bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the difficulty of laparoscopic cholecystectomy during COVID-19 pandemic using externally validated prediction models: A retrospective cohort study
Authors: Hatampour Kasra , Ebrahimian Manoochehr , Zamani Amir , Zardoui Arshia , Ramezani Amirreza , Ghahremanloo Kimia , Mirhashemi Seyed Hadi , Soori Mohsen , Rashnoo Fariborz , Asil Rouzbeh Shadidi , Hajinasrollah Esmaeil 
Published: November 2023

Abstract

Introduction
During the COVID-19 pandemic, elective surgeries suspension, led to delayed hospital visits for non-emergent diseases like acute cholecystitis. Although nonsurgical treatment was successful in numerous cases, there are some warnings about the progression of the disease to more advanced stages for laparoscopy. In this study, we aimed to find out if COVID-19 had adverse effects on the difficulty of laparoscopic cholecystectomy (LC).

Methods
In a retrospective cohort study at a referral center for minimally-invasive surgeries, medical records from February 2019 to February 2020 (before the pandemic) and from February 2020 until 2021 (during the outbreak) were reviewed and various data were extracted. Using two different preoperative scoring systems, we estimated the rate of difficulty of LCs, and the results compared to each other with appropriate statistical methods.

Results
A total of 531 LCs were performed. Pre-COVID and post-COVID patients had a mean age of 46 ± 15 and 44 ± 14 years old, respectively, and less than 35 % of patients in each group were males. LCs decreased notably during the pandemic (161 vs. 369, p < 0.001). Besides, elective surgeries were reduced in this period (36.6 % vs. 55.7 %, p < 0.001). Despite no significant changes in operation duration (123 ± 42 vs. 129 ± 40, p = 0.16), scoring models revealed a remarkable change in difficulties.

Conclusion
Using two well-established scoring models, we concluded that LCs were done with less difficulty during that period. However, there was a remarkable decrease in elective surgeries, and higher volume studies are required to confirm our results.

Highlights
A Shallow‐Deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model
Authors: Khouider B. , Goswami B. B. , Phani R. , Majda A. J. 
Published: November 2023

AbstractCumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.
The Temperature Control of Cloud Adiabatic Fraction and Coverage
Authors: Lu Xin , Mao Feiyue , Rosenfeld Daniel , Zhu Yannian , Zang Lin , Pan Zengxin , Gong Wei 
Published: November 2023

AbstractThe fraction of cloud water compared to its adiabatic value is defined as the adiabatic fraction, fad. The accuracy of cloud representation in climate models is highly sensitive to mixing rate, manifested in fad. Here, we present the first fad distribution of marine boundary layer clouds over global oceans, retrieved by satellite observations. The fad is shown to decrease exponentially with cloud base temperature (CBT) and cloud depth, in agreement with the increasing evaporation capacity of entrained warmer air. Cloud cover decreases with increasing CBT, but to a much lesser extent than fad. The dependence of fad on CBT has little dependence on relative humidity or precipitation. The relationship between CBT and fad highlights the importance of CBT as a core control factor on cloud evaporation. The simultaneous decrease in cloud water content and cover with increasing CBT can lead to positive cloud feedback, resulting in greater future climate warming.
Asymmetry of AMOC Hysteresis in a State‐Of‐The‐Art Global Climate Model
Authors: van Westen René M. , Dijkstra Henk A. 
Published: November 2023

AbstractWe study hysteresis properties of the Atlantic Meridional Overturning Circulation (AMOC) under a slowly‐varying North Atlantic (20°N–50°N) freshwater flux forcing in state‐of‐the‐art global climate model (GCM), the Community Earth System Model. Results are presented of a full hysteresis simulation (4,400 model years) and show that there is a hysteresis width of about 0.4 Sv. This demonstrates that an AMOC collapse and recovery do not only occur in conceptual and idealized climate models, but also in a state‐of‐the‐art GCM. The AMOC recovery is about a factor six faster than the AMOC collapse and this asymmetry is due to the major effect of the North Atlantic sea‐ice distribution on the AMOC recovery. The results have implications for projections of possible future AMOC behavior and for explaining relatively rapid climate transitions in the geological past.
Summertime Near‐Surface Temperature Biases Over the Central United States in Convection‐Permitting Simulations
Authors: Qin Hongchen , Klein Stephen A. , Ma Hsi‐Yen , Van Weverberg Kwinten , Feng Zhe , Chen Xiaodong , Best Martin , Hu Huancui , Leung L. Ruby , Morcrette Cyril J. , Rumbold Heather , Webster Stuart 
Published: November 2023

AbstractConvection‐Permitting Model (CPM) simulations of the Central United States climate for the summer of 2011 are studied to understand the causes of warm biases in 2‐m air temperature (T2m) and related underestimates of precipitation including that from mesoscale convective systems (MCSs). Based on 10 CPM simulations and 9 coarser‐resolution model simulations, we quantify contributions from evaporative fraction (EF) and radiation to the T2m bias with both types of models overestimating T2m largely because they underestimate EF. The performance of CPMs in capturing MCS characteristics (frequency, rainfall, propagation) varies. The pre‐summer precipitation bias has large correlation with mean summertime T2m bias but the relationship between summertime MCS mean rainfall bias and T2m bias is non‐monotonic. Analysis of lifting condensation level deficit and convective available potential energy suggests that models with T2m warm biases and low EF have too dry and stable boundary layers, inhibiting the formation of clouds, precipitation and MCSs. Among the CPMs with differing model formulations (e.g., transpiration, infiltration, cloud macrophysics and microphysics), evidence suggests that altering the land‐surface model is more effective than altering the atmospheric model in reducing T2m biases. These results demonstrate that land‐atmosphere interactions play a very important role in determining the summertime climate of the Central United States.
Fast Calculation on Atmospheric Rayleigh Scattering Extinction Optical Depth for Day/Night Band Radiative Transfer Model With Periodic Lunar Illumination
Authors: Liu Shuyue , Min Min , Di Di 
Published: November 2023

AbstractRayleigh scattering effect inspired by tiny atmospheric molecules generates significant extinction at relatively short wavelength, such as Day/Night Band (DNB) covering visible (VIS, 0.4–0.76 μm) and near‐infrared (NIR, 0.76–1.0 μm) wavelengths. This salient extinction effect coupled with periodic changes in lunar illumination and wide DNB will further lead to increased complexity in nocturnal fast radiative transfer model (RTM) calculation of DNB. For these reasons, this study is aimed at developing a precise and robust fast calculation method on Rayleigh scattering extinction optical depth (RayOD) for pertinent fast RTM calculation of DNB. Firstly, we coupled the lunar spectral irradiance model and the parameterized Rayleigh scattering extinction calculation module into a RTM for forward simulations. Moreover, we find that the errors in DNB‐averaged RayOD calculated from the classical fast algorithm from RTTOV (Radiative Transfer for TOVS) of training the DNB instrument coefficients (about 20% of relative error in reflectance) and the parameterization method using the central wavelength of DNB (about 5%) are too large to be tolerable in fast RTM. Finally, to address this issue, we skillfully conceptualize a new equivalent optimal central wavelength algorithm to retrieve a dynamically wavelength in DNB using observation scattering and lunar phase angles for rapidly calculating DNB‐averaged RayOD. The relative errors in simulated reflectance from coupled RTM aforementioned are subtle nuances, which are about 10−5∼10−6 order of magnitude. Besides, this robust algorithm can also correct the relative error of about 1% at dark surface caused by periodic changes in lunar illumination.
10Be Exposure Age Dating of Moraine Boulders and Glacially Polished Bedrock Surfaces in Karakoram and Ladakh Ranges, NW Himalaya: Implications in Quaternary Glaciation Studies
Authors: Jena Partha Sarathi , Bhushan Ravi , Sharma Shubhra , Dabhi Ankur J. , Ajay Shivam , Raj Harsh , Juyal Navin 
Published: November 2023

AbstractTerrestrial cosmogenic nuclide (TCN) dating has emerged as one of the most useful techniques in the last two decades for quantifying geomorphological processes and building the chronology of late Quaternary glacial advances/retreats. The chronology based on TCN and optically stimulated luminescence (OSL) dating of glacial landforms from the northwestern (NW) Himalaya suggests that glaciers responded to a complex interaction between temperature and moisture essentially derived from either of the climate systems, the Indian Summer Monsoon (ISM) and the Mid‐latitude Westerlies (MLW). The discrepancies between the TCN ages obtained on moraine boulders/bedrock surfaces, and the OSL ages on the stratigraphically equivalent deposits, highlighted the need for a detailed investigation. The present study attempts to build the chronology of Quaternary glaciation events in the Karakoram and Ladakh Ranges using TCN dating of stratigraphically constrained moraine boulders and striated bedrock surfaces. The TCN ages from glacially eroded surfaces (GES) having prominent striations are narrowly clustered around the Marine Isotopic Stage‐2 (MIS‐2). Agreement between GES TCN ages and OSL ages on the stratigraphically equivalent moraines suggests negligible geological inheritance. The glacial advance during MIS‐2 can be attributed to the combined effect of reduction in north hemispheric insolation and enhanced westerly precipitation. However, relict non‐glacial surfaces and moraine boulders with minimal ice flow modifications yield wide age distributions, most likely suggesting denudational events (interglacials) and/or contribution from tributary valley flanks.
NINJ1 is activated by cell swelling to regulate plasma membrane permeabilization during regulated necrosis
Authors: Dondelinger Yves , Priem Dario , Huyghe Jon , Delanghe Tom , Vandenabeele Peter , Bertrand Mathieu J. M. 
Published: November 2023

AbstractPlasma membrane permeabilization (PMP) is a defining feature of regulated necrosis. It allows the extracellular release of damage-associated molecular patterns (DAMPs) that trigger sterile inflammation. The pore forming molecules MLKL and GSDMs drive PMP in necroptosis and pyroptosis, respectively, but the process of PMP remains unclear in many other forms of regulated necrosis. Here, we identified NINJ1 as a crucial regulator of PMP and consequent DAMP release during ferroptosis, parthanatos, H2O2-induced necrosis and secondary necrosis. Importantly, the membrane-permeabilizing function of NINJ1 takes place after the metabolic death of the cells and is independent of the pore-forming molecules MLKL, GSDMD and GSDME. During ferroptosis, NINJ1 acts downstream of lipid peroxidation, which suggested a role for reactive oxygen species (ROS) in NINJ1 activation. Reactive oxygen species were however neither sufficient nor required to trigger NINJ1-dependent PMP. Instead, we found that NINJ1 oligomerization is induced by the swelling of the cell and that its permeabilizing potential still requires an addition, and yet to be discovered, activation mechanism.
Iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway
Authors: Li Hong-Ying , Wei Ting-Ting , Zhuang Miao , Tan Cheng-Ye , Xie Tian-Hua , Cai Jiping , Yao Yong , Zhu Lingpeng 
Published: November 2023

AbstractCellular senescence is a hallmark of aging and has been linked to age-related diseases. Age-related macular degeneration (AMD), the most common aging-related retinal disease, is prospectively associated with retinal pigment epithelial (RPE) senescence. However, the mechanism of RPE cell senescence remains unknown. In this study, tert-butyl hydroperoxide (TBH)-induced ARPE-19 cells and D-galactose-treated C57 mice were used to examine the cause of elevated iron in RPE cell senescence. Ferric ammonium citrate (FAC)-treated ARPE-19 cells and C57 mice were used to elucidated the mechanism of iron overload-induced RPE cell senescence. Molecular biology techniques for the assessment of iron metabolism, cellular senescence, autophagy, and mitochondrial function in vivo and in vitro. We found that iron level was increased during the senescence process. Ferritin, a major iron storage protein, is negatively correlated with intracellular iron levels and cell senescence. NCOA4, a cargo receptor for ferritinophagy, mediates degradation of ferritin and contributes to iron accumulation. Besides, we found that iron overload leads to mitochondrial dysfunction. As a result, mitochondrial DNA (mtDNA) is released from damaged mitochondria to cytoplasm. Cytoplasm mtDNA activates the cGAS-STING pathway and promotes inflammatory senescence-associated secretory phenotype (SASP) and cell senescence. Meanwhile, iron chelator Deferoxamine (DFO) significantly rescues RPE senescence and retinopathy induced by FAC or D-gal in mice. Taken together, these findings imply that iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway. Inhibiting iron accumulation may represent a promising therapeutic approach for age-related diseases such as AMD.
Intravitreal anti-vascular endothelial growth factor injections in pregnancy and breastfeeding: a case series and systematic review of the literature
Authors: Ong Ariel Yuhan , Kiire Christine A. , Frise Charlotte , Bakr Yasmin , de Silva Samantha R. 
Published: November 2023

Abstract
Introduction
Anti-vascular endothelial growth factor (anti-VEGF) agents may occasionally need to be considered for sight-threatening macular pathology in pregnant and breastfeeding women. This is controversial due to the dearth of data on systemic side effects for mother and child. We aimed to expand the evidence base to inform management.

Methods
Retrospective case series of pregnant and breastfeeding women treated with intravitreal anti-VEGF injections at Oxford Eye Hospital between January 2015 and December 2022. In addition, we conducted a systematic review and combined eligible cases in a narrative synthesis.

Results
We treated six pregnant women with anti-VEGF for diabetic macular oedema(DMO) (n = 5) or choroidal neovascularisation (CNV) (n = 1). Four received ranibizumab whilst two (not known to be pregnant) received aflibercept. Patients known to be pregnant underwent counselling by an obstetric physician. Five pregnancies resulted in live births. Combining our cases with those previously published, treatment of 41 pregnant women (42 pregnancies) are reported. Indications for treatment included CNV (n = 28/41,68%), DMO (n = 7/41,17%) and proliferative diabetic retinopathy (n = 6/41,15%). Bevacizumab (n = 22/41,54%) and ranibizumab (n = 17/41,41%) were given more frequently than aflibercept (n = 2/41,5%). Many (n = 16/41,40%) were unaware of their pregnancy when treated. Most pregnancies resulted in live births (n = 34/42,81%). First trimester miscarriages (n = 5/42,12%) and stillbirths (n = 3/42,7%) mostly occurred in women with significant risk factors.

Conclusion
Intravitreal anti-VEGF injections may not necessarily compromise obstetric outcomes, although clear associations cannot be drawn due to small numbers and confounders from high rates of first trimester miscarriages in general and inherently high-risk pregnancies. It may be worth considering routinely investigating pregnancy and breastfeeding status in women of childbearing age prior to each injection, as part of anti-VEGF treatment protocols.
Effect of Bergmeister papilla on disc parameters in spectral domain optical coherence tomography
Authors: Chun Yeoun Sook , Moon Nam Ju , Kim Ungsoo Samuel , Yeo Joon Hyung , Jeong Jae Hoon 
Published: November 2023

Abstract
Objectives
To investigate the morphological characteristics of Bergmeister papilla (BMP), a persistent hyaloid remnant tissue, and its effects on the measurements and repeatability of spectral-domain optical coherence tomography (OCT).

Subjects/Methods
The subjects of this prospective cross-sectional study including 83 patients with BMP and 76 unaffected individuals, all had open-angle structures. Images, including a 5-line raster and three consecutive optic disc cube scans centred on the optic disc, were acquired using the Cirrus high-definition OCT. BMP’s structural characteristics were classified based on the raster scan images, and repeatability of acquiring optic nerve head and retinal nerve fibre layer parameters acquisition was analysed by calculating the test-retest standard deviation (Sw), coefficient of variance (CV), and intraclass correlation coefficient.

Results
BMPs (n = 83) were categorised into lifting edge (LE) type (63.9%, n = 53), which partially covers the edge of the optic nerve head, and covering disc (CD) type (36.1%, n = 30), which completely covers the cupping area like a cap. The average cup-to-disc ratio (0.58 ± 0.21), vertical cup-to-disc ratio (0.55 ± 0.21), and cup volume (0.22 ± 0.22) of the CD type were lower than those of the LE type (0.66 ± 0.13, 0.64 ± 0.13, and 0.4 ± 0.27, respectively; all P < 0.05). Tolerability indices for repeatability of cup volume (Sw = 0.40 and CV = 0.36) and inferonasal (4 o’clock) retinal nerve fibre layer (Sw = 0.27 and CV = 0.25) in LE-type BMPs exceeded the cut-off value (0.22) and demonstrated stronger correlation with BMP location than that of the controls.

Conclusion
Caution should be exercised when interpreting OCT findings in eyes with BMP, as BMP can introduce a pitfall in OCT imaging.
Perioperative outcomes of penile prosthesis implantation in Germany: results from the GRAND study
Authors: Pyrgidis Nikolaos , Schulz Gerald B. , Chaloupka Michael , Volz Yannic , Pfitzinger Paulo L. , Rodler Severin , Berg Elena , Weinhold Philipp , Jokisch Friedrich , Stief Christian G. , Becker Armin J. , Marcon Julian 
Published: November 2023

AbstractWe aimed to assess the recommended annual hospital volume for inflatable penile prosthesis implantation (PPI) and to provide evidence on perioperative outcomes of semi-rigid and inflatable PPI in Germany. We used the GeRmAn Nationwide inpatient Data (GRAND) from 2005 to 2021 and report the largest study to date with 7,222 patients. 6,818 (94.4%) patients underwent inflatable and 404 (5.6%) semi-rigid PPI. Inflatable PPI was significantly associated with shorter length of hospital stay (difference of 2.2 days, 95%CI: 1.6–2.7, p < 0.001), lower odds of perioperative urinary tract infections (5.5% versus 9.2%; OR: 0.58, 95%CI: 0.41–0.84, p = 0.003) and surgical wound infections (1% versus 2.5%; OR: 0.42, 95%CI: 0.22–0.88, p = 0.012) compared to semi-rigid PPI. Overall, 4255 (62.4%) inflatable PPIs were undertaken in low- ( < 20 PPI/year) and 2563 (37.6%) in high-volume ( ≥ 20 PPI/year) centers. High-volume centers were significantly associated with shorter length of hospital stay (difference of 1.4 days, 95%CI: 1.2–1.7, p < 0.001) compared to low-volume centers. Our findings suggest that inflatable PPI leads to a shorter length of hospital stay and lower rates of perioperative urinary tract and surgical wound infections compared to semi-rigid PPI. Patients undergoing surgery in high-volume centers for inflatable PPI are discharged earlier from the hospital.
Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints
Authors: Chen Qinchang , Chuai Guohui , Zhang Haihang , Tang Jin , Duan Liwen , Guan Huan , Li Wenhui , Li Wannian , Wen Jiaying , Zuo Erwei , Zhang Qing , Liu Qi 
Published: November 2023

AbstractThe powerful CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. In this study, we propose to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and present CRISOT, an integrated tool suite containing four related modules, i.e., CRISOT-FP, CRISOT-Score, CRISOT-Spec, CRISORT-Opti for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. Our comprehensive computational and experimental tests reveal that CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations. In addition, CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems. Collectively, CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing.