bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Channel‐Spanning Engineered Logjam Structures on Channel Hydrodynamics
Authors: Müller S. , Follett E. M. , Ouro P. , Wilson C. A. M. E. 
Published: December 2022

AbstractNature‐based solutions to flood risk management, such as engineered logjams (ELJs), contribute to the reintroduction of wood in rivers. As part of stream restoration, and utilized in tributaries, ELJs increase upstream water levels, causing the flow to spill onto surrounding floodplains, resulting in the desynchronization of peak flows in a river network. To understand the effect of ELJs on local river hydrodynamics, we experimentally investigate the flow field upstream and downstream of six ELJs, using acoustic Doppler velocimetry and flow visualization. We consider channel‐spanning structures designed with a gap (b0) underneath, allowing unhindered baseflow. Our results revealed that upstream of the logjams, flow diverted toward the lower gap, creating a primary jet exiting underneath the structures, whose strength depends on the physical logjam design. Maximum jet velocities remained constant until a downstream distance of 4b0 for all logjams. The upper wake was structure‐dependent, with logjam structures allowing distinct internal flow paths generating secondary jets, which influenced near wake decay (x < 4b0) and turbulent mixing. The highest turbulence in the near wake was found for the non‐porous and short, porous logjam designs, while the upper wake of all long, porous logjams was characterized by low turbulent kinetic energy levels. Far wake decay (x > 4b0) was self‐similar for all logjams and resulted in near flow recovery at downstream streamwise distances greater than 35b0. ELJs are likely to enhance bed shear stress, increasing the risk of local scour and sediment mobilization. Our study expands the current knowledge of ELJ hydrodynamics and highlights potential implications for the riverine ecosystem.
Impacts of Subgrid Temperature Distribution Along Elevation Bands in Snowpack Modeling: Insights From a Suite of Andean Catchments
Authors: Murillo Octavio , Mendoza Pablo A. , Vásquez Nicolás , Mizukami Naoki , Ayala Álvaro 
Published: December 2022

AbstractThe implementation of elevation bands is a popular strategy to account for topographic heterogeneities in snowpack modeling. Here, we characterize the implications of subgrid temperature distribution along elevation bands through numerical experiments in nine mountainous basins of the Andes Cordillera, central Chile. Specifically, we analyze outputs from the Variable Infiltration Capacity model with six different setups: no elevation bands (i.e., flat grid cells; benchmark model) and elevation bands with vertical discretizations of 1,000, 750, 500, 200, and 100 m. The analyses are conducted in a wet period (April/1982–March/1987), dry period (April/2010–March/2015) and a climatological period (April/1982–March/2015). The results show that adding elevation bands yields little variations in simulated monthly or daily streamflow; however, there are important effects on the partitioning of precipitation between snowfall and rainfall, snowmelt, sublimation, and the spatial variability in 1 September snow water equivalent (SWE), suggesting a form of model‐structure equifinality. Vertical temperature distribution generally yields less basin‐averaged snowmelt and more (less) catchment‐scale sublimation across water‐limited (energy‐limited) basins. Further, the implications of subgrid temperature distribution vary with the analysis period: fluxes are more affected during the wet period, while variations in 1 September SWE are more noticeable during the dry period. In general, the effects of topographic temperature distribution are reduced with increasing vertical discretization and can differ among catchments. Finally, the grid cells that yield the largest sensitivities to vertical discretization have relatively more humid conditions, large intra‐annual variations in the water/energy budget, lower mean altitude, elevation ranges >1,000 m, and steep slopes (>15°).
Perinatal and neonatal outcomes for fetoscopic laser ablation for the treatment of twin twin transfusion syndrome at a single center
Authors: Ling Diamond , Phelps Alexandra , Tate Tabitha , Adefisoye James , Mehra Suwan , Prazad Preetha 
Published: December 2022

Abstract
Objective
To describe the perinatal and neonatal outcomes of fetal laser ablation (FLA) for the treatment of twin-twin transfusion syndrome (TTTS) in our single center institution.

Study design
Retrospective study of 76 treated pregnant women. Procedural complications, perinatal and neonatal outcomes analyzed. Differences in outcomes between two procedural techniques, selective and Solomon, compared.

Results
FLA occurred at median gestational age (GA) of 20.8 weeks (IQR 18.1–22.9) with low incidence of procedural complications (5.3%). High survival rate with delivery of at least one neonate (96%) [95% CI: 88.9–99.2%]; 73.7% [95% CI: 62.3–83.1%] were twins. Median GA at birth was 33.1 weeks (IQR 28.0–35.0). Neonatal mortality and morbidities were 9.4% and 48.3% of cases respectively, and associated with lower GA. Solomon cases had comparatively higher median GA, and lower incidences of neonatal morbidities.

Conclusion
Our small single center study showed favorable outcomes for using the Solomon technique in the treatment of TTTS.
Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi
Authors: Stirrup Rachel , Mausz Michaela A , Silvano Eleonora , Murphy Andrew , Guillonneau Richard , Quareshy Mussa , Rihtman Branko , Ferretjans Maria Aguilo , He Ruo , Todd Jonathan D , Chen Feng , Scanlan David J , Chen Yin 
Published: December 2022

Abstract
Lipids play a crucial role in maintaining cell integrity and homeostasis with the surrounding environment. Cosmopolitan marine roseobacter clade (MRC) and SAR11 clade bacteria are unique in that, in addition to glycerophospholipids, they also produce an array of amino acid-containing lipids that are conjugated with beta-hydroxy fatty acids through an amide bond. Two of these aminolipids, the ornithine aminolipid (OL) and the glutamine aminolipid (QL), are synthesized using the O-acetyltransferase OlsA. Here, we demonstrate that OL and QL are present in both the inner and outer membranes of the Gram-negative MRC bacterium Ruegeria pomeroyi DSS-3. In an olsA mutant, loss of these aminolipids is compensated by a concurrent increase in glycerophospholipids. The inability to produce aminolipids caused significant changes in the membrane proteome, with the membrane being less permeable and key nutrient transporters being downregulated while proteins involved in the membrane stress response were upregulated. Indeed, the import of 14C-labelled choline and dimethylsulfoniopropionate, as a proxy for the transport of key marine nutrients across membranes, was significantly impaired in the olsA mutant. Moreover, the olsA mutant was significantly less competitive than the wild type (WT) being unable to compete with the WT strain in co-culture. However, the olsA mutant unable to synthesize these aminolipids is less susceptible to phage attachment. Together, these data reveal a critical role for aminolipids in the ecophysiology of this important clade of marine bacteria and a trade-off between growth and avoidance of bacteriophage attachment.
Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma
Authors: Murumägi Astrid , Ungureanu Daniela , Khan Suleiman , Arjama Mariliina , Välimäki Katja , Ianevski Aleksandr , Ianevski Philipp , Bergström Rebecka , Dini Alice , Kanerva Anna , Koivisto-Korander Riitta , Tapper Johanna , Lassus Heini , Loukovaara Mikko , Mägi Andrus , Hirasawa Akira , Aoki Daisuke , Pietiäinen Vilja , Pellinen Teijo , Bützow Ralf , Aittokallio Tero , Kallioniemi Olli 
Published: December 2022

AbstractMany efforts are underway to develop novel therapies against the aggressive high-grade serous ovarian cancers (HGSOCs), while our understanding of treatment options for low-grade (LGSOC) or mucinous (MUCOC) of ovarian malignancies is not developing as well. We describe here a functional precision oncology (fPO) strategy in epithelial ovarian cancers (EOC), which involves high-throughput drug testing of patient-derived ovarian cancer cells (PDCs) with a library of 526 oncology drugs, combined with genomic and transcriptomic profiling. HGSOC, LGSOC and MUCOC PDCs had statistically different overall drug response profiles, with LGSOCs responding better to targeted inhibitors than HGSOCs. We identified several subtype-specific drug responses, such as LGSOC PDCs showing high sensitivity to MDM2, ERBB2/EGFR inhibitors, MUCOC PDCs to MEK inhibitors, whereas HGSOCs showed strongest effects with CHK1 inhibitors and SMAC mimetics. We also explored several drug combinations and found that the dual inhibition of MEK and SHP2 was synergistic in MAPK-driven EOCs. We describe a clinical case study, where real-time fPO analysis of samples from a patient with metastatic, chemorefractory LGSOC with a CLU-NRG1 fusion guided clinical therapy selection. fPO-tailored therapy with afatinib, followed by trastuzumab and pertuzumab, successfully reduced tumour burden and blocked disease progression over a five-year period. In summary, fPO is a powerful approach for the identification of systematic drug response differences across EOC subtypes, as well as to highlight patient-specific drug regimens that could help to optimise therapies to individual patients in the future.
Body composition, physical activity, and quality of life in pediatric patients with inflammatory bowel disease on anti-TNF therapy—an observational follow-up study
Authors: Boros Kriszta Katinka , Veres Gábor , Cseprekál Orsolya , Pintér Hajnalka Krisztina , Richter Éva , Cseh Áron , Dezsőfi-Gottl Antal , Arató András , Reusz György , Dohos Dóra , Müller Katalin Eszter 
Published: December 2022

Abstract
Background
Poor outcome of inflammatory bowel disease (IBD) is associated with malnutrition. Our aim was to compare body composition (BC) and physical activity (PA) between patients with IBD and healthy controls, and to assess the changes in BC, PA and health related quality of life (HRQoL) in children with IBD during anti-TNF therapy.

Methods
32 children with IBD (21 with Crohn’s disease (CD), (age: 15.2 ± 2.6 years, 9 male) and 11 with ulcerative colitis (UC), (age: 16.4 ± 2.2 years, 5 male) participated in this prospective, observational follow up study conducted at Semmelweis University, Hungary. As control population, 307 children (age: 14.3 ± 2.1) (mean ± SD) were included. We assessed BC via bioelectric impedance, PA and HRQoL by questionnaires at initiation of anti-TNF therapy, and at two and six months later. The general linear model and Friedman test were applied to track changes in each variable.

Results
During follow-up, the fat-free mass Z score of children with CD increased significantly (-0.3 vs 0.1, p = 0.04), while the BC of patients with UC did not change. PA of CD patients was lower at baseline compared to healthy controls (1.1 vs. 2.4), but by the end of the follow up the difference disappeared.

Conclusions
The fat-free mass as well as PA of CD patients increased during the first six months of anti-TNF treatment. As malnutrition and inactivity affects children with IBD during an important physical and mental developmental period, encouraging them to engage in more physical activity, and monitoring nutritional status should be an important goal in patient care.
Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses
Authors: Ecke Frauke , Han Barbara A. , Hörnfeldt Birger , Khalil Hussein , Magnusson Magnus , Singh Navinder J. , Ostfeld Richard S. 
Published: December 2022

AbstractPopulation fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species’ synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world.
Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase
Authors: Cui Ning , Zhang Jun-Tao , Li Zhuolin , Liu Xiao-Yu , Wang Chongyuan , Huang Hongda , Jia Ning 
Published: December 2022

AbstractThe RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMPcrRNA and gRAMPcrRNA-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions −1 and −2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity.
Direct retrieval of Zernike-based pupil functions using integrated diffractive deep neural networks
Authors: Goi Elena , Schoenhardt Steffen , Gu Min 
Published: December 2022

AbstractRetrieving the pupil phase of a beam path is a central problem for optical systems across scales, from telescopes, where the phase information allows for aberration correction, to the imaging of near-transparent biological samples in phase contrast microscopy. Current phase retrieval schemes rely on complex digital algorithms that process data acquired from precise wavefront sensors, reconstructing the optical phase information at great expense of computational resources. Here, we present a compact optical-electronic module based on multi-layered diffractive neural networks printed on imaging sensors, capable of directly retrieving Zernike-based pupil phase distributions from an incident point spread function. We demonstrate this concept numerically and experimentally, showing the direct pupil phase retrieval of superpositions of the first 14 Zernike polynomials. The integrability of the diffractive elements with CMOS sensors shows the potential for the direct extraction of the pupil phase information from a detector module without additional digital post-processing.
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
Authors: Kjær Kurt H. , Winther Pedersen Mikkel , De Sanctis Bianca , De Cahsan Binia , Korneliussen Thorfinn S. , Michelsen Christian S. , Sand Karina K. , Jelavić Stanislav , Ruter Anthony H. , Schmidt Astrid M. A. , Kjeldsen Kristian K. , Tesakov Alexey S. , Snowball Ian , Gosse John C. , Alsos Inger G. , Wang Yucheng , Dockter Christoph , Rasmussen Magnus , Jørgensen Morten E. , Skadhauge Birgitte , Prohaska Ana , Kristensen Jeppe Å. , Bjerager Morten , Allentoft Morten E. , Coissac Eric ,   PhyloNorway Consortium, Alsos Inger Greve , Coissac Eric , Rouillard Alexandra , Simakova Alexandra , Fernandez-Guerra Antonio , Bowler Chris , Macias-Fauria Marc , Vinner Lasse , Welch John J. , Hidy Alan J. , Sikora Martin , Collins Matthew J. , Durbin Richard , Larsen Nicolaj K. , Willerslev Eske 
Published: December 2022

AbstractLate Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6(eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
A transcriptional switch controls sex determination in Plasmodium falciparum
Authors: Gomes A. R. , Marin-Menendez A. , Adjalley S. H. , Bardy C. , Cassan C. , Lee M. C. S. , Talman A. M. 
Published: December 2022

AbstractSexual reproduction and meiotic sex are deeply rooted in the eukaryotic tree of life, but mechanisms determining sex or mating types are extremely varied and are only well characterized in a few model organisms1. In malaria parasites, sexual reproduction coincides with transmission to the vector host. Sex determination is non-genetic, with each haploid parasite capable of producing either a male or a female gametocyte in the human host2. The hierarchy of events and molecular mechanisms that trigger sex determination and maintenance of sexual identity are yet to be elucidated. Here we show that the male development 1 (md1) gene is both necessary and sufficient for male fate determination in the human malaria parasitePlasmodium falciparum. We show that Md1 has a dual function stemming from two separate domains: in sex determination through its N terminus and in male development from its conserved C-terminal LOTUS/OST-HTH domain. We further identify a bistable switch at themd1locus, which is coupled with sex determination and ensures that the male-determining gene is not expressed in the female lineage. We describe one of only a few known non-genetic mechanisms of sex determination in a eukaryote and highlight Md1 as a potential target for interventions that block malaria transmission.
Nonstationary footprints of ENSO in the Mekong River Delta hydrology
Authors: Watanabe Takaaki K. , Phan Tung Thanh , Yamazaki Atsuko , Chiang Hong-Wei , Shen Chuan-Chou , Doan Lam Dinh , Watanabe Tsuyoshi 
Published: December 2022

AbstractThe Mekong River Delta (MRD) is an essential agricultural area for the worldwide rice supply. Floods and droughts triggered by El Niño southern oscillation (ENSO) have been threatening sustenance in the MRD. Sustainable food supplies require understanding the response of the MRD hydrology to the changing ENSO behaviour in recent decades. Here, we reconstructed the annual rainfall maxima in the MRD using the oceanic paleoclimate proxy from coral skeletons and compared them with ENSO indexes. Annual minima of coral-based seawater oxygen isotope (δ18Osw) correlated with annual rainfall maxima, which allowed to extend rainfall data from 1924 to the recent. The annual rainfall maxima based on δ18Osw negatively correlated with the central Pacific El Niño index. This suggested that La Niña and central Pacific El Niño events lead to heavy and light rainy seasons. The heavy rainy season had more serious impacts in recent decades, which likely increases the flood risk. In contrast, the frequency and rainfall amount of the light rainy season has not changed significantly, although a catastrophic drought has hit the MRD. Our finding concludes that the impact of the ENSO event on MRD hydrology is inconsistent in the past century.
Live imaging of apoptotic signaling flow using tunable combinatorial FRET-based bioprobes for cell population analysis of caspase cascades
Authors: Suzuki Miho , Shindo Yutaka , Yamanaka Ryu , Oka Kotaro 
Published: December 2022

AbstractUnderstanding cellular signaling flow is required to comprehend living organisms. Various live cell imaging tools have been developed but challenges remain due to complex cross-talk between pathways and response heterogeneities among cells. We have focused on multiplex live cell imaging for statistical analysis to address the difficulties and developed simple multiple fluorescence imaging system to quantify cell signaling at single-cell resolution using Förster Resonance Energy Transfer (FRET)-based chimeric molecular sensors comprised of fluorescent proteins and dyes. The dye-fluorescent protein conjugate is robust for a wide selection of combinations, facilitating rearrangement for coordinating emission profile of molecular sensors to adjust for visualization conditions, target phenomena, and simultaneous use. As the molecular sensor could exhibit highly sensitive in detection for protease activity, we customized molecular sensor of caspase-9 and combine the established sensor for caspase-3 to validate the system by observation of caspase-9 and -3 dynamics simultaneously, key signaling flow of apoptosis. We found cumulative caspase-9 activity rather than reaction rate inversely regulated caspase-3 execution times for apoptotic cell death. Imaging-derived statistics were thus applied to discern the dominating aspects of apoptotic signaling unavailable by common live cell imaging and proteomics protein analysis. Adopted to various visualization targets, the technique can discriminate between rivalling explanations and should help unravel other protease involved signaling pathways.