bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening of potential immune-related genes expressed during sepsis using gene sequencing technology
Authors: Tian Ye , Wang Chenglin , Lu Qiangyong , Zhang Chuan , Hu Lin , Ling Jiamei , Chen Muhu , Hu Yingchun 
Published: March 2023

AbstractTo screen potential pivotal targets in sepsis through peripheral blood. Septic patients (n = 23) and healthy volunteers (n = 10) were enrolled according to SEPSIS 3.0. Peripheral blood was collected within 24 h of enrollment, RNA-seq was performed on the peripheral blood. The sequencing data was screened for DEGs (p < 0.01; logFC ≥ 2). PPI, WGCNA and survival curve analysis were used to identify potential targets. Then, 5 PBMC samples were conducted by single-cell sequencing for cell lineage location. Finally, mouse sepsis model and clinic samples were performed to verify the targets gene using RNA-seq and RT-PCR, respectively. Compared to the control group, 1007 DEGs were found in septic group. BCL9L, BCL11B, CD247, CD96, MAFG and SAMD3 were in the core of network. These six genes correlated to the survival rate of septic patients and they were mainly expressed in T cells, except that MAFG was located in monocyte cell. The expression levels of six key genes were confirmed by animal and clinical samples. BCL9L, BCL11B, CD247, CD96 and SAMD3 were decreased in sepsis and mainly expressed in the T cell; while MAFG increased in sepsis and localizes to monocytes. These genes may be therapeutic targets for sepsis.
Determination of the fate of Cholecalciferol injected by the basis of 25D3 plasma concentration
Authors: Mousavi Rad Seyed Ali , Haji Hajikolaei Mohammad Rahim , Nouri Mohammad , Seyfi Abad Shapouri Masoud Reza , Ghorbanpoor Masoud 
Published: March 2023

AbstractSun exposure in bovines is believed to be the most important route of 25D3synthesis in suitable latitudes. In some situations, e.g. breeding systems, solar radiation cannot reach or penetrate into the skin and thus causes the 25D3deficiency. Because of the critical effect of vitamin D on the immune and endocrine systems, the plasma must be enriched with 25D3in a short period of time. In such a condition, injection of Cholecalciferol has been recommended. However, to our knowledge, the certain dose of Cholecalciferol injection for rapid 25D3plasma enrichment has not been verified. On the other hand, it seems that the basis 25D3concentration can influence or shift the 25D3metabolism at the injection time. In the same line, the present study, designed to induce the different basis 25D3concentration in treatment groups, aimed at investigating the effect of Cholecalciferol intramuscularly injection with the intermediate dose (11,000 IU/kg) on the calves' plasma 25D3with different basis 25D3. Besides, an attempt was made to clarify the time that 25D3reaches the sufficient concentration after injection in different treatment groups. To do this, twenty calves of 3 to 4 months old were chosen for the farm with semi-industrial elements. Furthermore, the effect of optional sun exposure/deprivation and Cholecalciferol injection on the 25D3concentration variations was assayed. To do this, the calves were divided into four groups. Groups A and B were unconstrained to choose sun to expose or shadow in a semi-roofed place, but groups C and D were restricted to the completely dark barn. The interference of the digestive system in supplying vitamin D was minimized through dietary. All groups had a different basic concentration (25D3) on the day 21 of the experiment. At this time, groups A and C received the intermediate dose of (11,000 IU/kg) Cholecalciferol intramuscularly (IM). After Cholecalciferol injection, the effects of basis 25D3concentration on the details of variation and fate of plasma concentration of 25D3were investigated. The data collected from the two groups C and D showed that sun deprivation without any vitamin D supplementation, could rapidly and severely deplete the plasma from 25D3. Cholecalciferol injection could not immediately increase the 25D3in the groups C and A. However, this injection enriches the 25D3to sufficient value after two weeks if the basis 25D3of plasma is insufficient, i.e. less than 30 ng/mL. Moreover, the injection of Cholecalciferol could not significantly increase the 25D3concentration in the group A that had a sufficient basis 25D3concentration. Therefore, it is concluded that the variation of 25D3in plasma, after injection of Cholecalciferol, depends on its basic level at the time of injection.
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation
Authors: Guo Hao-Bo , Varaljay Vanessa A. , Kedziora Gary , Taylor Kimberly , Farajollahi Sanaz , Lombardo Nina , Harper Eric , Hung Chia , Gross Marie , Perminov Alexander , Dennis Patrick , Kelley-Loughnane Nancy , Berry Rajiv 
Published: March 2023

AbstractDespite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence fromAcidimicrobiaceae TMED77(T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two Fe4S4iron-sulfur clusters for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility in complex with the ligands, i.e., in their native states. Therefore, an apo-protein predicted by AF2 is actually a holo-protein awaiting ligands.
A Bayesian multi-proxy contribution to the socioeconomic, political, and cultural history of late medieval Capitanata (southern Italy)
Authors: Cocozza Carlo , Teegen Wolf-Rüdiger , Vigliarolo Ilaria , Favia Pasquale , Giuliani Roberta , Muntoni Italo Maria , Oione Domenico , Clemens Lukas , Groß Marcus , Roberts Patrick , Lubritto Carmine , Fernandes Ricardo 
Published: March 2023

AbstractMedieval southern Italy is typically viewed as a region where political, religious, and cultural systems coexisted and clashed. Written sources often focus on elites and give an image of a hierarchical feudal society supported by a farming economy. We undertook an interdisciplinary study combining historical and archaeological evidence with Bayesian modelling of multi-isotope data from human (n = 134) and faunal (n = 21) skeletal remains to inform on the socioeconomic organisation, cultural practices, and demographics of medieval communities in Capitanata (southern Italy). Isotopic results show significant dietary differences within local populations supportive of marked socioeconomic hierarchies. Bayesian dietary modelling suggested that cereal production, followed by animal management practices, was the economic basis of the region. However, minor consumption of marine fish, potentially associated with Christian practices, revealed intra-regional trade. At the site of Tertiveri, isotope-based clustering and Bayesian spatial modelling identified migrant individuals likely from the Alpine region plus one Muslim individual from the Mediterranean coastline. Our results align with the prevailing image of Medieval southern Italy but they also showcase how Bayesian methods and multi-isotope data can be used to directly inform on the history of local communities and of the legacy that these left.
Casson nanoliquid film flow over an unsteady moving surface with time-varying stretching velocity
Authors: Vanitha G. P. , Shobha K. C. , Mallikarjun B. Patil , Mahabaleshwar U. S. , Bognár Gabriella 
Published: March 2023

AbstractPresent study explains about unsteady Casson nanoliquid film flow over a surface moving with velocity $$U_w=\lambda x/t$$

U
w

=
λ
x
/
t

. The governing momentum equation is reduced to ODE by using corresponding similarity transformation, which is then tackled by employing numerical technique. The problem is analysed for both two-dimensional film flow and axisymmetric film flow. The exact solution is derived which satisfies the governing equation. It is noted that solution exists only for a specified scale of the moving surface parameter $$\lambda$$
λ
. ie., $$\lambda \ge -1/2$$

λ
≥
-
1
/
2

for two-dimensional flow and $$\lambda \le -1/4$$

λ
≤
-
1
/
4

for axisymmetric flow. The velocity increases first and reaches the maximum velocity and then decreases to the boundary condition. Streamlines are also analysed for both axisymmetric and two-dimensional flow patterns by considering the stretching ($$\lambda >0$$

λ
>
0

) and shrinking wall conditions ($$\lambda <0$$

λ
<
0

). Study has been made for large values of wall moving parameter $$\lambda$$
λ
. The aim of this investigation is to analyse the Casson nanoliquid film flow which finds applications in industries like coating of sheet or wire, laboratories, painting, many more.
Increased empathic distress in adults is associated with higher levels of childhood maltreatment
Authors: Benz Annika B. E. , Dimitroff Stephanie J. , Jeggle Christin , Gaertner Raphaela J. , Meier Maria , Unternaehrer Eva , Bentele Ulrike U. , Denk Bernadette F. , Klink Elea S. C. , Pruessner Jens C. 
Published: March 2023

AbstractWhile many studies investigated basic facets of empathy, less is known about the association with early life adversity (ELA). To investigate a possible association of empathy with ELA, we assessed self-reported ELA, using the Childhood Trauma Questionnaire (CTQ), the Parental Bonding Instrument (PBI) for mother and father, and empathy, using the Interpersonal Reactivity Index (IRI), in a sample of N = 228 (83% female, agemean = 30.51 ± 9.88 years, agerange = 18–60). Further, we measured willingness to donate a certain percentage of study compensation to a charity as an index of prosocial behavior. In line with our hypotheses that stated a positive association of empathy with ELA, increased levels of emotional, physical, and sexual abuse, and emotional and physical neglect were positively correlated with personal distress in response to others’ suffering. Likewise, higher parental overprotection and lower parental care were related to higher personal distress. Furthermore, while participants with higher levels of ELA tended to donate more money on a merely descriptive level, only higher levels of sexual abuse were significantly related to larger donations after correction for multiple statistical tests. Other facets of the IRI (empathic concern, perspective taking and fantasy) were not related to any other ELA measure. This suggests ELA only affects levels of personal distress.
Only empathy-related traits, not being mimicked or endorphin release, influence social closeness and prosocial behavior
Authors: Rauchbauer Birgit , Jank Gabriela , Dunbar Robin I. M. , Lamm Claus 
Published: March 2023

AbstractSeminal studies suggest that being mimicked increases experienced social closeness and prosocial behavior to a mimicking confederate (i.e., interaction partner). Here we reexamine these results by considering the role of empathy-related traits, an indirect proxy for endorphin uptake, and their combined effects as an explanation for these results. 180 female participants were mimicked or anti-mimicked in an interaction with a confederate. The effects of being mimicked versus anti-mimicked in relation to empathy-related traits and endorphin release (assessed indirectly via pain tolerance) on experienced closeness and prosocial behavior were assessed using Bayesian analyses. Our results suggest that high individual empathy-related traits increase social closeness to the anti-mimicking and mimicking confederate and to one’s romantic partner, as compared to mimicry alone. Results furthermore strongly suggest that high individual empathy-related traits increase prosocial behavior (donations and willingness to help) as compared to mimicry alone. These findings extend previous work by highlighting that empathy-related traits are more influential in creating positive effects on social closeness and prosocial behavior than a one-shot mimicking encounter.
Acute and chronic stress alter behavioral laterality in dogs
Authors: Salgirli Demirbas Yasemin , Isparta Sevim , Saral Begum , Keskin Yılmaz Nevra , Adıay Deniz , Matsui Hiroshi , Töre-Yargın Gülşen , Musa Saad Adam , Atilgan Durmus , Öztürk Hakan , Kul Bengi Cinar , Şafak C. Etkin , Ocklenburg Sebastian , Güntürkün Onur 
Published: March 2023

AbstractDogs are one of the key animal species in investigating the biological mechanisms of behavioral laterality. Cerebral asymmetries are assumed to be influenced by stress, but this subject has not yet been studied in dogs. This study aims to investigate the effect of stress on laterality in dogs by using two different motor laterality tests: the Kong™ Test and a Food-Reaching Test (FRT). Motor laterality of chronically stressed (n = 28) and emotionally/physically healthy dogs (n = 32) were determined in two different environments, i.e., a home environment and a stressful open field test (OFT) environment. Physiological parameters including salivary cortisol, respiratory rate, and heart rate were measured for each dog, under both conditions. Cortisol results showed that acute stress induction by OFT was successful. A shift towards ambilaterality was detected in dogs after acute stress. Results also showed a significantly lower absolute laterality index in the chronically stressed dogs. Moreover, the direction of the first paw used in FRT was a good predictor of the general paw preference of an animal. Overall, these results provide evidence that both acute and chronic stress exposure can change behavioral asymmetries in dogs.
SMAD2/3 signaling in the uterine epithelium controls endometrial cell homeostasis and regeneration
Authors: Kriseman Maya L. , Tang Suni , Liao Zian , Jiang Peixin , Parks Sydney E. , Cope Dominique I. , Yuan Fei , Chen Fengju , Masand Ramya P. , Castro Patricia D. , Ittmann Michael M. , Creighton Chad J. , Tan Zhi , Monsivais Diana 
Published: March 2023

AbstractThe regenerative potential of the endometrium is attributed to endometrial stem cells; however, the signaling pathways controlling its regenerative potential remain obscure. In this study, genetic mouse models and endometrial organoids are used to demonstrate that SMAD2/3 signaling controls endometrial regeneration and differentiation. Mice with conditional deletion of SMAD2/3 in the uterine epithelium using Lactoferrin-iCre develop endometrial hyperplasia at 12-weeks and metastatic uterine tumors by 9-months of age. Mechanistic studies in endometrial organoids determine that genetic or pharmacological inhibition of SMAD2/3 signaling disrupts organoid morphology, increases the glandular and secretory cell markers, FOXA2 and MUC1, and alters the genome-wide distribution of SMAD4. Transcriptomic profiling of the organoids reveals elevated pathways involved in stem cell regeneration and differentiation such as the bone morphogenetic protein (BMP) and retinoic acid signaling (RA) pathways. Therefore, TGFβ family signaling via SMAD2/3 controls signaling networks which are integral for endometrial cell regeneration and differentiation.
Rare sugar l-sorbose exerts antitumor activity by impairing glucose metabolism
Authors: Xu Hui-Lin , Zhou Xiaoman , Chen Shuai , Xu Si , Li Zijie , Nakanishi Hideki , Gao Xiao-Dong 
Published: March 2023

AbstractRare sugars are monosaccharides with low natural abundance. They are structural isomers of dietary sugars, but hardly be metabolized. Here, we report that rare sugar l-sorbose induces apoptosis in various cancer cells. As a C-3 epimer of d-fructose, l-sorbose is internalized via the transporter GLUT5 and phosphorylated by ketohexokinase (KHK) to produce l-sorbose-1-phosphate (S-1-P). Cellular S-1-P inactivates the glycolytic enzyme hexokinase resulting in attenuated glycolysis. Consequently, mitochondrial function is impaired and reactive oxygen species are produced. Moreover, l-sorbose downregulates the transcription of KHK-A, a splicing variant of KHK. Since KHK-A is a positive inducer of antioxidation genes, the antioxidant defense mechanism in cancer cells can be attenuated by l-sorbose-treatment. Thus, l-sorbose performs multiple anticancer activities to induce cell apoptosis. In mouse xenograft models, l-sorbose enhances the effect of tumor chemotherapy in combination with other anticancer drugs. These results demonstrate l-sorbose as an attractive therapeutic reagent for cancer treatment.
Rough capillary rise
Authors: Panter Jack R. , Konicek Andrew R. , King Mark A. , Jusufi Arben , Yeganeh Mohsen S. , Kusumaatmaja Halim 
Published: March 2023

AbstractCapillary rise within rough structures is a wetting phenomenon that is fundamental to survival in biological organisms, deterioration of our built environment, and performance of numerous innovations, from 3D microfluidics to carbon capture. Here, to accurately predict rough capillary rise, we must couple two wetting phenomena: capillary rise and hemiwicking. Experiments, simulations, and theory demonstrate how this coupling challenges our conventional understanding and intuitions of wetting and roughness. Firstly, the critical contact angle for hemiwicking becomes separation-dependent so that hemiwicking can vanish for even highly wetting liquids. Secondly, the rise heights for perfectly wetting liquids can differ between smooth and rough systems, even with the same 0∘ contact angle. Finally, the raised liquid volumes are substantially increased in rough compared to smooth systems. To explain and predict all rise heights and volumes with quantitative accuracy, we present the Dual-Rise model that is valid for general roughness, liquids, and surface wettabilities.
A two‐stage algorithm for vehicle routing problem with charging relief in post‐disaster
Authors: Liu Qixing , Xu Peng , Wu Yuhu , Shen Tielong 
Published: March 2023

AbstractThis paper first investigates emergency transportation for power recovery in post‐disaster. The problem is formulated as a mixed‐integer linear programming model called vehicle routing problem with charging relief (VRPCR). The battery state of charge () implies the working hours that the battery can provide. The goal is to make a set of shelters charge before the battery of shelters reaches the minimum bound over time. To this end, a two‐stage algorithm is developed to deal with the problem. In stage I, a reduced road network is obtained from a leading road network by the A‐star search algorithm. Subsequently, to determine the order of power delivery with charging operations at shelters by enhanced genetic algorithm (EGA) in stage II. To evaluate this strategy, the detailed complexity analysis of the three algorithms and results tested on a realistic disaster scenario shows the performance of the A‐star search algorithm for VRPCR that outperforms the Dijkstra and Floyd algorithms. In addition, the EGA is applied to Solomon's benchmarks compared with the state‐of‐the‐art heuristic algorithms, which indicates a better performance of EGA. A real case obtained from a disaster scenario in Ichihara City, Japan is also conducted. Simulation results demonstrate that the method can achieve satisfactory solutions.
Evaluation of the Effectiveness of Systemic Inflammatory Indices in the Diagnosis of Respiratory Distress Syndrome in Preterm with Gestational Age of ≤32 Weeks
Authors: Cakir Ufuk , Tugcu Ali Ulas , Tayman Cuneyt , Yildiz Duran 
Published: March 2023

Objective It is not yet known whether systemic inflammatory indices affect the development of respiratory distress syndrome (RDS) in premature infants. We aimed to evaluate the relationship between systemic inflammatory indices obtained on the first day of life and the development of RDS in premature infants.
Study Design Premature infants with gestational age of ≤32 weeks were included in the study. Six systemic inflammatory indices involving neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), systemic immune-inflammation index (SII), pan-immune-inflammation value (PIV), and systemic inflammation response index (SIRI) were measured in the first 1 hour after birth and compared in premature infants with and without RDS.
Results A total of 931 premature infants, 579 infants in the RDS group and 352 infants in the non-RDS group, were included in the study. MLR, PLR, and SIRI values were similar between the groups (p > 0.05 for all parameters). NLR, PIV, and SII values in the RDS group were significantly higher than those in the non-RDS group (p = 0.005, p = 0.011, and p < 0.001, respectively). In the predictivity of RDS, the AUC value of SII was 0.842 and the cut-off value was ≥78.200. Multiple logistic analysis showed that a higher level of SII (≥78.2) was independently associated with RDS (odds ratio: 3.03, 95% confidence interval: 1.761–5.301).
Conclusion Our results demonstrated that a higher SII level (≥78.2) may be a predictor for the development of RDS in premature infants with gestational age of ≤32 weeks.
Key Points
A Natural Language Processing Model to Identify Confidential Content in Adolescent Clinical Notes
Authors: Rabbani Naveed , Bedgood Michael , Brown Conner , Steinberg Ethan , Goldstein Rachel L. , Carlson Jennifer L. , Pageler Natalie , Morse Keith E. 
Published: March 2023

Abstract
Background The 21st Century Cures Act mandates the immediate, electronic release of health information to patients. However, in the case of adolescents, special consideration is required to ensure that confidentiality is maintained. The detection of confidential content in clinical notes may support operational efforts to preserve adolescent confidentiality while implementing information sharing.
Objectives This study aimed to determine if a natural language processing (NLP) algorithm can identify confidential content in adolescent clinical progress notes.
Methods A total of 1,200 outpatient adolescent progress notes written between 2016 and 2019 were manually annotated to identify confidential content. Labeled sentences from this corpus were featurized and used to train a two-part logistic regression model, which provides both sentence-level and note-level probability estimates that a given text contains confidential content. This model was prospectively validated on a set of 240 progress notes written in May 2022. It was subsequently deployed in a pilot intervention to augment an ongoing operational effort to identify confidential content in progress notes. Note-level probability estimates were used to triage notes for review and sentence-level probability estimates were used to highlight high-risk portions of those notes to aid the manual reviewer.
Results The prevalence of notes containing confidential content was 21% (255/1,200) and 22% (53/240) in the train/test and validation cohorts, respectively. The ensemble logistic regression model achieved an area under the receiver operating characteristic of 90 and 88% in the test and validation cohorts, respectively. Its use in a pilot intervention identified outlier documentation practices and demonstrated efficiency gains over completely manual note review.
Conclusion An NLP algorithm can identify confidential content in progress notes with high accuracy. Its human-in-the-loop deployment in clinical operations augmented an ongoing operational effort to identify confidential content in adolescent progress notes. These findings suggest NLP may be used to support efforts to preserve adolescent confidentiality in the wake of the information blocking mandate.