bluuebunny/crossref_metadata_2025_split huggingface dataset:
All insects matter: a review of 160 entomology cases from 1993 to 2007 in Switzerland—part I (Diptera)
Authors: Hodecek Jiri , Fumagalli Luca , Jakubec Pavel 
Published: December 2023

Abstract
Necrophagous Diptera are the most important group of insects used for the purposes of forensic entomology. While the most utilized fly family in this context is the family Calliphoridae, there are several other families that can be of great importance during real-case investigations. This article analyzes the necrophagous flies of all families recorded from 160 real cases in Switzerland between 1993 and 2007. A total of 56 species belonging to 16 families was identified with Calliphoridae being the most dominant family (90.63% of all cases), followed by Muscidae (26.25%), Sarcophagidae (19.38%), Phoridae (14.38%), and Fanniidae (12.50%). For specimens that were difficult to identify morphologically, a new PCR primer has been specifically designed for the amplification of a short, informative COI barcode in degraded museum samples of forensically important Diptera taxa. The richest family in terms of species was the family Muscidae with 16 species. Fannia fuscula (Fallen) and Fannia monilis (Haliday) were recorded from human cadavers for the first time. The study highlights the importance of different fly families in forensic investigation, enhancing our comprehension of their prevalence and dispersion in real cases in Central Europe. The results pave the way for additional exploration, especially regarding the involvement of less frequently observed species in forensic entomology.
Salvage surgery for mesenteric lymph node metastasis by resection of the first jejunal flap and reconstruction with the second jejunal flap
Authors: Kitano Daiki , Hashikawa Kazunobu , Furukawa Tatsuya , Nomura Tadashi , Tamagawa Kotaro , Sakakibara Shunsuke , Nibu Ken-ichi , Terashi Hiroto 
Published: December 2023

Abstract
We report a case of a second free jejunal transfer to treat metastasis in the mesenteric lymph node of the first jejunal flap. A 73-year-old man underwent total pharyngolaryngectomy, bilateral neck dissection, and free jejunal transfer for recurrent hypopharyngeal cancer [left pyriform sinus, pT2N0, moderately differentiated squamous cell carcinoma (SCC)] after radiotherapy. Seven years post-surgery, he underwent transoral videolaryngoscopic surgery for oropharyngeal cancer (soft palate, pT1N0, well-differentiated SCC). Ten years after the first jejunal transfer, metastasis was found in the mesenteric lymph node surrounding the jejunal flap’s vascular pedicle. Under general anesthesia, resection of the first jejunum including the affected lymph node, and second jejunal transfer were performed. Lymph node pathological examination revealed poorly differentiated SCC, compatible with pharyngeal cancer metastasis. After neck dissection and jejunal flap transfer, lymphatic collateral pathways toward the flap’s mesenteric lymph node might form. Possibly, hypopharyngeal or oropharyngeal cancer metastasized via this pathway.
A new simple and innovative technique for surgical drains fixation
Authors: Alsherawi Abeer , Al-Mohannadi Fatima Saoud , Ahmed Mohamed Badie 
Published: December 2023

Abstract
Seroma is a common complication post many plastic surgery procedures. To overcome this issue, drain insertion became a standard of care in many procedures. Existing methods for fixing the drain like the Roman sandal, purse string, and mesentery have limitations, including loosening and skin problems. A new, innovative, and efficient drain fixation technique is introduced in this paper. It involves using silk or similar non-absorbable sutures in a simple five-step process. This method ensures secure drain placement without undesirable outcomes. It avoids the need to force a knot over the skin, reducing the risk of skin damage or necrosis. In conclusion, the study introduces a straightforward, safe, and effective drain fixation method, reducing risks associated with fluid accumulation after surgery.
Reprogramming the translatome during daily light transitions as affected by cytosolic glyceraldehyde-3-phosphate dehydrogenases GAPC1/C2
Authors: Wegener Melanie , Persicke Marcus , Dietz Karl-Josef 
Published: December 2023

Abstract
Dark–light and light–dark transitions during the day are switching points of leaf metabolism that strongly affect the regulatory state of the cells, and this change is hypothesized to affect the translatome. The cytosolic glyceraldehyde-3-phosphate dehydrogenases GAPC1 and GAPC2 function in glycolysis, and carbohydrate and energy metabolism, but GAPC1/C2 also shows moonlighting functions in gene expression and post-transcriptional regulation. In this study we examined the rapid reprogramming of the translatome that occurs within 10 min at the end of the night and the end of the day in wild-type (WT) Arabidopsis and a gapc1/c2 double-knockdown mutant. Metabolite profiling compared to the WT showed that gapc1/c2 knockdown led to increases in a set of metabolites at the start of day, particularly intermediates of the citric acid cycle and linked pathways. Differences in metabolite changes were also detected at the end of the day. Only small sets of transcripts changed in the total RNA pool; however, RNA-sequencing revealed major alterations in polysome-associated transcripts at the light-transition points. The most pronounced difference between the WT and gapc1/c2 was seen in the reorganization of the translatome at the start of the night. Our results are in line with the proposed hypothesis that GAPC1/C2 play a role in the control of the translatome during light/dark transitions.
On the Use of a Cluster Identification Method and a Statistical Approach for Analyzing Atom Probe Tomography Data for GP Zones in Al–Zn–Mg(–Cu) Alloys
Authors: Shah Sohail , Thronsen Elisabeth , De Geuser Frederic , Hatzoglou Constantinos , Marioara Calin D , Holmestad Randi , Holmedal Bjørn 
Published: December 2023

Abstract
Early-stage clustering in two Al–Mg–Zn(–Cu) alloys has been investigated using atom probe tomography and transmission electron microscopy. Cluster identification by the isoposition method and a statistical approach based on the pair correlation function have both been applied to estimate the cluster size, composition, and volume fraction from atom probe data sets. To assess the accuracy of the quantification of clusters of different mean sizes, synthesized virtual data sets were used, accounting for a simulated degraded spatial resolution. The quality of the predictions made by the two complementary methods is discussed, considering the experimental and simulated data sets.
Color Standardization and Stain Intensity Calibration for Whole Slide Image-Based Immunohistochemistry Assessment
Authors: Ohnishi Chie , Ohnishi Takashi , Ibrahim Kareem , Ntiamoah Peter , Ross Dara , Yamaguchi Masahiro , Yagi Yukako 
Published: December 2023

Abstract
Automated quantification of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) using whole slide imaging (WSI) is expected to eliminate subjectivity in visual assessment. However, the color intensity in WSI varies depending on the staining process and scanner device. Such variations affect the image analysis results. This paper presents methods to diminish the influence of color variation produced in the staining process using a calibrator slide consisting of peptide-coated microbeads. The calibrator slide is stained along with tissue sample slides, and the 3,3′-diaminobenzidine (DAB) color intensities of the microbeads are used for calibrating the color variation of the sample slides. An off-the-shelf image analysis tool is employed for the automated assessment, in which cells are classified by the thresholds for the membrane staining. We have adopted two methods for calibrating the color variation based on the DAB color intensities obtained from the calibrator slide: (1) thresholds for classifying the DAB membranous intensity are adjusted, and (2) the color intensity of WSI is corrected. In the experiment, the calibrator slides and tissue of breast cancer slides were stained together on different days and used to test our protocol. With the proposed protocol, the discordance in the HER2 evaluation was reduced to one slide out of 120 slides.
Limits of water maser kinematics: insights from the high-mass protostar AFGL 5142-MM1
Authors: Rosli Zulfazli , Burns Ross A , Nazri Affan Adly , Sugiyama Koichiro , Hirota Tomoya , Kim Kee-Tae , Yonekura Yoshinori , Tie Liu , Orosz Gabor , Chibueze James Okwe , Sobolev Andrey M , Kang Ji Hyun , Lee Chang Won , Hwang Jihye , Mohammad Hafieduddin , Hashim Norsiah , Abidin Zamri Zainal 
Published: December 2023

ABSTRACT
Multi-epoch very long baseline interferometry (VLBI) observations measure three-dimensional water maser motions in protostellar outflows, enabling analysis of inclination and velocity. However, these analyses assume that water masers and shock surfaces within outflows are co-propagating. We compare VLBI data on maser-traced bow shocks in the high-mass protostar AFGL 5142-MM1, from seven epochs of archival data from the VLBI Exploration of Radio Astrometry (VERA), obtained from 2014 April to 2015 May, and our newly conducted data from the KVN and VERA Array (KaVA), obtained in 2016 March. We find an inconsistency between the expected displacement of the bow shocks and the motions of individual masers. The separation between two opposing bow shocks in AFGL 5142-MM1 was determined to be 337.17 ± 0.07 mas in the KaVA data, which is less than an expected value of 342.1 ± 0.7 mas based on extrapolation of the proper motions of individual maser features measured by VERA. Our measurements imply that the bow shock propagates at a velocity of 24 ± 3 km s−1, while the individual masing gas clumps move at an average velocity of 55 ± 5 km s−1; that is ,the water masers are moving in the outflow direction at double the speed at which the bow shocks are propagating. Our results emphasize that investigations of individual maser features are best approached using short-term high-cadence VLBI monitoring, while long-term monitoring on timescales comparable to the lifetimes of maser features is better suited to tracing the overall evolution of shock surfaces. Observers should be aware that masers and shock surfaces can move relative to each other, and that this can affect the interpretation of protostellar outflows.
Pre- and post-processing of cluster galaxies out to 5 × R200: the extreme case of A2670
Authors: Piraino-Cerda Franco , Jaffé Yara L , Lourenço Ana C , Crossett Jacob P , Salinas Vicente , Kim Duho , Sheen Yun-Kyeong , Kelkar Kshitija , Pallero Diego , Bravo-Alfaro Hector 
Published: December 2023

ABSTRACT
We study galaxy interactions in the large-scale environment around A2670, a massive (M200 = $8.5 \pm 1.2~\times 10^{14} \, \mathrm{{M}_{\odot }}$) and interacting galaxy cluster at z = 0.0763. We first characterize the environment of the cluster out to 5× R200 and find a wealth of substructures, including the main cluster core, a large infalling group, and several other substructures. To study the impact of these substructures (pre-processing) and their accretion into the main cluster (post-processing) on the member galaxies, we visually examined optical images to look for signatures indicative of gravitational or hydrodynamical interactions. We find that ∼21 per cent of the cluster galaxies have clear signs of disturbances, with most of those (∼60 per cent) likely being disturbed by ram pressure. The number of ram-pressure stripping candidates found (101) in A2670 is the largest to date for a single system, and while they are more common in the cluster core, they can be found even at &gt;4 × R200, confirming cluster influence out to large radii. In support of a pre-processing scenario, most of the disturbed galaxies follow the substructures found, with the richest structures having more disturbed galaxies. Post-processing also seems plausible, as many galaxy–galaxy mergers are seen near the cluster core, which is not expected in relaxed clusters. In addition, there is a comparable fraction of disturbed galaxies in and outside substructures. Overall, our results highlight the complex interplay of gas stripping and gravitational interactions in actively assembling clusters up to 5 × R200, motivating wide-area studies in larger cluster samples.
Synchrotron emission on FIRE: equipartition estimators of magnetic fields in simulated galaxies with spectrally resolved cosmic rays
Authors: Ponnada Sam B , Panopoulou Georgia V , Butsky Iryna S , Hopkins Philip F , Skalidis Raphael , Hummels Cameron , Quataert Eliot , Kereš Dušan , Faucher-Giguère Claude-André , Su Kung-Yi 
Published: December 2023

ABSTRACT
Synchrotron emission is one of few observable tracers of galactic magnetic fields (B) and cosmic rays (CRs). Much of our understanding of B in galaxies comes from utilizing synchrotron observations in conjunction with several simplifying assumptions of equipartition models, however, it remains unclear how well these assumptions hold, and what B these estimates physically represent. Using Feedback in Realistic Environments project simulations which self-consistently evolve CR proton, electron, and positron spectra from MeV to TeV energies, we present the first synthetic synchrotron emission predictions from simulated L* galaxies with ‘live’ spectrally resolved CR-magnetohydrodynamic. We find that synchrotron emission can be dominated by relatively cool and dense gas, resulting in equipartition estimates of B with fiducial assumptions underestimating the ‘true’ B in the gas that contributes the most emission by factors of 2–3 due to small volume-filling factors. Motivated by our results, we present an analytical framework that expands upon equipartition models for estimating B in a multiphase medium. Comparing our spectrally resolved synchrotron predictions to simpler spectral assumptions used in galaxy simulations with CRs, we find that spectral evolution can be crucial for accurate synchrotron calculations towards galactic centres, where loss terms are large.
Pumping and sliding of droplets steered by a hydrogel pattern for atmospheric water harvesting
Authors: Zhang Wei , Ji Qinghua , Zhang Gong , Gu Zhenao , Wang Haozhi , Hu Chengzhi , Liu Huijuan , Ren Zhiyong Jason , Qu Jiuhui 
Published: December 2023

ABSTRACT
Atmospheric water harvesting is an emerging strategy for decentralized and potable water supplies. However, water nucleation and microdroplet coalescence on condensing surfaces often result in surface flooding owing to the lack of a sufficient directional driving force for shedding. Herein, inspired by the fascinating properties of lizards and catfish, we present a condensing surface with engineered hydrogel patterns that enable rapid and sustainable water harvesting through the directional pumping and drag-reduced sliding of water droplets. The movement of microscale condensed droplets is synergistically driven by the surface energy gradient and difference in Laplace pressure induced by the arch hydrogel patterns. Meanwhile, the superhydrophilic hydrogel surface can strongly bond inner-layer water molecules to form a lubricant film that reduces drag and facilitates the sliding of droplets off the condensing surface. Thus, this strategy is promising for various water purification techniques based on liquid–vapor phase-change processes.
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
Authors: Zhang Dezhi , She Huishang , Wang Shangyu , Wang Haitao , Li Shi , Cheng Yalin , Song Gang , Jia Chenxi , Qu Yanhua , Rheindt Frank E , Olsson Urban , Alström Per , Lei Fumin 
Published: December 2023

Abstract
Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski’s bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which—in combination—support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance
Authors: Avadhanula Vasanthi , Agustinho Daniel Paiva , Menon Vipin Kumar , Chemaly Roy F , Shah Dimpy P , Qin Xiang , Surathu Anil , Doddapaneni Harshavardhan , Muzny Donna M , Metcalf Ginger A , Cregeen Sara Javornik , Gibbs Richard A , Petrosino Joseph F , Sedlazeck Fritz J , Piedra Pedro A 
Published: December 2023

Abstract
Respiratory syncytial virus (RSV) infection in immunocompromised individuals often leads to prolonged illness, progression to severe lower respiratory tract infection, and even death. How the host immune environment of the hematopoietic stem cell transplant (HCT) adults can affect viral genetic variation during an acute infection is not understood well. In the present study, we performed whole genome sequencing of RSV/A or RSV/B from samples collected longitudinally from HCT adults with normal (&lt;14 days) and delayed (≥14 days) RSV clearance who were enrolled in a ribavirin trial. We determined the inter-host and intra-host genetic variation of RSV and the effect of mutations on putative glycosylation sites. The inter-host variation of RSV is centered in the attachment (G) and fusion (F) glycoprotein genes followed by polymerase (L) and matrix (M) genes. Interestingly, the overall genetic variation was constant between normal and delayed clearance groups for both RSV/A and RSV/B. Intra-host variation primarily occurred in the G gene followed by non-structural protein (NS1) and L genes; however, gain or loss of stop codons and frameshift mutations appeared only in the G gene and only in the delayed viral clearance group. Potential gain or loss of O-linked glycosylation sites in the G gene occurred both in RSV/A and RSV/B isolates. For RSV F gene, loss of N-linked glycosylation site occurred in three RSV/B isolates within an antigenic epitope. Both oral and aerosolized ribavirin did not cause any mutations in the L gene. In summary, prolonged viral shedding and immune deficiency resulted in RSV variation, especially in structural mutations in the G gene, possibly associated with immune evasion. Therefore, sequencing and monitoring of RSV isolates from immunocompromised patients are crucial as they can create escape mutants that can impact the effectiveness of upcoming vaccines and treatments.
Quantitative comparison of presenilin protein expression reveals greater activity of PS2‐γ‐secretase
Authors: Eccles Melissa K. , Main Nathan , Carlessi Rodrigo , Armstrong Ayeisha Milligan , Sabale Miheer , Roberts‐Mok Brigid , Tirnitz‐Parker Janina E. E. , Agostino Mark , Groth David , Fraser Paul E. , Verdile Giuseppe 
Published: December 2023

Abstractγ‐secretase processing of amyloid precursor protein (APP) has long been of interest in the pathological progression of Alzheimer's disease (AD) due to its role in the generation of amyloid‐β. The catalytic component of the enzyme is the presenilins of which there are two homologues, Presenilin‐1 (PS1) and Presenilin‐2 (PS2). The field has focussed on the PS1 form of this enzyme, as it is typically considered the more active at APP processing. However, much of this work has been completed without appropriate consideration of the specific levels of protein expression of PS1 and PS2. We propose that expression is an important factor in PS1‐ and PS2‐γ‐secretase activity, and that when this is considered, PS1 does not have greater activity than PS2. We developed and validated tools for quantitative assessment of PS1 and PS2 protein expression levels to enable the direct comparison of PS in exogenous and endogenous expression systems, in HEK‐293 PS1 and/or PS2 knockout cells. We show that exogenous expression of Myc‐PS1‐NTF is 5.5‐times higher than Myc‐PS2‐NTF. Quantitating endogenous PS protein levels, using a novel PS1/2 fusion standard we developed, showed similar results. When the marked difference in PS1 and PS2 protein levels is considered, we show that compared to PS1‐γ‐secretase, PS2‐γ‐secretase has equal or more activity on APP and Notch1. This study has implications for understanding the PS1‐ and PS2‐specific contributions to substrate processing, and their potential influence in AD pathogenesis.
Clinical Predictors of Major Intrathoracic Injury in Pediatric Blunt Trauma
Authors: Gunnink Stephen M. , Butz Alysa M. , Griep Jordan , Starrs Mary , Ponkowski Michael , Parker Jessica L. , Benner Christopher 
Published: December 2023

Objectives
Blunt trauma in pediatric patients accounts for a significant proportion of pediatric death from traumatic injury. Currently, there are no clinical decision-making tools available to guide imaging choice in the evaluation of pediatric patients with blunt thoracic trauma (BTT). This study aimed to analyze the rates of missed major intrathoracic injuries on chest x-ray (CXR) and identify clinical risk factors associated with major intrathoracic injuries to formulate a clinical decision-making tool for computed tomography (CT) use in pediatric patients with BTT.

Methods
We performed a retrospective single-center study using an institutional trauma database of pediatric patients. Inclusion criteria included age, blunt trauma, and patients who received a CXR and thoracic CT within 24 hours of presentation. Thoracic CT findings were graded as major, minor, or none, and comparison CXR was used to determine the rate of missed thoracic injuries. Eighty-four patient variables were then collected, and clinically relevant variables associated with major intrathoracic injuries were placed in a logistic regression model to determine the best predictors of major injury in pediatric BTT patients.

Results
A total of 180 patients (48.3%) had CXR that missed an injury that was seen on thoracic CT. In our cohort, 20 patients (5.4%) had major injuries that were missed on CXR. Characteristics correlating with major thoracic injuries were older age (odds ratio [OR], 1.125; 95% confidence interval [CI], 1.015–1.247), chest pain (OR, 4.907; 95% CI, 2.173–11.083), abnormal chest auscultation (OR, 3.564; 95% CI, 1.406–9.035), and tachycardia (OR, 2.876; 95% CI, 1.256–6.586). Using these 4 variables, receiver operating characteristic analysis revealed an area under the curve of 0.7903.

Conclusions
Pediatric BTT patients older than 15 years with tachycardia, chest pain, or abnormal chest auscultation are at increased risk for major intrathoracic injuries and may benefit from thoracic CT.