bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical characterisation of electron tunnelling from granular activated carbon to electron accepting organisms in direct interspecies electron transfer
Authors: Rao Rohan , Hu Jing , Lee Po-Heng 
Published: July 2022

AbstractDirect interspecies electron transfer (DIET) has been identified as an efficient metabolism between symbiotically interacting organisms. One method of DIET uses conductive materials (e.g., granular activated carbon (GAC)) as a medium to shuttle electrons from electron donating organisms (eg., Geobacter metallireducens) to electron accepting organisms (e.g., Geobacter sulfurreducens and Methanosarcina barkeri). Conductive materials such as GAC, become negatively charged in DIET processes due to reduction by electron donating organisms. This high excess electron density in GAC leads to quantum tunnelling of electrons being a significant electron transfer mechanism for DIET. Thus, a theoretical model obeying the Wentzel–Kramers–Brillouin (WKB) approximation and Fermi–Dirac statistics was developed and simulated. In the model, the electron tunnelling transfer barrier was described by an effective rectangular barrier. The result of our 1D tunnelling simulations indicates that within 29.4 nm of the GAC, tunnelling can sufficiently supply electrons from GAC to G. sulfurreducens and M. barkeri. The phenomenon of tunnelling may also have significance as a stimulant of chemotaxis for G. sulfurreducens and other electron accepting microbes when attempting to adsorb onto GAC. This study sheds light on quantum tunnelling’s significant potential in both bacterium and archaeon DIET-centric processes.
Cone penetration index for soil behaviour type prediction
Authors: Sodré Denilson José Ribeiro 
Published: July 2022

AbstractSeveral approaches have been proposed to classify soil types using both cone and piezocone penetration tests. The chart relating the normalized cone resistance (Qtn) and the friction ratio (Fr) has proven to be the most reliable method. However, its practical use requires function fitting, where the chart is described by means of a soil behaviour type index. The currently available indexes for this chart, based on concentric circles and hyperbolas, lead to significant errors. Thus, to properly represent theQtn–Frchart, this study proposes new soil behaviour type indexes based on an analytical approach from a concentric logarithmic spiral approximation and a numerical approach from an exponential function approximation. The new indexes provide an improvement in the reproduction of the soil type zones while preserving the robustness of the original method. A discussion on the cone penetration test-based soil type classification is presented, along with a case example comparing the soil behaviour indexes in soil profiling.
Subduction age and stress state control on seismicity in the NW Pacific subducting plate
Authors: Pino Nicola Alessandro , Convertito Vincenzo , Godano Cataldo , Piromallo Claudia 
Published: July 2022

AbstractIntermediate depth (70–300 km) and deep (> 300 km) earthquakes have always been puzzling Earth scientists: their occurrence is a paradox, since the ductile behavior of rocks and the high confining pressure with increasing depths would theoretically preclude brittle failure and frictional sliding. The mechanisms proposed to explain deep earthquakes, mainly depending on the subducting plate age and stress state, are generally expressed by single parameters, unsuitable to comprehensively account for differences among distinct subduction zones or within the same slab. We analyze the Kurile and Izu–Bonin intraslab seismicity and detail the Gutenberg–Richter b-value along the subducted planes, interpreting its variation in terms of stress state, analogously to what usually done for shallow earthquakes. We demonstrate that, despite the slabs different properties (e.g., lithospheric age, stress state, dehydration rate), in both cases deep earthquakes are restricted to depths characterized by equal age from subduction initiation and are driven by stress regimes affected by the persistence of the metastable olivine wedge.
Repatriation of a historical North Atlantic right whale habitat during an era of rapid climate change
Authors: O’Brien O. , Pendleton D. E. , Ganley L. C. , McKenna K. R. , Kenney R. D. , Quintana-Rizzo E. , Mayo C. A. , Kraus S. D. , Redfern J. V. 
Published: July 2022

AbstractClimate change is affecting species distributions in space and time. In the Gulf of Maine, one of the fastest-warming marine regions on Earth, rapid warming has caused prey-related changes in the distribution of the critically endangered North Atlantic right whale (Eubalaena glacialis). Concurrently, right whales have returned to historically important areas such as southern New England shelf waters, an area known to have been a whaling ground. We compared aerial survey data from two time periods (2013–2015; 2017–2019) to assess trends in right whale abundance in the region during winter and spring. Using distance sampling techniques, we chose a hazard rate key function to model right whale detections and used seasonal encounter rates to estimate abundance. The mean log of abundance increased by 1.40 annually between 2013 and 2019 (p = 0.004), and the mean number of individuals detected per year increased by 2.23 annually between 2013 and 2019 (R2 = 0.69, p = 0.001). These results demonstrate the current importance of this habitat and suggest that management options must continually evolve as right whales repatriate historical habitats and potentially expand to new habitats as they adapt to climate change.
Association of serum s-adenosylmethionine, s-adenosylhomocysteine, and their ratio with the risk of dementia and death in a community
Authors: Mihara Akane , Ohara Tomoyuki , Hata Jun , Chen Sanmei , Honda Takanori , Tamrakar Sonam , Isa Akiko , Wang Dongmei , Shimizu Kuniyoshi , Katakura Yoshinori , Yonemoto Koji , Nakao Tomohiro , Kitazono Takanari , Ninomiya Toshiharu 
Published: July 2022

AbstractWe examined the association of serum s-adenosylmethionine (SAM), s-adenosylhomocysteine (SAH) (methionine metabolites), and their ratio on the risk of dementia and death in a community-dwelling population of older Japanese individuals. 1371 residents of Hisayama, Japan, aged 65 years or older and without dementia, were followed for a median of 10.2 years (2007–2017). We divided serum SAM, SAH, and SAM/SAH ratio into quartiles. Cox proportional hazards models were used to estimate the hazard ratios (HRs) and their 95% confidence intervals (CIs) of serum SAM, SAH, and SAM/SAH ratio levels on the risk of a composite outcome of all-cause dementia or death, and each outcome. During the follow-up, 635 participants developed all-cause dementia and/or died, of which 379 participants developed dementia and 394 deaths occurred. The multivariable-adjusted HRs of the composite outcome decreased significantly with increasing serum SAM levels (Pfor trend = 0.01), while they increased significantly with higher serum SAH levels (Pfor trend = 0.03). Higher serum SAM/SAH ratio levels were significantly associated with a lower risk of the composite outcome (Pfor trend = 0.002), as well as with lower risk of each outcome. Our findings suggest that the balance of methionine metabolites may closely associate with the risk of dementia and death.
APOA1 mRNA and protein in kidney renal clear cell carcinoma correlate with the disease outcome
Authors: Zeng Wei , Xiong Guoguang , Hua Li , Hu Yugang , Guo Xufeng , Peng Xiulan 
Published: July 2022

AbstractRenal cancer is one of the most common malignant tumors with high mortality, and kidney renal clear cell carcinoma (KIRC) is the most common type of renal cancer. We attempted to evaluate the clinical and prognostic significance of Apolipoprotein A1 (APOA1) mRNA and protein in KIRC patients. Clinical data along with RNA-sequencing data were downloaded from UCSC Xena. The Human Protein Atlas database was searched to reveal APOA1 protein expression profiles in KIRC and normal renal tissues. The TIMER database was applied to determine the correlations of APOA1 with immune cells and PD-1 and PD-L1 in KIRC. Ninety-one cases of KIRC patients and 93 healthy controls from our hospital were enrolled for clinical validation. Levels of APOA1 mRNA in KIRC tissues (N = 535) are not only lower than the levels in normal renal tissues (N = 117), but also in paired normal renal tissues (N = 72). High expression of APOA1 mRNA at the time of surgery was correlated with worse overall survival (OS) (HR 1.66; p = 0.037) and disease-free survival (DFS) (HR 1.65; p = 0.047), and APOA1 DNA methylation was linked to worse OS (HR 2.1; p = 0.001) rather than DFS (HR 1.12; p = 0.624) in KIRC patients. Concentrations of preoperative serum APOA1 protein were markedly decreased in KIRC patients compared to healthy controls (p < 0.01), and low levels of APOA1 protein predicted less favorable OS than those with high levels (HR = 2.84, p = 0.0407). APOA1 negatively correlated with various immune cell infiltrates and PD-L1 expression (r = − 0.283, p = 2.74e−11) according to the TIMER database. Low levels of APOA1 mRNA at the time of surgery predict favorable survival in KIRC patients. Our results provide insights to identify a novel prognostic index with great clinical utility.
Wildfire plumes in the Western US are reaching greater heights and injecting more aerosols aloft as wildfire activity intensifies
Authors: Wilmot Taylor Y. , Mallia Derek V. , Hallar A. Gannet , Lin John C. 
Published: July 2022

AbstractBy producing a first-of-its-kind, decadal-scale wildfire plume rise climatology in the Western U.S. and Canada, we identify trends toward enhanced plume top heights, aerosol loading aloft, and near-surface smoke injection throughout the American West. Positive and significant plume trends suggest a growing impact of Western US wildfires on air quality at the local to continental scales and support the notion that wildfires may have an increasing impact on regional climate. Overlap of identified trends with regions of increasing wildfire emissions and burn severity suggests a link to climate driven trends toward enhanced wildfire activity. Further, time series of plume activity point to a possible acceleration of trends over recent years, such that the future impacts to air quality and regional climate may exceed those suggested by a linear fit to the multi-decadal data. These findings have significant implications for human health and exacerbate concern for the climate–wildfire connection.
Impact of an electronic alert system for pediatric sepsis screening a tertiary hospital experience
Authors: Alturki Abdullah , Al-Eyadhy Ayman , Alfayez Ali , Bendahmash Abdulrahman , Aljofan Fahad , Alanzi Fawaz , Alsubaie Hadeel , Alabdulsalam Moath , Alayed Tareq , Alofisan Tariq , Alnajem Afnan 
Published: July 2022

AbstractThis study aimed to assess the potential impact of implementing an electronic alert system (EAS) for systemic inflammatory syndrome (SIRS) and sepsis in pediatric patients mortality. This retrospective study had a pre and post design. We enrolled patients aged ≤ 14 years who were diagnosed with sepsis/severe sepsis upon admission to the pediatric intensive care unit (PICU) of our tertiary hospital from January 2014 to December 2018. We implemented an EAS for the patients with SIRS/sepsis. The patients who met the inclusion criteria pre-EAS implementation comprised the control group, and the group post-EAS implementation was the experimental group. Mortality was the primary outcome, while length of stay (LOS) and mechanical ventilation in the first hour were the secondary outcomes. Of the 308 enrolled patients, 147 were in the pre-EAS group and 161 in the post-EAS group. In terms of mortality, 44 patients in the pre-EAS group and 28 in the post-EAS group died (p 0.011). The average LOS in the PICU was 7.9 days for the pre-EAS group and 6.8 days for the post-EAS group (p 0.442). Considering the EAS initiation time as the “zero time”, early recognition of SIRS and sepsis via the EAS led to faster treatment interventions in post-EAS group, which included fluid boluses with median (25th, 75th percentile) time of 107 (37, 218) min vs. 30 (11,112) min, p < 0.001) and time to initiate antimicrobial therapy median (25th, 75th percentile) of 170.5 (66,320) min vs. 131 (53,279) min, p 0.042). The difference in mechanical ventilation in the first hour of admission was not significant between the groups (25.17% vs. 24.22%, p 0.895). The implementation of the EAS resulted in a statistically significant reduction in the mortality rate among the patients admitted to the PICU in our study. An EAS can play an important role in saving lives and subsequent reduction in healthcare costs. Further enhancement of systematic screening is therefore highly recommended to improve the prognosis of pediatric SIRS and sepsis. The implementation of the EAS, warrants further validation in multicenter or national studies.
Cell-free DNA 5-hydroxymethylcytosine is an emerging marker of acute myeloid leukemia
Authors: Shao Jianming , Wang Sihan , West-Szymanski Diana , Karpus Jason , Shah Shilpan , Ganguly Siddhartha , Smith Janice , Zu Youli , He Chuan , Li Zejuan 
Published: July 2022

AbstractAberrant changes in 5-hydroxymethylcytosine (5hmC) are a unique epigenetic feature in many cancers including acute myeloid leukemia (AML). However, genome-wide analysis of 5hmC in plasma cell-free DNA (cfDNA) remains unexploited in AML patients. We used a highly sensitive and robust nano-5hmC-Seal technology and profiled genome-wide 5hmC distribution in 239 plasma cfDNA samples from 103 AML patients and 81 non-cancer controls. We developed a 5hmC diagnostic model that precisely differentiates AML patients from controls with high sensitivity and specificity. We also developed a 5hmC prognostic model that accurately predicts prognosis in AML patients. High weighted prognostic scores (wp-scores) in AML patients were significantly associated with adverse overall survival (OS) in both training (P = 3.31e−05) and validation (P = 0.000464) sets. The wp-score was also significantly associated with genetic risk stratification and displayed dynamic changes with varied disease burden. Moreover, we found that high wp-scores in a single gene, BMS1 and GEMIN5 predicted OS in AML patients in both the training set (P = 0.023 and 0.031, respectively) and validation set (P = 9.66e−05 and 0.011, respectively). Lastly, our study demonstrated the genome-wide landscape of DNA hydroxymethylation in AML and revealed critical genes and pathways related to AML diagnosis and prognosis. Our data reveal plasma cfDNA 5hmC signatures as sensitive and accurate markers for AML diagnosis and prognosis. Plasma cfDNA 5hmC analysis will be an effective and minimally invasive tool for AML management.
Net greenhouse gas balance with cover crops in semi-arid irrigated cropping systems
Authors: Acharya Pramod , Ghimire Rajan , Paye Wooiklee S. , Ganguli Amy C. , DelGrosso Stephen J. 
Published: July 2022

AbstractClimate smart agriculture has been emphasized for mitigating anthropogenic greenhouse gas (GHG) emissions, yet the mitigation potential of individual management practices remain largely unexplored in semi-arid cropping systems. This study evaluated the effects of different winter cover crop mixtures on CO2 and N2O emissions, net GHG balance (GHGnet), greenhouse gas intensity (GHGI), yield-scaled GHG emissions, and soil properties in irrigated forage corn (Zea mays L.) and sorghum (Sorghum bicolor L. Moench) rotations. Four cover crop treatments: (1) grasses, brassicas, and legumes mixture (GBL), (2) grasses and brassicas mixture (GB), (3) grasses and legumes mixture (GL), and (4) a no-cover crop (NCC) control, each replicated four times under corn and sorghum phase of the rotations, were tested in the semi-arid Southern Great Plains of USA. Results showed 5–10 times higher soil respiration with cover crop mixtures than NCC during the cover crop phase and no difference during the cash crop phase. The average N2O-N emission in NCC was 44% lower than GL and 77% lower than GBL in corn and sorghum rotations. Cash crop yield was 13–30% greater in cover crop treatments than NCC, but treatment effects were not observed for GHGnet, yield-scaled emissions, and GHGI. Integrating cover crops could be a climate smart strategy for forage production in irrigated semi-arid agroecosystems.
On the spectral closeness and residual spectral closeness of graphs
Authors: Zheng Lu , Zhou Bo 
Published: July 2022

The spectral closeness of a graph G is defined as the spectral radius of the closeness matrix of G, whose (u, v)-entry for vertex u and vertex v is 2−dG(u,v) if u ≠ v and 0 otherwise, where dG(u, v) is the distance between u and v in G. The residual spectral closeness of a nontrivial graph G is defined as the minimum spectral closeness of the subgraphs of G with one vertex deleted. We propose local grafting operations that decrease or increase the spectral closeness and determine those graphs that uniquely minimize and/or maximize the spectral closeness in some families of graphs. We also discuss extremal properties of the residual spectral closeness.
Blutbasierte Biomarker zur Optimierung der Früh- und
Differentialdiagnostik der Alzheimer-Demenz
Authors: Hansen Niels , Rauter Carolin , Wiltfang Jens 
Published: July 2022

Zusammenfassung
Ziele der Studie Die Demenz bei Alzheimer-Krankheit ist eine globale
Herausforderung. Studien weisen auf Blutbiomarker zur Diagnose der
Alzheimer-Krankheit als eine minimal invasive, schnellere,
kostengünstigere und daher zukunftsträchtige Methode hin. Ziel
dieser Übersicht ist es, Studien zu vielversprechenden Biomarkern der
Alzheimer-Krankheit darzustellen.
Methodik Für diese Übersichtsarbeit wurden aktuelle
Studien zusammengestellt.
Ergebnisse Immunassays mit anschließender Massenspektrometrie und
solche mit immunmagnetischer Reduktion sind aussichtsreiche Methoden für
die Bestimmung von Amyloid-ß 42 (Aß42) und Amyloid-ß 40
(Aß40) für die Bildung der Ratio von
Aß42/Aß40 zur blutbasierten Früh- und
Differentialdiagnostik der Alzheimer-Krankheit. Die Amyloid-ß
(Aß) Peptide im Blutplasma sind ein potentieller Marker der
Aß-Pathologie, da sie mit der Aß-Pathologie im Gehirn
korrelieren. Das mittels der Simoa Technologie bestimmte phosphorylierte
Tau-Protein 181 (p-tau181), das phosphorylierte Tau Protein 231 (p-tau231) und
das phosphorylierte Tau Protein 217 (p-tau217) im Blut sind vielversprechend
hinsichtlich einer möglichen Optimierung der Früh- und
Differentialdiagnostik der Alzheimer-Krankheit und sind Marker einer
Tau-Pathologie im Gehirn. Die Neurofilamente Leichtketten (Nfl) und das saure
Gliafaserprotein (GFAP) sind als Zusatzmarker hilfreich, um eine axonale und
astrogliale Hirnschädigung bei Alzheimer-Krankheit zu beurteilen. GFAP
im Blut könnte vor allem als Zusatzmarker zur Frühdiagnostik und
Prädiktion des Verlaufs der Alzheimer-Krankheit sinnvoll sein.
Schlussfolgerungen Blutbasierte Biomarker sind ein wichtiger Schritt in
Richtung einer weniger invasiven und kostengünstigeren Diagnostik der
Alzheimer-Krankheit. Die Ratio Aß42/Aß40, das p-tau181,
das p-tau217, das p-tau231, die Nfl und das GFAP sind vielversprechende
Blutbiomarker unter Beachtung der AT(N) Klassifikation der Alzheimer-Krankheit.
Hochdurchsatzfähige Methoden sollten in großen Kohorten und
Metanalysen evaluiert werden. Zudem sollten Konsensus Kriterien mit
einheitlichen Protokollen mit Normwerten zur Messung dieser Biomarker erstellt
werden. Die Etablierung der AT(N) Klassifikation der Alzheimer-Krankheit im Blut
ist unter Berücksichtigung ethischer Gesichtspunkte sowie des Alzheimer
Phänotyps ein wichtiger Baustein für die Implementierung einer
minimal-invasiven Präzisionsmedizin.
Outcomes of balloon vs basket catheter for clearance of choledocholithiasis: a systematic review and meta-analysis
Authors: Sharma Ruchi , Sharma Vikram , Singhal Umang , Sanaka Madhusudhan 
Published: July 2022

Abstract
Background and study aims Endoscopic retrograde cholangiopancreatography (ERCP) is the mainstay for treatment of choledocholithiasis. It is unclear whether balloon or basket catheters are better for extraction of stones ≤ 10 mm in size. We performed a meta-analysis of studies comparing rates of complete stone extraction and adverse events after ERCP using balloon vs basket catheters for bile duct stones ≤ 10 mm in size.
Methods Cochrane database, PubMed, Web of Science, and Embase were searched from inception to October 2021. Randomized control trials comparing outcomes of balloon vs basket catheter were included. Data extraction of articles was carried out by two authors using predefined inclusion criteria. Metanalysis was carried out using the Revman 5.4.1. software using a random-effects model.
Results Three studies with a total of 508 patients were included in the final analysis. For common bile duct stones ≤ 10 mm, balloon catheters had higher complete stone clearance rates than basket catheters (relative risk 1.1, confidence interval 1.03, 1.18, P = 0.006). Heterogeneity among studies was low (Tau2  = 0.0; P = 0.47, I2  = 0 %). There was no difference in the rate of complications.
Conclusions Meta-analysis of three studies indicates that balloon catheters have a higher success rate compared to basket catheters for complete stone extraction for choledocholithiasis ≤ 10 mm with no significant difference in the rate of complications.
DxGenerator: An Improved Differential Diagnosis Generator for Primary Care Based on MetaMap and Semantic Reasoning
Authors: Sanaeifar Ali , Eslami Saeid , Ahadi Mitra , Kahani Mohsen , Vakili Arki Hassan 
Published: July 2022

Abstract
Background In recent years, researchers have used many computerized interventions to reduce medical errors, the third cause of death in developed countries. One of such interventions is using differential diagnosis generators in primary care, where physicians may encounter initial symptoms without any diagnostic presuppositions. These systems generate multiple diagnoses, ranked by their likelihood. As such, these reports' accuracy can be determined by the location of the correct diagnosis in the list.
Objective This study aimed to design and evaluate a novel practical web-based differential diagnosis generator solution in primary care.
Methods In this research, a new online clinical decision support system, called DxGenerator, was designed to improve diagnostic accuracy; to this end, an attempt was made to converge a semantic database with the unified medical language system (UMLS) knowledge base, using MetaMap tool and natural language processing. In this regard, 120 diseases of gastrointestinal organs causing abdominal pain were modeled into the database. After designing an inference engine and a pseudo-free-text interactive interface, 172 patient vignettes were inputted into DxGenerator and ISABEL, the most accurate similar system. The Wilcoxon signed ranked test was used to compare the position of correct diagnoses in DxGenerator and ISABEL. The α level was defined as 0.05.
Results On a total of 172 vignettes, the mean and standard deviation of correct diagnosis positions improved from 4.2 ± 5.3 in ISABEL to 3.2 ± 3.9 in DxGenerator. This improvement was significant in the subgroup of uncommon diseases (p-value < 0.05).
Conclusion Using UMLS knowledge base and MetaMap Tools can improve the accuracy of diagnostic systems in which terms are entered in a free text manner. Applying these new methods will help the medical community accept medical diagnostic systems better.