bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual elastography ultrasound via generative adversarial network for breast cancer diagnosis
Authors: Yao Zhao , Luo Ting , Dong YiJie , Jia XiaoHong , Deng YinHui , Wu GuoQing , Zhu Ying , Zhang JingWen , Liu Juan , Yang LiChun , Luo XiaoMao , Li ZhiYao , Xu YanJun , Hu Bin , Huang YunXia , Chang Cai , Xu JinFeng , Luo Hui , Dong FaJin , Xia XiaoNa , Wu ChengRong , Hu WenJia , Wu Gang , Li QiaoYing , Chen Qin , Deng WanYue , Jiang QiongChao , Mou YongLin , Yan HuanNan , Xu XiaoJing , Yan HongJu , Zhou Ping , Shao Yang , Cui LiGang , He Ping , Qian LinXue , Liu JinPing , Shi LiYing , Zhao YaNan , Xu YongYuan , Zhan WeiWei , Wang YuanYuan , Yu JinHua , Zhou JianQiao 
Published: February 2023

AbstractElastography ultrasound (EUS) imaging is a vital ultrasound imaging modality. The current use of EUS faces many challenges, such as vulnerability to subjective manipulation, echo signal attenuation, and unknown risks of elastic pressure in certain delicate tissues. The hardware requirement of EUS also hinders the trend of miniaturization of ultrasound equipment. Here we show a cost-efficient solution by designing a deep neural network to synthesize virtual EUS (V-EUS) from conventional B-mode images. A total of 4580 breast tumor cases were collected from 15 medical centers, including a main cohort with 2501 cases for model establishment, an external dataset with 1730 cases and a portable dataset with 349 cases for testing. In the task of differentiating benign and malignant breast tumors, there is no significant difference between V-EUS and real EUS on high-end ultrasound, while the diagnostic performance of pocket-sized ultrasound can be improved by about 5% after V-EUS is equipped.
A deep learning approach reveals unexplored landscape of viral expression in cancer
Authors: Elbasir Abdurrahman , Ye Ying , Schäffer Daniel E. , Hao Xue , Wickramasinghe Jayamanna , Tsingas Konstantinos , Lieberman Paul M. , Long Qi , Morris Quaid , Zhang Rugang , Schäffer Alejandro A. , Auslander Noam 
Published: February 2023

AbstractAbout 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
Surface engineering of inorganic solid-state electrolytes via interlayers strategy for developing long-cycling quasi-all-solid-state lithium batteries
Authors: Kim Ju-Sik , Yoon Gabin , Kim Sewon , Sugata Shoichi , Yashiro Nobuyoshi , Suzuki Shinya , Lee Myung-Jin , Kim Ryounghee , Badding Michael , Song Zhen , Chang JaeMyung , Im Dongmin 
Published: February 2023

AbstractLithium metal batteries (LMBs) with inorganic solid-state electrolytes are considered promising secondary battery systems because of their higher energy content than their Li-ion counterpart. However, the LMB performance remains unsatisfactory for commercialization, primarily owing to the inability of the inorganic solid-state electrolytes to hinder lithium dendrite propagation. Here, using an Ag-coated Li6.4La3Zr1.7Ta0.3O12 (LLZTO) inorganic solid electrolyte in combination with a silver-carbon interlayer, we demonstrate the production of stable interfacially engineered lab-scale LMBs. Via experimental measurements and computational modelling, we prove that the interlayers strategy effectively regulates lithium stripping/plating and prevents dendrite penetration in the solid-state electrolyte pellet. By coupling the surface-engineered LLZTO with a lithium metal negative electrode, a high-voltage positive electrode with an ionic liquid-based liquid electrolyte solution in pouch cell configuration, we report 800 cycles at 1.6 mA/cm2 and 25 °C without applying external pressure. This cell enables an initial discharge capacity of about 3 mAh/cm2 and a discharge capacity retention of about 85%.
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex
Authors: Soni Komal , Sivadas Anusree , Horvath Attila , Dobrev Nikolay , Hayashi Rippei , Kiss Leo , Simon Bernd , Wild Klemens , Sinning Irmgard , Fischer Tamás 
Published: February 2023

AbstractThe S. pombe orthologue of the human PAXT connection, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex that targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identify and characterise the interaction between Pla1 and the MTREC complex core component Red1 and analyse the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex shows that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations show that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction is also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3’-end processing machineries.
Lipid-droplet associated mitochondria promote fatty-acid oxidation through a distinct bioenergetic pattern in male Wistar rats
Authors: Talari Noble Kumar , Mattam Ushodaya , Meher Niroj Kumar , Paripati Arun Kumar , Mahadev Kalyankar , Krishnamoorthy Thanuja , Sepuri Naresh Babu V. 
Published: February 2023

AbstractMitochondria empower the liver to regulate lipid homeostasis by enabling fatty acid oxidation during starvation and lipogenesis during nutrient-rich conditions. It is unknown if mitochondria can seamlessly regulate these two distinct processes or if two discrete populations of mitochondria achieve these two functions in the liver. For the first time in the liver, we report the isolation of two distinct populations of mitochondria from male Wistar rats on an ad-libitum diet: cytoplasmic mitochondria and lipid droplet-associated mitochondria. Our studies show that while lipid droplet mitochondria exhibit higher fatty acid oxidation and are marked by enhanced levels of pACC2, MFN2, and CPT1 activity, cytoplasmic mitochondria are associated with higher respiration capacity. Notably, lipid droplet-associated mitochondria isolated from a non-alcoholic fatty liver disease (NAFLD) rat model are compromised for fatty acid oxidation. We demonstrate the importance of functional segregation of mitochondria as any aberration in lipid droplet-associated mitochondria may lead to NAFLD.
Asymmetric eROSITA bubbles as the evidence of a circumgalactic medium wind
Authors: Mou Guobin , Sun Dongze , Fang Taotao , Wang Wei , Zhang Ruiyu , Yuan Feng , Sofue Yoshiaki , Wang Tinggui , He Zhicheng 
Published: February 2023

AbstractThe eROSITA bubbles are detected via the instrument with the same name. The northern bubble shows noticeable asymmetric features, including distortion to the west and enhancement in the eastern edge, while the southern counterpart is significantly dimmer. Their origins are debated. Here, we performed hydrodynamic simulations showing that asymmetric eROSITA bubbles favor a dynamic, circumgalactic medium wind model, but disfavor other mechanisms such as a non-axisymmetric halo gas or a tilted nuclear outflow. The wind from the east by north direction in Galactic coordinates blows across the northern halo with a velocity of about 200 km s−1, and part of it enters the southern halo. This creates a dynamic halo medium and redistributes both density and metallicity within. This naturally explains the asymmetric bubbles in both the morphology and surface brightness. Our results suggest that our Galaxy is accreting low-abundance circumgalactic medium from one side while providing outflow feedback.
Origami-inspired perovskite X-ray detector by printing and folding
Authors: Mescher Henning , Schackmar Fabian , Huber Robert , Eggers Helge , Zuber Marcus , Hamann Elias , Gramlich Georg , Dangelmaier Julian , Zhang Qiaoshuang , Rösch Andres Georg , Zwick Thomas , Hernandez-Sosa Gerardo , Paetzold Ulrich W. , Lemmer Uli 
Published: February 2023

AbstractX-ray detectors are of pivotal importance for the scientific and technological progress in a wide range of medical, industrial, and scientific applications. Here, we take advantage of the printability of perovskite-based semiconductors and achieve a high X-ray sensitivity combined with the potential of an exceptional high spatial resolution by our origami-inspired folded perovskite X-ray detector. The high performance of our device is reached solely by the folded detector architecture and does not require any photolithography. The design and fabrication of a foldable perovskite sensor array is presented and the detector is characterized as a planar and as a folded device. Exposed to 50 kVp−150 kVp X-ray radiation, the planar detector reaches X-ray sensitivities of 25−35 μC/(Gyaircm2), whereas the folded detector achieves remarkably increased X-ray sensitivities of several hundred μC/(Gyaircm2) and a record value of 1409 μC/(Gyaircm2) at 150 kVp without photoconductive gain. Finally, the potential of an exceptional high spatial resolution of the folded detector of more than 20 lp/mm under 150 kVp X-ray radiation is demonstrated.
Comparison of clinical outcomes in patients with schizophrenia following different long-acting injectable event-driven initiation strategies
Authors: Correll Christoph U. , Benson Carmela , Emond Bruno , Patel Charmi , Lafeuille Marie-Hélène , Lin Dee , Morrison Laura , Ghelerter Isabelle , Lefebvre Patrick , Mavros Panagiotis 
Published: February 2023

AbstractThis retrospective study evaluated the benefit of following different long-acting injectable (LAI) initiation strategies based on the timing of behavioral and clinical events among Medicaid beneficiaries with schizophrenia. Adults with schizophrenia initiating oral antipsychotics (OAPs) after 12 months without antipsychotic use or schizophrenia-related inpatient/emergency room (ER) visits (index date) were identified. Patients were categorized into four event-driven LAI initiation strategy cohorts based on observed sequences of behavioral (i.e., OAP adherence) and clinical (i.e., schizophrenia-related inpatient/ER visits) events between index and LAI initiation or censoring—strategy #1: adherent to OAPs without schizophrenia-related inpatient/ER visits; strategy #2: nonadherent to OAPs without schizophrenia-related inpatient/ER visits; strategy #3: one schizophrenia-related inpatient/ER visit; strategy #4: ≥2 schizophrenia-related inpatient/ER visits. Clinical outcomes (i.e., all-cause inpatient/ER visits) were evaluated between OAP initiation and end of follow-up. Comparisons between LAI initiation strategy cohorts were conducted using a dynamic marginal structural model adjusting for baseline characteristics and time-varying confounders. Among 13,444 eligible patients, 13.1%, 53.6%, 15.7%, and 17.6% were following strategies #1–4, respectively; of these, 21.9%, 4.3%, 9.2%, and 6.5% started an LAI (the remaining were censored). Strategy #1 was associated with a greater clinical benefit, with 43%, 69%, and 80% fewer inpatient days (all p < 0.05); and 57%, 59%, and 79% fewer ER visits (all p < 0.01) vs strategies #2–4, respectively; the clinical benefit was also observed for strategy #2 vs #3–4. Therefore, starting an LAI prior to OAP nonadherence or occurrence of a schizophrenia-related inpatient/ER visit was associated with fewer all-cause inpatient days of inpatient stay and ER visits.
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms
Authors: Chakravarty Suchana , Hong Christian I. , Csikász-Nagy Attila 
Published: February 2023

AbstractTemperature compensation and robustness to biological noise are two key characteristics of the circadian clock. These features allow the circadian pacemaker to maintain a steady oscillation in a wide range of environmental conditions. The presence of a time-delayed negative feedback loop in the regulatory network generates autonomous circadian oscillations in eukaryotic systems. In comparison, the circadian clock of cyanobacteria is controlled by a strong positive feedback loop. Positive feedback loops with substrate depletion can also generate oscillations, inspiring other circadian clock models. What makes a circadian oscillatory network robust to extrinsic noise is unclear. We investigated four basic circadian oscillators with negative, positive, and combinations of positive and negative feedback loops to explore network features necessary for circadian clock resilience. We discovered that the negative feedback loop system performs the best in compensating temperature changes. We also show that a positive feedback loop can reduce extrinsic noise in periods of circadian oscillators, while intrinsic noise is reduced by negative feedback loops.
Assessing ternary materials for fluoride-ion batteries
Authors: McTaggart Don H. , Sundberg Jack D. , McRae Lauren M. , Warren Scott C. 
Published: February 2023

AbstractAlthough lithium-ion batteries have transformed energy storage, there is a need to develop battery technologies with improved performance. Fluoride-ion batteries (FIBs) may be promising alternatives in part due to their high theoretical energy density and natural elemental abundance. However, electrode materials for FIBs, particularly cathodes, have not been systematically evaluated, limiting rapid progress. Here, we evaluate ternary fluorides from the Materials Project crystal structure database to identify promising cathode materials for FIBs. Structures are further assessed based on stability and whether fluorination/defluorination occurs without unwanted disproportionation reactions. Properties are presented for pairs of fluorinated/defluorinated materials including theoretical energy densities, cost approximations, and bandgaps. We aim to supply a dataset for extracting property and structural trends of ternary fluoride materials that may aid in the discovery of next-generation battery materials.
Soil, leaf and fruit nutrient data for pear orchards located in the Circum-Bohai Bay and Loess Plateau regions
Authors: Sun Mingde , Zhao Yanyan , Liang Zhenxu , Wu Yang , Du Ruirui , Liu Jun , Yu Futong , Liu Songzhong 
Published: February 2023

AbstractThe data described in this paper were collected from the Circum-Bohai Bay and Loess Plateau regions of northern China. Soil, leaf and fruit nutrients from 225 typical pear orchards in these regions were measured. Soil data included pH, organic matter, total N, alkaline hydrolysable N, available P and available K concentrations of 3 different soil layers, 0–20 cm, 20–40 cm and 40–60 cm, from different orchards. Leaf and fruit data included N, P, K, Ca, Fe, Mn, Cu, Zn and B concentrations of pear trees from different orchards. These data can be used to assess the soil nutrient supply and leaf and fruit nutrient status of pear orchards in two major producing areas, Circum-Bohai Bay and Loess Plateau. Additionally, this dataset provides data to support the development of regionalized and standardized soil nutrient management programs for pear orchards, as well as regionalized layouts of the main varieties in the two producing areas.
Quantum machine learning with differential privacy
Authors: Watkins William M. , Chen Samuel Yen-Chi , Yoo Shinjae 
Published: February 2023

AbstractQuantum machine learning (QML) can complement the growing trend of using learned models for a myriad of classification tasks, from image recognition to natural speech processing. There exists the potential for a quantum advantage due to the intractability of quantum operations on a classical computer. Many datasets used in machine learning are crowd sourced or contain some private information, but to the best of our knowledge, no current QML models are equipped with privacy-preserving features. This raises concerns as it is paramount that models do not expose sensitive information. Thus, privacy-preserving algorithms need to be implemented with QML. One solution is to make the machine learning algorithm differentially private, meaning the effect of a single data point on the training dataset is minimized. Differentially private machine learning models have been investigated, but differential privacy has not been thoroughly studied in the context of QML. In this study, we develop a hybrid quantum-classical model that is trained to preserve privacy using differentially private optimization algorithm. This marks the first proof-of-principle demonstration of privacy-preserving QML. The experiments demonstrate that differentially private QML can protect user-sensitive information without signficiantly diminishing model accuracy. Although the quantum model is simulated and tested on a classical computer, it demonstrates potential to be efficiently implemented on near-term quantum devices [noisy intermediate-scale quantum (NISQ)]. The approach’s success is illustrated via the classification of spatially classed two-dimensional datasets and a binary MNIST classification. This implementation of privacy-preserving QML will ensure confidentiality and accurate learning on NISQ technology.
Updated meta-analysis on intraoperative inspired fraction of oxygen and the risk of surgical site infection in adults undergoing general and regional anesthesia
Authors: El Maleh Yoann , Fasquel Charlotte , Quesnel Christophe , Garnier Marc 
Published: February 2023

AbstractThis updated meta-analysis aims at exploring whether the use of systematic high vs low intraoperative oxygen fraction (FiO2) may decrease the incidence of postoperative surgical site infection during general (GA) or regional anesthesia (RA). PubMed, Cochrane CENTRAL, ClinicalTrials.gov databases were searched from January 1st, 1999 and July, 1st 2022, for randomized and quasi-randomized controlled trials that included patients in a high and low FiO2 groups and reported the incidence of SSI. The meta-analysis was conducted with a DerSimonian and Laird random-effects model. Thirty studies (24 for GA and 6 for RA) totaling 18,055 patients (15,871 for GA and 2184 for RA) were included. We have low-to-moderate-quality evidence that high FiO2 (mainly 80%) was not associated with a reduction of SSI incidence compared to low FiO2 (mainly 30%) in all patients (RR 0.90, 95%CI 0.79–1.03). Moderate inconsistency existed between studies (I2 = 38%). Subgroup analyses showed a moderate protective effect in patients undergoing GA (RR 0.86, 95%CI 0.75–0.99) (low level of evidence), while high FiO2 was not associated with a reduction of SSI in patients undergoing RA (RR 1.17, 95%CI 0.90–1.52) (moderate level of evidence). Sensitivity analyses restricted to patients ventilated without nitrous oxide (n = 20 studies), to patients operated from abdominal surgeries (n = 21 studies), and to patients suffering from deep SSI (n = 13 studies), all showed the absence of any significant effect of high FiO2. As a conclusion there is no compelling evidence that high FiO2 can improve postoperative patient’s outcome on its own when good SSI prevention practices are properly applied. Recent well-designed and adequately powered randomized controlled trials add further weight to these results.
Separate lifetime signatures of macaque S cones, M/L cones, and rods observed with adaptive optics fluorescence lifetime ophthalmoscopy
Authors: Huynh Khang T. , Walters Sarah , Foley Emma K. , Hunter Jennifer J. 
Published: February 2023

AbstractIn the retina, several molecules involved in metabolism, the visual cycle, and other roles exhibit intrinsic fluorescence. The overall properties of retinal fluorescence depend on changes to the composition of these molecules and their environmental interactions due to transient functional shifts, especially in disease. This behooves the understanding of the origins and deviations of these properties within the multilayered retina at high lateral and axial resolution. Of particular interest is the fluorescence lifetime, a potential biomarker of function and disease independent of fluorescence intensity that can be measured in the retina with adaptive optics fluorescence lifetime ophthalmoscopy (AOFLIO). This work demonstrates the utility of the phasor method of analysis, an alternate approach to traditional multiexponential fitting, to evaluate photoreceptor two-photon excited AOFLIO data and separate them based on functional differences. Phasor analysis on fluorescence lifetime decay data allowed the repeatable segregation of S from M/L cones, likely from differences in functional or metabolic demands. Furthermore, it is possible to track the lifetime changes in S cones after photodamage. Phasor analysis increases the sensitivity of AOFLIO to functional differences between cells and has the potential to improve our understanding of pathways involved in normal and diseased conditions at the cellular scale throughout the retina.
In-situ atomic level observation of the strain response of graphene lattice
Authors: Juo Jz-Yuan , Shin Bong Gyu , Stiepany Wolfgang , Memmler Marko , Kern Klaus , Jung Soon Jung 
Published: February 2023

AbstractStrain is inevitable in two-dimensional (2D) materials, regardless of whether the film is suspended or supported. However, the direct measurement of strain response at the atomic scale is challenging due to the difficulties of maintaining both flexibility and mechanical stability at low temperature under UHV conditions. In this work, we have implemented a compact nanoindentation system with a size of $$\sim $$
∼
160 mm$$^2$$

2

$$\times $$
×
5.2 mm in a scanning tunneling microscope (STM) sample holder, which enables the reversible control of strain and gate electric field. A combination of gearbox and piezoelectric actuator allowed us to modulate the depth of the indentation continuously with nanometer precision. The 2D materials were transferred onto the polyimide film. Pd clamp was used to enhance the strain transfer from the polyimide from to the 2D layers. Using this unique technique, strain response of graphene lattice were observed at atomic precision. In the relaxed graphene, strain is induced mainly by local curvature. However, in the strained graphene with tented structure, the lattice parameters become more sensitive to the indentor height change and stretching strain is increased additionally. Moreover, the gate controllability is confirmed by measuring the dependence of the STM tip height on gate voltage.