conditional on a variety level of scenarios. The findings implied that low-risk immunity profiles of booster doses increased the peak cases averted versus medium- and high-risk counterparts. The effect was most salient for the former paired with enhancing the rollout rate of doses, followed by the medium- and then high-risk scenarios. Positive and temporarily durable aversion effects for the low-risk, in contrast, negative trade-offs and decreasing aversion effects for the suboptimal scenarios were observed. While there are heterogeneities in vaccines, public strategies, social efforts, and other considerations, this work can provide an evidence-based rationale for the long-term trade-off analysis of vaccination.
A systematic review and meta-analysis of participant characteristics in the prevention of gestational diabetes: a summary of evidence for precision medicine
Authors: Lim Siew , Takele Wubet Worku , Vesco Kimberly K , Redman Leanne ,   ADA PMDI GDM prevention working group, Josefson Jami 
Published: April 2023

AbstractBackground and aimsPrecision prevention involves using the unique characteristics of a particular group to determine their responses to preventive interventions. This study aimed to systematically evaluate the participant characteristics associated with interventions in gestational diabetes mellitus (GDM) prevention.MethodsWe searched MEDLINE, EMBASE, and Pubmed to identify lifestyle (diet, physical activity, or both), metformin, myoinositol/inositol and probiotics interventions of GDM prevention published up to May 24, 2022.ResultsFrom 10347 studies, 116 studies (n=40940 women) were included. Physical activity resulted in greater GDM reduction in participants with a normal body mass index (BMI) at baseline compared to obese BMI (risk ratio, 95% confidence interval: 0.06 [0.03, 0.14] vs 0.68 [0.26, 1.60]). Diet and physical activity interventions resulted in greater GDM reduction in participants without polycystic ovary syndrome (PCOS) than those with PCOS (0.62 [0.47, 0.82] vs 1.12 [0.78-1.61]) and in those without a history of GDM than those with unspecified history (0.62 [0.47, 0.81] vs 0.85 [0.76, 0.95]). Metformin interventions were more effective in participants with PCOS than those with unspecified status (0.38 [0.19, 0.74] vs 0.59 [0.25, 1.43]), or when commenced preconception than during pregnancy (0.22 [0.11, 0.45] vs 1.15 [0.86-1.55]). Parity, history of having a large-for-gestational-age infant or family history of diabetes had no effect.ConclusionsGDM prevention through metformin or lifestyle differs according to some individual characteristics. Future research should include trials commencing preconception and provide results stratified by participant characteristics including social and environmental factors, clinical traits, and other novel risk factors to predict GDM prevention through interventions.Plain language summaryPrecision prevention involves using a group’s unique context to determine their responses to preventive interventions. This study aimed to evaluate the participant characteristics associated with interventions in GDM prevention. We searched medical literature databases to identify lifestyle (diet, physical activity), metformin, myoinositol/inositol and probiotics interventions. A total of 116 studies (n=40903 women) were included. Diet and physical activity interventions resulted in greater GDM reduction in participants without polycystic ovary syndrome (PCOS) and those without a history of GDM. Metformin interventions resulted in greater GDM reduction in participants with PCOS or when started during the preconception period. Future research should include trials starting in the preconception period, and provide results stratified by participant characteristics to predict GDM prevention through interventions.
A neural basis of choking under pressure
Authors: Smoulder Adam L. , Marino Patrick J. , Oby Emily R. , Snyder Sam E. , Miyata Hiroo , Pavlovsky Nick P. , Bishop William E. , Yu Byron M. , Chase Steven M. , Batista Aaron P. 
Published: April 2023

AbstractIncentives tend to drive improvements in performance. But when incentives get too high, we can “choke under pressure” and underperform when it matters most. What neural processes might lead to choking under pressure? We studied Rhesus monkeys performing a challenging reaching task in which they underperform when an unusually large “jackpot” reward is at stake. We observed a collapse in neural information about upcoming movements for jackpot rewards: in the motor cortex, neural planning signals became less distinguishable for different reach directions when a jackpot reward was made available. We conclude that neural signals of reward and motor planning interact in the motor cortex in a manner that can explain why we choke under pressure.One-Sentence SummaryIn response to exceptionally large reward cues, animals can “choke under pressure”, and this corresponds to a collapse in the neural information about upcoming movements.
Fortuitous events in the evolution of Light-dependent Protochlorophyllide Oxidoreductase
Authors: Vedalankar Pratishtha , Tripathy Baishnab C 
Published: April 2023

AbstractLight-dependent protochlorophyllide oxidoreductase (LPOR) is a nuclear-encoded photoenzyme in many photosynthetic organisms. LPOR originated in primitive cyanobacterial ancestors during the great oxygenation event that was detrimental to the existence of the oxygen-sensitive LIPOR that prevailed in anoxygenic Earth. Both LIPOR and LPOR catalyse reduction of protochlorophyllide to chlorophyllide in the penultimate step of chlorophyll biosynthesis. Except for angiosperms and gnetophytes several oxygenic phototrophs harbour both LIPOR and LPOR. The coexistence of LIPOR and LPOR in certain phototrophs provides niche spaces for organisms in unconducive environment. The selection pressure of increased O2concentration, changing light quality and quantity at different depths of the ocean, nutrient status of water, gene reorganization during several endosymbiotic events, horizontal gene transfer, LIPOR gene loss and multiple duplication events played a major role in the evolution and diversification of LPOR and its isoforms in photosynthetic and non-photosynthetic organisms. In the absence of LIPOR angiosperms become vulnerable to protochlorophyllide-sensitized and light-induced oxidative stress mediated by singlet oxygen. To overcome the photo-damage PORA was expressed abundantly in the plastids of etiolated plants. PORB evolved to take over the function of vanishing PORA isoform in light. Brassicales evolved PORC to protect plants from high light and other environmental stresses.HighlightsProtochlorophyllide oxidoreductase is an important photo-enzyme in angiosperms that needs light as a substrate for the synthesis of chlorophylls. Therefore, angiosperms cannot green in dark although several algae and lower green plants can synthesize chlorophyll in dark due to the presence of light-independent protochlorophyllide oxidoreductase (LIPOR).In response to climate change, during the great oxygenation event light-dependent protochlorophyllide oxidoreductase (LPOR) evolved due to the O2-induced selection pressure that inactivated the oxygen-sensitive LIPOR.Increased O2concentration, changing light quality and quantity at different depths of ocean, gene reorganization during several endosymbiotic events, selective LIPOR gene loss and multiple duplication events played a major role in the evolution and diversification of LPOR and its isoforms in phototrophs.Phylogenetic studies indicate that LPOR genes have been overwhelmingly horizontally transferred between phototrophs and also non phototrophic organisms.Presence of LPOR in non-photosynthetic organisms, Mycobacterium and certain fungi suggests that LPOR may have some other reductive functions in these organisms.
Asymmetric patterns of nucleosome positioning sequences in protein-coding regions
Authors: Kato Hiroaki , Shimizu Mitsuhiro , Urano Takeshi 
Published: April 2023

ABSTRACTAlthough nucleosome positioning is key to epigenetic regulation, how the DNA sequence contributes to positioning remains elusive, especially in the context of transcription direction. Analysis of nucleotide bases with respect to the nucleosomal DNA coordinates requires precise nucleosomal mapping information on the genome. However, currently available base-pair-resolution nucleosome maps based on cysteine-mediated chemical cleavage do not fully satisfy the requirement due to method-specific cleavage biases. Here, we generated a chimeric nucleosomal DNA model to achieve less-biased prediction. The model revealed that yeast protein-coding sequences have higher affinity for the promoter-proximal half of nucleosomes than for the distal half. Strikingly, peaks of calculated affinity scores for the promoter-proximal half periodically matched the first few nucleosome positions. Detailed analysis of nucleotide bases revealed that the AA dinucleotide in the left side of the top strand contributes to nucleosome detection frequency in intergenic regions, while the complementary dinucleotide TT is preferred in the other side. In contrast, the sense strand is AA-rich throughout the nucleosome coordinate in protein-coding regions, which is consistent with asymmetric affinity. These data suggest that eukaryotes have evolved DNA sequences with asymmetric affinity for nucleosome formation to maintain epigenetic integrity of protein-coding regions.
Sperm Whales Demographics in the Gulf of Alaska and Bering Sea/Aleutian Islands: An Overlooked Female Habitat
Authors: Posdaljian Natalie , Solsona-Berga Alba , Hildebrand John A. , Soderstjerna Caroline , Wiggins Sean M. , Lenssen Kieran , Baumann-Pickering Simone 
Published: April 2023

AbstractSperm whales exhibit sexual dimorphism and sex-specific latitudinal segregation. Females and their young form social groups and are usually found in temperate and tropical latitudes, while males forage at higher latitudes. Historical whaling data and rare sightings of social groups in high latitude regions of the North Pacific, such as the Gulf of Alaska (GOA) and Bering Sea/Aleutian Islands (BSAI), suggest a more nuanced distribution than previously understood. Sperm whales are the most sighted and recorded cetacean in marine mammal surveys in these regions but capturing their demographic composition and habitat use has proven challenging. This study detects sperm whale presence using passive acoustic data from seven sites in the GOA and BSAI from 2010 to 2019. Differences in click characteristics between males and females (i.e., inter-click and inter-pulse interval) was used as a proxy for animal size/sex to derive time series of animal detections. Generalized additive models with generalized estimation equations demonstrate how spatiotemporal patterns differ between the sexes. Social groups were present at all recording sites with the largest relative proportion at two seamount sites in the GOA and an island site in the BSAI. We found that the seasonal patterns of presence varied for the sexes and between the sites. Male presence was highest in the summer and lowest in the winter, conversely, social group peak presence was in the winter for the BSAI and in the spring for the GOA region, with the lowest presence in the summer months. This study demonstrates that social groups are not restricted to lower latitudes and capture their present-day habitat use in the North Pacific. It highlights that sperm whale distribution is more complex than accounted for in management protocol and underscores the need for improved understanding of sperm whale demographic composition to better understand the impacts of increasing anthropogenic threats, particularly climate change.
Oncolytic Newcastle disease virus enhanced apoptosis in colorectal cancer cell lines
Authors: Ginting Teridah Ernala , Hidayat Nur Rahmaniah , Cornelia Vina , Larasati Young Othiwi , Zarkasie Kamaluddin , Yusuf Irawan 
Published: April 2023

AbstractColorectal cancer (CRC) is a deadly disease with a high prevalence and mortality rate worldwide. Previous investigations have shown that Newcastle disease virus (NDV) exhibits oncolytic activity and antitumor immunostimulation properties on several types of tumor cells but not normal cells. This study aims to examine NDV oncolytic activity against two kinds of human CRC cell lines, i.e., HCT116 and SW620, as well as its ability to induce apoptosis. The results showed that CRC cell lines were susceptible to NDV LaSota strain and the mechanism of death was due to caspase-dependent pathways apoptosis, followed by interferon signaling competence. NDV-induced proinflammatory cytokines in CRC cells might have contributed to apoptosis mechanism. Therefore, further investigation is recommended, using the findings obtained in this study as a basis for an animal CRC model.
Evaluation of nanopore sequencing on polar bodies for routine pre-implantation genetic testing for aneuploidy
Authors: Oberle Anna , Hanzer Franziska , Kokocinski Felix , Ennemoser Anna , Carli Luca , Vaccari Enrico , Hengstschläger Markus , Feichtinger Michael 
Published: April 2023

Structured AbstractBACKGROUNDPGT-A using polar body (PB) biopsy derives a clinical benefit by reducing the number of embryo transfers and miscarriage rates but is currently not cost-efficient. Nanopore sequencing technology opens possibilities by providing cost-efficient, fast sequencing results with uncomplicated sample preparation workflows.METHODSIn this comparative experimental study, 102 pooled PB samples from 20 patients were analyzed for aneuploidy using nanopore sequencing technology and compared with aCGH results generated as part of the clinical routine. Samples were sequenced on a Nanopore MinION machine for up to 9 hours for 6 pooled PB samples. Whole-chromosome copy-numbers were called by a custom bioinformatic analysis software. Automatically called results were compared to aCGH results.RESULTSOverall, 96/99 samples were consistently detected as euploid or aneuploid in both methods (concordance=97.0%, sensitivity = 0.957, specificity = 1.0, PPV = 1.0, NPV = 0.906). On chromosomal level, concordance reached 98.7%. Chromosomal aneuploidies analyzed in this trial covered all 23 chromosomes with 98 trisomies, and 97 monosomies in 70 aCGH samples.The whole nanopore workflow is feasible in under 5 hours (for one sample) with maximum time of 16 hours (for 12 samples), enabling fresh PB-euploid embryo transfer. Material cost of 150€/sample possibly enable cost-efficient aneuploidy screening.CONCLUSIONSThis is the first study, systematically comparing nanopore sequencing for aneuploidy of PBs with standard detection methods. High concordance rates confirmed feasibility of nanopore technology for this application. Additionally, the fast and cost-efficient workflow reveals clinical utility of this technology, making PB PGT-A clinically attractive.
Bexmarilimab-induced macrophage activation leads to treatment benefit in solid tumors: the phase I/II first-in-human MATINS trial
Authors: Rannikko Jenna H. , Verlingue Loic , de Miguel Maria , Pasanen Annika , Robbrecht Debbie , Skytta Tanja , Iivanainen Sanna , Shetty Shishir , Ma Yuk Ting , Graham Donna M. , Arora Sukeshi Patel , Jaakkola Panu , Yap Christina , Xiang Yujuan , Mandelin Jami , Karvonen Matti K. , Jalkanen Juho , Karaman Sinem , Koivunen Jussi P. , Minchom Anna , Hollmén Maija , Bono Petri 
Published: April 2023

AbstractClever-1 expression in macrophages contributes to impaired antigen presentation and suppression of anti-tumor immunity. This first-in-human trial was designed to investigate the safety and tolerability of Clever-1 blockade in patients with treatment-refractory solid tumors and to assess preliminary anti- tumor efficacy, pharmacodynamics, and immunologic correlates. Bexmarilimab was well tolerated with no observed dose limiting toxicities in part I (n=30) and no additional safety signals in part II (n=108). Disease control (DC) rates of 25-40% were observed in cutaneous melanoma, gastric, hepatocellular, estrogen receptor positive breast, and biliary tract cancers, which associated with improved survival in a landmark analysis. High pre-treatment intra-tumoral Clever-1 staining and low circulating TNFα correlated with DC. Digital spatial profiling of DC and non-DC tumors with next generation sequencing showed bexmarilimab-induced macrophage activation and robust stimulation of IFNγ and T-cell receptor signaling selectively in DC patients. These data suggest that bexmarilimab therapy is well-tolerated and show that macrophage targeting can promote tumor control in late stage cancer.HighlightsTargeting Clever-1 with bexmarilimab is well toleratedDisease control in late stage cancer can be achieved with bexmarilimab monotherapyLow baseline immune activation associates with bexmarilimab benefitBexmarilimab converts intratumoral macrophages to support adaptive immune responses
Associations betweenin vitro,in vivoandin silicocell classes in mouse primary visual cortex
Authors: Wei Yina , Nandi Anirban , Jia Xiaoxuan , Siegle Joshua H. , Denman Daniel , Lee Soo Yeun , Buchin Anatoly , Geit Werner Van , Mosher Clayton P. , Olsen Shawn , Anastassiou Costas A. 
Published: April 2023

AbstractThe brain consists of many cell classes yetin vivoelectrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modalin vitroproperties from experiments within vivorecorded units via computational modeling and optotagging experiments. We found two one-channel and six multi-channel clusters in mouse visual cortex with distinctin vivoproperties in terms of activity, cortical depth, and behavior. We used biophysical models to map the two one- and the six multi-channel clusters to specificin vitroclasses with unique morphology, excitability and conductance properties that explain their distinct extracellular signatures and functional characteristics. These concepts were tested in ground-truth optotagging experiments with two inhibitory classes unveiling distinctin vivoproperties. This multi-modal approach presents a powerful way to separatein vivoclusters and infer their cellular properties from first principles.
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Authors: Stevens Lewis , Martinez-Ugalde Isaac , King Erna , Wagah Martin , Absolon Dominic , Bancroft Rowan , Gonzalez de la Rosa Pablo , Hall Jessica L , Kieninger Manuela , Kloch Agnieszka , Pelan Sarah , Robertson Elaine , Pedersen Amy B , Abreu-Goodger Cei , Buck Amy H , Blaxter Mark 
Published: April 2023

AbstractHost-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to increased fitness of rare alleles, resulting in negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Despite their economic and ecological importance, there is limited evidence for balancing selection in parasitism-relevant genes in parasitic nematodes. Here, we sequenced the genomes of several individuals ofHeligmosomoides bakeri, a parasite of house mice that is a well-established model parasitic nematode, andHeligmosomoides polygyrus, a closely related parasite of wood mice. We combined our single nematode genome assemblies with chromatin conformation capture (Hi-C) libraries derived from pools of individuals to generate chromosome-level reference genomes for both species. AlthoughH. bakeriis commonly referred to asH. polygyrusin the literature, their genomes show levels of divergence that are consistent with millions of years of independent evolution. We found that theH. bakerigenome, which we expected to be highly homozygous through inbreeding, contained hundreds of hyper-divergent haplotypes, similar to those recently reported in free-living nematodes. Within these haplotypes, we found an enrichment of protein families that interact with the host immune response, including protease inhibitors and transthyretin-related proteins. We also found that many of these haplotypes originated prior to the divergence betweenH. bakeriandH. polygyrus, suggesting that they have been maintained since the last common ancestor of the two species by long-term balancing selection. Together, our results suggest that selection pressures exerted on parasites by their hosts have led to unexpected modes and levels of genetic diversity in the genomes of these economically and ecologically important species.