bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence-enhanced quantum chemical method with broad applicability
Authors: Zheng Peikun , Zubatyuk Roman , Wu Wei , Isayev Olexandr , Dral Pavlo O. 
Published: December 2021

AbstractHigh-level quantum mechanical (QM) calculations are indispensable for accurate explanation of natural phenomena on the atomistic level. Their staggering computational cost, however, poses great limitations, which luckily can be lifted to a great extent by exploiting advances in artificial intelligence (AI). Here we introduce the general-purpose, highly transferable artificial intelligence–quantum mechanical method 1 (AIQM1). It approaches the accuracy of the gold-standard coupled cluster QM method with high computational speed of the approximate low-level semiempirical QM methods for the neutral, closed-shell species in the ground state. AIQM1 can provide accurate ground-state energies for diverse organic compounds as well as geometries for even challenging systems such as large conjugated compounds (fullerene C60) close to experiment. This opens an opportunity to investigate chemical compounds with previously unattainable speed and accuracy as we demonstrate by determining geometries of polyyne molecules—the task difficult for both experiment and theory. Noteworthy, our method’s accuracy is also good for ions and excited-state properties, although the neural network part of AIQM1 was never fitted to these properties.
Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones
Authors: Beman J. M. , Vargas S. M. , Wilson J. M. , Perez-Coronel E. , Karolewski J. S. , Vazquez S. , Yu A. , Cairo A. E. , White M. E. , Koester I. , Aluwihare L. I. , Wankel S. D. 
Published: December 2021

AbstractOceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and 15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs.
Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure
Authors: Zhou Jia , Hu Qinli , Xiao Xinlong , Yao Deqiang , Ge Shenghong , Ye Jin , Li Haojie , Cai Rujie , Liu Renyang , Meng Fangang , Wang Chao , Zhu Jian-Kang , Lei Mingguang , Xing Weiman 
Published: December 2021

AbstractPhosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. SPX1 an inhibit the PHR2 transcription factor to maintain Pi homeostasis. How SPX1 recognizes an InsP molecule and represses transcription activation by PHR2 remains unclear. Here we show that, upon binding InsP6, SPX1 can disrupt PHR2 dimers and form a 1:1 SPX1-PHR2 complex. The complex structure reveals that SPX1 helix α1 can impose a steric hindrance when interacting with the PHR2 dimer. By stabilizing helix α1, InsP6allosterically decouples the PHR2 dimer and stabilizes the SPX1-PHR2 interaction. In doing so, InsP6further allows SPX1 to engage with the PHR2 MYB domain and sterically block its interaction with DNA. Taken together, our results suggest that, upon sensing the surrogate signals of phosphate, SPX1 inhibits PHR2 via a dual mechanism that attenuates dimerization and DNA binding activities of PHR2.
Circular functional analysis of OCT data for precise identification of structural phenotypes in the eye
Authors: Ali Md. Hasnat , Wainwright Brian , Petersen Alexander , Jonnadula Ganesh B. , Desai Meghana , Rao Harsha L. , Srinivas M. B. , Jammalamadaka S. Rao , Senthil Sirisha , Pyne Saumyadipta 
Published: December 2021

AbstractProgressive optic neuropathies such as glaucoma are major causes of blindness globally. Multiple sources of subjectivity and analytical challenges are often encountered by clinicians in the process of early diagnosis and clinical management of these diseases. In glaucoma, the structural damage is often characterized by neuroretinal rim (NRR) thinning of the optic nerve head, and other clinical parameters. Baseline structural heterogeneity in the eyes can play a key role in the progression of optic neuropathies, and present challenges to clinical decision-making. We generated a dataset of Optical Coherence Tomography (OCT) based high-resolution circular measurements on NRR phenotypes, along with other clinical covariates, of 3973 healthy eyes as part of an established clinical cohort of Asian Indian participants. We introduced CIFU, a new computational pipeline for CIrcular FUnctional data modeling and analysis. We demonstrated CIFU by unsupervised circular functional clustering of the OCT NRR data, followed by meta-clustering to characterize the clusters using clinical covariates, and presented a circular visualization of the results. Upon stratification by age, we identified a healthy NRR phenotype cluster in the age group 40–49 years with predictive potential for glaucoma. Our dataset also addresses the disparity of representation of this particular population in normative OCT databases.
Thirty-day hospital readmission prediction model based on common data model with weather and air quality data
Authors: Ryu Borim , Yoo Sooyoung , Kim Seok , Choi Jinwook 
Published: December 2021

AbstractAlthough several studies have attempted to develop a model for predicting 30-day re-hospitalization, few attempts have been made for sufficient verification and multi-center expansion for clinical use. In this study, we developed a model that predicts unplanned hospital readmission within 30 days of discharge; the model is based on a common data model and considers weather and air quality factors, and can be easily extended to multiple hospitals. We developed and compared four tree-based machine learning methods: decision tree, random forest, AdaBoost, and gradient boosting machine (GBM). Above all, GBM showed the highest AUC performance of 75.1 in the clinical model, while the clinical and W-score model showed the best performance of 73.9 for musculoskeletal diseases. Further, PM10, rainfall, and maximum temperature were the weather and air quality variables that most impacted the model. In addition, external validation has confirmed that the model based on weather and air quality factors has transportability to adapt to other hospital systems.
The role of eye movements in perceiving vehicle speed and time-to-arrival at the roadside
Authors: Sudkamp Jennifer , Bocian Mateusz , Souto David 
Published: December 2021

AbstractTo avoid collisions, pedestrians depend on their ability to perceive and interpret the visual motion of other road users. Eye movements influence motion perception, yet pedestrians’ gaze behavior has been little investigated. In the present study, we ask whether observers sample visual information differently when making two types of judgements based on the same virtual road-crossing scenario and to which extent spontaneous gaze behavior affects those judgements. Participants performed in succession a speed and a time-to-arrival two-interval discrimination task on the same simple traffic scenario—a car approaching at a constant speed (varying from 10 to 90 km/h) on a single-lane road. On average, observers were able to discriminate vehicle speeds of around 18 km/h and times-to-arrival of 0.7 s. In both tasks, observers placed their gaze closely towards the center of the vehicle’s front plane while pursuing the vehicle. Other areas of the visual scene were sampled infrequently. No differences were found in the average gaze behavior between the two tasks and a pattern classifier (Support Vector Machine), trained on trial-level gaze patterns, failed to reliably classify the task from the spontaneous eye movements it elicited. Saccadic gaze behavior could predict time-to-arrival discrimination performance, demonstrating the relevance of gaze behavior for perceptual sensitivity in road-crossing.
Efficacy and immunogenicity of different BCG doses in BALB/c and CB6F1 mice when challenged with H37Rv or Beijing HN878
Authors: Khatri Bhagwati , Keeble James , Dagg Belinda , Kaveh Daryan A. , Hogarth Philip J. , Ho Mei Mei 
Published: December 2021

AbstractTwo strains of mice (BALB/c and CB6F1) were vaccinated with a range of Bacille Calmette-Guérin (BCG) Danish doses from 3 × 105to 30 CFU/mouse, followed by aerosol infection withMtb(H37Rv or West-Beijing HN878 strain). The results indicated that both strains of mice when infected with HN878 exhibited significant protection in their lungs with BCG doses at 3 × 105—3000 CFU (BALB/c) and 3 × 105—300 CFU (CB6F1). Whereas, a significant protection was seen in both strains of mice with BCG doses at 3 × 105—300 CFU when infected with H37Rv. A significant increase in the frequencies of BCG-specific IFNγ+IL2+TNFα+CD4 T cells in the BCG doses at 3 × 105—3000 CFU (BALB/c) and 3 × 105—300 CFU (CB6F1) was seen. The IFNγ+IL2+TNFα+CD4 T cells correlated with theMtbburden in the lungs of HN878 infected mice (BALB/c and CB6F1) whereas, IFNγ+TNFα+CD4 T cells correlated with the BALB/c mice infected with H37Rv or HN878. The BCG dose at 3000 CFU (an equivalent single human dose in the mice by body weight) is protective in both strains of mice infected with H37Rv or HN878 and may serve an interesting dose to test new TB vaccine in a preclinical animal model.
Emerging trends of therapy related myeloid neoplasms following modern cancer therapeutics in the United States
Authors: Singh Abhay , Herr Megan M. , Griffiths Elizabeth A. , Przespolewski Amanda , Faber Mark G. , Mrad Chebli , Wang Eunice S. , Hahn Theresa , Thota Swapna 
Published: December 2021

AbstractClonal hematopoiesis (CH) is a risk factor for the development of therapy-related myelodysplastic syndromes (tMDS) and acute myeloid leukemia (tAML). Adoption of targeted-immunotherapeutics since 2011, may alter the risk of CH progression to tMDS/AML. To study this, we evaluated risk of tMDS and tAML in 667 588 ≥ 1-year survivors of non-small cell lung cancer (NSCLC), renal cell carcinoma (RCC), melanoma and multiple-myeloma (MM) diagnosed during: 2000–2005, 2006–2010 and 2011–2016. The risk of tMDS increased significantly after NSCLC across all time periods (Ptrend = 0.002) while tAML risk decreased from 2006–2010 to 2011–2016, coinciding with increasing use of non-chemotherapeutic agents. tAML risk after RCC decreased (Ptrend = 0.007) whereas tMDS risk did not significantly change over time. After melanoma, tMDS and tAML risks were similar to the general population. tMDS and tAML risk after MM increased from the first to second time-period, however, only risk of tMDS decreased during last period. We report diverging trends in the risk of tAML and tMDS after adoption of modern cancer therapies for specific cancers. It is imperative to further explore impact of contemporary treatment strategies on clonal evolution. Modern treatments via their discrete mechanism of actions on pre-existing CH may alter the risk of subsequent tMDS and tAML.
Experimental investigation of size broadening of a Kα x-ray source produced by high intensity laser pulses
Authors: Gambari M. , Clady R. , Videau L. , Utéza O. , Ferré A. , Sentis M. 
Published: December 2021

AbstractThe size of a hard Kα x-ray source ($${\mathrm{E}}_{{\rm{K}}_{\rm{\alpha }}}$$

E

K
α

= 17.48 keV) produced by a high intensity femtosecond laser interacting with a solid molybdenum target is experimentally investigated for a wide range of laser intensity (I ~ 1017–2.8 × 1019 W/cm2) and for four values of the temporal contrast ratio (6.7 × 107 < CR < 3.3 × 1010). Results point out the size enlargement of the x-ray source with the increase of laser intensity and with the deterioration of temporal contrast. It amounts up to sixteen times the laser spot size at the highest laser intensity and for the lowest temporal contrast ratio. Using hydrodynamic simulations, we evaluate the density scale length of the pre-plasma L/λ just before the main pulse peak. This allows us to show that a direct correlation with the laser absorption mechanisms is not relevant to explain the large size broadening. By varying the thickness of the molybdenum target down to 4 µm, the impact of hot electron scattering inside the solid is also proved irrelevant to explain the evolution of both the x-ray source size and the Kα photon number. We deduce that the most probable mechanism yielding to the broadening of the source size is linked to the creation of surface electromagnetic fields which confine the hot electrons at the solid surface. This assumption is supported by dedicated experiments where the evolution of the size enlargement of the x-ray source is carefully studied as a function of the laser focal spot size for the highest contrast ratio.
Changes in resting-state measures of prostate cancer patients exposed to androgen deprivation therapy
Authors: Plata-Bello Julio , Plata-Bello Ana , Pérez-Martín Yaiza , López-Curtis David , Acosta-López Silvia , Modroño Cristián , Concepción-Massip Tomás 
Published: December 2021

AbstractThe aim of the present work is to describe the differences in rs-fMRI measures (Amplitude of low frequency fluctuations [ALFF], Regional Homogeneity [ReHo] and Functional Connectivity [FC]) between patients exposed to Androgen deprivation therapy (ADT) and a control group. Forty-nine ADT patients and fifteen PC-non-ADT patients (Controls) were included in the study. A neuropsychological evaluation and a resting-state fMRI was performed to evaluate differences in ALFF and ReHo. Region of interest (ROI) analysis was also performed. ROIs were selected among those whose androgen receptor expression (at RNA-level) was the highest. FC analysis was performed using the same ROIs. Higher ALFF in frontal regions and temporal regions was identified in Controls than in ADT patients. In the ROI analysis, higher activity for Controls than ADT patients was shown in the left inferior frontal gyrus and in the left precentral gyrus. Lower ALFF in the right hippocampus and the lateral geniculate nucleus of the right thalamus was identified for Controls than ADT patients. Higher ReHo was observed in Controls in the left parietal-occipital area. Finally, ADT patients presented an increase of FC in more regions than Controls. These differences may reflect an impairment in brain functioning in ADT users.
Notch signaling and natural killer cell infiltration in tumor tissues underlie medulloblastoma prognosis
Authors: Liang Kung-Hao , Chang Che-Chang , Wu Kuo-Sheng , Yu Alice L. , Sung Shian-Ying , Lee Yi-Yen , Liang Muh-Lii , Chen Hsin-Hung , Fen Jun-Jeng , Chao Meng-En , Liao Yi-Ting , Wong Tai-Tong 
Published: December 2021

AbstractMedulloblastoma is the most common embryonic brain tumor in children. We investigated a cohort of 52 Asian medulloblastoma patients aged between 0 and 19 years old, who received surgical resections and post-resection treatments in the Taipei Medical University Hospital and the Taipei Veterans General Hospital. Genome-wide RNA sequencing was performed on fresh-frozen surgical tissues. These data were analyzed using the CIBERSORTx immune deconvolution software. Two external clinical and molecular datasets from United States (n = 62) and Canada (n = 763) were used to evaluate the transferability of the gene-signature scores across ethnic populations. The abundance of 13 genes, including DLL1, are significantly associated with overall survival (All Cox regression P < 0.001). A gene-signature score was derived from the deep transcriptome, capable of indicating patients’ subsequent tumor recurrence (Hazard Ratio [HR] 1.645, confidence interval [CI] 1.337–2.025, P < 0.001) and mortality (HR 2.720, CI 1.798–4.112, P < 0.001). After the adjustment of baseline clinical factors, the score remains indicative of recurrence-free survival (HR 1.604, CI 1.292–1.992, P < 0.001) and overall survival (HR 2.781, CI 1.762–4.390, P < 0.001). Patients stratified by this score manifest not only distinct prognosis but also different molecular characteristics: Notch signaling ligands and receptors are comparatively overexpressed in patients with poorer prognosis, while tumor infiltrating natural killer cells are more abundant in patients with better prognosis. Additionally, immunohistochemical staining showed the DLL1 protein, a major ligand in the Notch signaling pathway, and the NCAM1 protein, a representative biomarker of natural killer cells, are present in the surgical tissues of patients of four molecular subgroups, WNT, SHH, Group 3 and Group 4. NCAM1 RNA level is also positively associated with the mutation burden in tumor (P = 0.023). The gene-signature score is validated successfully in the Canadian cohort (P = 0.009) as well as its three molecular subgroups (SHH, Group 3 and Group 4; P = 0.047, 0.018 and 0.040 respectively). In conclusion, pediatric medullablastoma patients can be stratified by gene-signature scores with distinct prognosis and molecular characteristics. Ligands and receptors of the Notch signaling pathway are overexpressed in the patient stratum with poorer prognosis. Tumor infiltrating natural killer cells are more abundant in the patient stratum with better prognosis.
Computational fluid dynamics modeling of cough transport in an aircraft cabin
Authors: Zee Malia , Davis Angela C. , Clark Andrew D. , Wu Tateh , Jones Stephen P. , Waite Lindsay L. , Cummins Joshua J. , Olson Nels A. 
Published: December 2021

AbstractTo characterize the transport of respiratory pathogens during commercial air travel, Computational Fluid Dynamics simulations were performed to track particles expelled by coughing by a passenger assigned to different seats on a Boeing 737 aircraft. Simulation data were post-processed to calculate the amounts of particles inhaled by nearby passengers. Different airflow rates were used, as well as different initial conditions to account for random fluctuations of the flow field. Overall, 80% of the particles were removed from the cabin in 1.3–2.6 min, depending on conditions, and 95% of the particles were removed in 2.4–4.6 min. Reducing airflow increased particle dispersion throughout the cabin but did not increase the highest exposure of nearby passengers. The highest exposure was 0.3% of the nonvolatile mass expelled by the cough, and the median exposure for seats within 3 feet of the cough discharge was 0.1%, which was in line with recent experimental testing.
Experiences in treatment of multiple sclerosis with natalizumab from a real-life cohort over 15 years
Authors: Auer Michael , Zinganell Anne , Hegen Harald , Bsteh Gabriel , Di Pauli Franziska , Berek Klaus , Fava Elena , Wurth Sebastian , Berger Thomas , Deisenhammer Florian 
Published: December 2021

AbstractNatalizumab (NTZ) has been used for treatment of highly active relapsing–remitting multiple sclerosis (MS). When stopping NTZ the risk of severe rebound phenomenon has to be considered. We aimed to investigate the use of NTZ in clinical routine and focused on identification of potential risk factors for disease reactivation after treatment discontinuation. At the Medical University of Innsbruck, Austria, we identified all MS patients who were treated with NTZ and performed a retrospective analysis on therapeutic decision making, disease course before, during and after treatment with NTZ and on risk factors for disease reactivation after NTZ discontinuation. 235 NTZ treated MS patients were included, of whom 105 had discontinued treatment. At NTZ start disease duration was 5.09 (IQR 2.09–10.57) years, average number of total relapses was 4 (IQR 3–6) and median EDSS 2.0 (range 0–6.5), whereby these values significantly decreased over time. Reduction of annualized relapse rate (ARR) on treatment was 93% and EDSS remained stable in 64%. In multivariate regression models only conversion to secondary progressive MS (SPMS) on treatment was significantly associated with lower risk of disease reactivation after NTZ, while ARR before treatment was associated with earlier disease reactivation. We could confirm the high therapeutic efficacy of NTZ which trends to be used earlier in the disease course nowadays. Discontinuation of NTZ seems safe only in patients who convert to SPMS during treatment, while higher ARR before NTZ increases the risk of disease reactivation after treatment discontinuation.
On the transience or stability of subthreshold psychopathology
Authors: Schreuder Marieke J. , Wigman Johanna T. W. , Groen Robin N. , Wichers Marieke , Hartman Catharina A. 
Published: December 2021

AbstractSymptoms of psychopathology lie on a continuum ranging from mental health to psychiatric disorders. Although much research has focused on progression along this continuum, for most individuals, subthreshold symptoms do not escalate into full-blown disorders. This study investigated how the stability of psychopathological symptoms (attractor strength) varies across severity levels (homebase). Data were retrieved from the TRAILS TRANS-ID study, where 122 at-risk young adults (mean age 23.6 years old, 57% males) monitored their mental states daily for a period of six months (± 183 observations per participant). We estimated each individual’s homebase and attractor strength using generalized additive mixed models. Regression analyses showed no association between homebases and attractor strengths (linear model: B = 0.02, p = 0.47, R2 < 0.01; polynomial model: B < 0.01, p = 0.61, R2 < 0.01). Sensitivity analyses where we (1) weighed estimates according to their uncertainty and (2) removed individuals with a DSM-5 diagnosis from the analyses did not change this finding. This suggests that stability is similar across severity levels, implying that subthreshold psychopathology may resemble a stable state rather than a transient intermediate between mental health and psychiatric disorder. Our study thus provides additional support for a dimensional view on psychopathology, which implies that symptoms differ in degree rather than kind.
Low parasite connectivity among three malaria hotspots in Thailand
Authors: Chang Hsiao-Han , Chang Meng-Chun , Kiang Mathew , Mahmud Ayesha S. , Ekapirat Nattwut , Engø-Monsen Kenth , Sudathip Prayuth , Buckee Caroline O. , Maude Richard J. 
Published: December 2021

AbstractIdentifying sources and sinks of malaria transmission is critical for designing effective intervention strategies particularly as countries approach elimination. The number of malaria cases in Thailand decreased 90% between 2012 and 2020, yet elimination has remained a major public health challenge with persistent transmission foci and ongoing importation. There are three main hotspots of malaria transmission in Thailand: Ubon Ratchathani and Sisaket in the Northeast; Tak in the West; and Yala in the South. However, the degree to which these hotspots are connected via travel and importation has not been well characterized. Here, we develop a metapopulation model parameterized by mobile phone call detail record data to estimate parasite flow among these regions. We show that parasite connectivity among these regions was limited, and that each of these provinces independently drove the malaria transmission in nearby provinces. Overall, our results suggest that due to the low probability of domestic importation between the transmission hotspots, control and elimination strategies can be considered separately for each region.