bluuebunny/crossref_metadata_2025_split huggingface dataset:
FGF1 alleviates LPS-induced acute lung injury via suppression of inflammation and oxidative stress
Authors: Dhlamini Qhaweni , Wang Wei , Feng Guifeng , Chen Aiping , Chong Lei , Li Xue , Li Quan , Wu Jin , Zhou Depu , Wang Jie , Zhang Hailin , Zhang Jin-San 
Published: June 2022

Abstract
Background
Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), are devastating clinical disorders with high mortality, and for which more effective therapies are urgently needed. FGF1, the prototype member of the FGF family, is shown to exert protective effects against injurious stimuli in multiple disease models. Here we aimed to evaluate whether FGF1 pretreatment is protective against LPS-induced ALI and elucidate the potential underlying mechanisms.

Methods
For drug-treated groups, C57B/6 mice received a single i.p. injection of FGF1 (1 mg/kg) 1 h before the LPS challenge or not. To induce the ALI model, the mice were treated by intratracheal instillation of LPS (5 mg/kg). Then, histopathological changes in lung tissues were assessed by hematoxylin and eosin staining and transmission electron microscopy. ELISA and qPCR assays were used to detect pro-inflammatory cytokine levels in BALF and lung tissues, respectively. The total number of inflammatory cells (neutrophils and macrophages) in BALF were counted using the Wright-Giemsa method. The expressions of reactive oxygen species (ROS) and malondialdehyde (MDA) were measured using their respective kits. Western blot and immunostaining were used to evaluate the expressions of antioxidants (Nrf-2, HO-1, SOD2, GPX4, and Catalase), as well as the inflammatory and/or apoptosis-related factors (TLR4, NF-κB, and Cleaved- caspase 3).

Results
FGF1 pretreatment significantly ameliorated the LPS-induced histopathological changes, reduced lung wet/dry ratios, ROS and MDA levels, total BALF protein, inflammatory cell infiltration, proinflammatory cytokine levels, and significantly increased the expression of antioxidant proteins (Nrf-2, HO-1, Catalase, and SOD2). In addition, FGF1 pretreatment significantly reduced the expression of TLR4 and cleaved- caspase 3, inhibited NF-κB activation, and reduced LPS-induced cell apoptosis.

Conclusions
Altogether, our results suggest that FGF1 pretreatment is protective against LPS-induced ALI through mediating anti-inflammatory and antioxidant effects, which may be attributed to the downregulation of TLR4 expression and inhibition of NF-κB activation, as well as promotion of antioxidant defenses. Therefore, FGF1 administration may prove beneficial in preventative strategies for ALI/ARDS.
Consistency of parent-report SLC6A1 data in Simons Searchlight with Provider-Based Publications
Authors: Bain Jennifer M. , Snyder LeeAnne Green , Helbig Katherine L. , Cooper Dominique D. , Chung Wendy K. , Goodspeed Kimberly 
Published: June 2022

Abstract
Background
SLC6A1-related disorder is a recently identified, rare, genetic neurodevelopmental disorder that is associated with loss-of-function variants in SLC6A1. This gene encodes GABA transporter type I that is responsible for re-uptake of GABA from the synapse into the pre-synaptic terminal or circulating neuroglia. Based upon retrospective review of published cases and available research databases including Epi25 collective and SLC6A1 Connect patient database, the phenotypic spectrum is broad and includes developmental delay, epilepsy, and autism or autistic traits. SLC6A1 is one of the genes included in the Simons Searchlight registry, which includes standardized data collection across genetically identified neurodevelopmental conditions.

Methods
In this study, we compare parent-report measures of phenotypic features in the Simons Searchlight registry to previously published, provider-reported cases to assess if parent-report measures are consistent with what has been reported in the literature.

Results
There were 116 participants in the provider-reported dataset compared to 43 individuals in the caregiver-reported dataset. Carriers in Searchlight had 83 unique pathogenic or likely pathogenic variants in SLC6A1, which were predominantly missense or nonsense variants. There was no significant difference between groups for the prevalence of developmental delay, ASD, or ADHD. Caregivers more often reported hypotonia, while epilepsy was slightly more frequently reported by providers.

Conclusions
We propose that standardized parent-report data collection methods are consistent with provider reports on many core features of SLC6A1-related disorder. The availability of patient registries and standardized natural history studies may fill an important need in clinical trial readiness programs, with larger sample sizes than smaller published case series.
Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches
Authors: Nunn Adam , Otto Christian , Fasold Mario , Stadler Peter F , Langenberger David 
Published: June 2022

AbstractBackgroundCalling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in the context of the genetic background. The confounding effect of bisulfite conversion however can be conceptually resolved by observing differences in allele counts on a per-strand basis, whereby artificial mutations are reflected by non-complementary base pairs.ResultsHerein, we present a computational pre-processing approach for adapting sequence alignment data, thus indirectly enabling downstream analysis on a per-strand basis using conventional variant calling software such as GATK or Freebayes. In comparison to specialised tools, the method represents a marked improvement in precision-sensitivity based on high-quality, published benchmark datasets for both human and model plant variants.ConclusionThe presented “double-masking” procedure represents an open source, easy-to-use method to facilitate accurate variant calling using conventional software, thus negating any dependency on specialised tools and mitigating the need to generate additional, conventional sequencing libraries alongside bisulfite sequencing experiments. The method is available athttps://github.com/bio15anu/revelioand an implementation with Freebayes is available athttps://github.com/EpiDiverse/SNP
Heat-inactivated Lacticaseibacillus paracasei N1115 alleviates the damage due to brain function caused by long-term antibiotic cocktail exposure in mice
Authors: Zhang Yujie , Liang Huijing , Wang Yimie , Cheng Ruyue , Pu Fangfang , Yang Yang , Li Jinxing , Wu Simou , Shen Xi , He Fang 
Published: June 2022

AbstractCritical development period of intestinal microbiota occurs concurrently with brain development, and their interaction is influenced by the microbiota–gut–brain axis. This study examined how antibiotics exposure affected gut microbiota and brain development and analyzed the possible benefits of heat-inactivated Lacticaseibacillus paracasei N1115 (N1115). Thirty neonatal male mice were randomly divided into three groups and treated with sterilized water (control), an antibiotic cocktail (Abx), or antibiotics plus heat-inactivated N1115 (Abx + N1115) for 84 days. We found that while the mRNA levels of GABAAα1, GABAb1, and glucocorticoid receptor (GR) in the hippocampus and brain-derived neurotrophic factor (BDNF), GABAAα1, GABAb1, and nerve growth factor (NGF) in the prefrontal cortex were higher, the mRNA levels of 5-HT1A were lower in the Abx group. The Abx + N1115 group had lower mRNA levels of GABAAα1, GABAb1, and GR in the hippocampus and BDNF, GABAb1, and NGF in the prefrontal cortex than the Abx group. The latency period was longer in the Morris water maze test while longer rest time was seen in tail suspension test in the Abx group than the control and Abx + N1115 groups. In the open field test, the moving time and distance of the Abx group were reduced. Further, the alpha-diversity indexes of the Abx and Abx + N1115 groups were significantly lower than the control. Further, long-term exposure to antibiotics disrupted the intestinal microbiota as evidenced by decreased Bacteroides, Firmicutes, and Lactobacillus, and increased Proteobacteria and Citrobacter. However, N1115 significantly decreased the abundance of Citrobacter when compared with those in the Abx group. These results indicate that antibiotics can substantially damage the intestinal microbiota and cognitive function, causing anxiety and depression, which can be alleviated by heat-inactivated N1115 via modulation of the microbiota–gut–brain axis.
Transition in plant–plant facilitation in response to soil water and phosphorus availability in a legume-cereal intercropping system
Authors: Zhu Shuang-Guo , Cheng Zheng-Guo , Yin Hai-Hong , Zhou Rui , Yang Yu-Miao , Wang Jing , Zhu Hao , Wang Wei , Wang Bao-Zhong , Li Wen-Bo , Tao Hong-Yan , Xiong You-Cai 
Published: June 2022

Abstract
Background
The tradeoff between negative and positive interactions of facilitated species and facilitators may depend on the degree of resource availability in agroecosystems. However, the rhizospheric mechanisms driving trade-offs that occur along phosphorus (P) and water availability gradients have not yet been systematically clarified. We established three types of root isolation conditions (no barrier, nylon barrier and solid barrier) at different P and water addition levels to address the above issue in a maize-grass pea intercropping system.

Results
The total yield and biomass net effect (NE) and the relative interaction index (RII) were significantly higher than 0 under all environmental conditions, demonstrating that plant-plant interactions generated positive effects in the intercropping system. The maize yield and biomass RII were 0.029–0.095 and 0.018–0.066, respectively, which indicated that maize growth was constantly facilitated. However, the RII for grass pea yield and biomass exhibited a different trend in comparison with maize. It was higher than 0 (as the facilitated species) under low soil P and moisture conditions and transitioned to values lower than 0 (facilitator species) under high P and moisture conditions, which showed that the type and intensity of plant-plant interactions steadily shifted with the applied stressors. Direct interactions decreased the maize rhizospheric soil pH by 1.5% and 1.9% under Low-P conditions. Notably, the rhizospheric soil acid and alkaline phosphatase secretions of maize and grass pea increased by 17.4–27.4% and 15.3–27.7%, respectively, in P-deficient soils. These results show that plant-plant interactions can effectively relieve P stress by mineralizing organophosphorus in P-deficient soils. Furthermore, the above tendency became more pronounced under drought-stressed conditions. The nylon barrier partially restricted the exchange and utilization of available nutrients and decreased the total yield and biomass by 1.8–7.8% and 1.1–7.8%, respectively. The presence of a solid barrier completely restricted interspecific rhizospheric interactions and decreased the total yield and biomass by 2.1–13.8% and 1.6–15.7%, respectively. Phytate and KH2PO4 addition intensified asymmetric interspecific competition, and grass pea was consistently subjected to competitive pressures.

Conclusion
Briefly, the tradeoff between facilitation and competition was driven by rhizospheric interactions, and the transition in the intensity and type of interaction was highly dependent on resource availability in a biologically diverse system.
Attitudes toward medicalization in childbirth and their relationship with locus of control and coping in a Spanish population
Authors: Espinosa Maite , Artieta-Pinedo Isabel , Paz-Pascual Carmen , Bully-Garay Paola , García-Álvarez Arturo ,   ema-Q. Group, Estalella Itziar , Trincado Mª José , Cabeza Inés , Gagnon Mari Pierre , Fernández Ana , Lozano Gorane , Villanueva Gemma , Sánchez Jesús , Maquibar Amaia , Moreno David , Legarra Catalina , Mulas Maria Jesús , Blas Mónica , Amorrortu Pilar , Alva Sonia 
Published: June 2022

AbstractThe dominant model of childbirth in most Western countries is medicalized childbirth. Women's beliefs about whether childbirth should be a medicalized process to a greater or lesser degree may be related, in addition to contextual factors, to internal factors. The objective of the study is to find out if women’s locus of control (LC) and stress coping strategies (CS) are related to having a more favourable or less favourable attitude towards medicalization (ATMC). A cross-sectional study was carried out with the participation of 248 women recruited in primary care centres by their midwives. All the women filled in answers on a mobile phone app with various different measurement instruments: the questionnaire created by Benyamini to evaluate their ATMC; the Spanish version of the Wallston MLC to evaluate their LC; and the Spanish adaptation of the “Revised Prenatal Coping Inventory (NuPCI)” scale for the assessment of their CS. The women presented a favourable attitude towards medicalization, with a mean ATMC score of 3.42. Both the LC and the CS of women during pregnancy are related to this attitude. Specifically, having an internal LC and using preparative CS both lower the probability of presenting a favourable attitude towards medicalization, while the lack of a paid job raises the probability. For each point in internal locus and preparatory coping, the ATMC score decreased by 0.02 and 0.23 points, respectively, while it increased by 0.18 for not having a paid job. The influence of these psychological factors must be taken into account in the development of content and interventions that promote a more natural birth.
Women´s experiences of preeclampsia as a condition of uncertainty: a qualitative study
Authors: Hansson Therése , Andersson Maria E. , Ahlström Gerd , Hansson Stefan R. 
Published: June 2022

Abstract
Background
Preeclampsia is a severe condition that annually affects about 3–8% of pregnancies worldwide. Preeclampsia is thereby one of the most common pregnancy complications for both mother and child. Despite that, there is limited research exploring the women´s perspective of experiencing preeclampsia.

Aim
The aim of this study was to describe women´s experiences of preeclampsia to improve the support and care given during and after pregnancy.

Methods
A qualitative descriptive interview study was undertaken. Nine women, diagnosed with preeclampsia, were recruited from a maternity unit in southern Sweden. The descriptive phenomenological method according to Amadeo Giorgi was used to analyse the data.

Results
The women´s experiences of PE were expressed as A condition of uncertainty, meaning that it was an unexpected and unknown situation. This main result consisted of 1) incomprehensible diagnosis message, 2) ambivalent feeling when the unexpected happens, 3) confusing contradictory messages, 4) appreciated support from the midwife, 5) need for continuous information. The nature of preeclampsia can sometimes deteriorate rapidly both for the mother and/or the child, often resulting in conversion from a planned vaginal spontaneous delivery to an emergency Caesarean section. The women narrated diffuse symptoms, and they experienced that they got contradictory information from different health care professionals regarding the severity of their disease. Detailed and continuous information is requested throughout the course of the disease, and the postpartum period.

Conclusion
This qualitative study reveal a need for improved clinical management. Health care professionals must be aware that women and their partners need detailed, consistent and repeated information about severity and prognosis to diminish the condition of uncertainty, confusion and fearful experience. The clinical implication would be a standardized preeclampsia education for pregnant women early on in the pregnancy, to raise awareness of preeclamptic symptoms. Furthermore, there is a need for harmonized guidelines and individualized support to the woman and her partner both at the antenatal care and the maternity ward and inpatient care at the hospital.
Adult height in pubertal boys with short stature treated with GH/letrozole: a hospital record-based retrospective study
Authors: Ma Yaping , Jia Ruofan , Xia Bingyang , Tang Bin , Xu Zhuangjian 
Published: June 2022

Abstract
Background
The growth potential in pubertal boys with short stature is limited by the effect of estrogen on epiphyseal fusion. This study aims to identify the efficacy and safety of the combination of growth hormone (GH) and letrozole on adult height (AH) in pubertal boys with short stature.

Methods
This is a retrospective record based study. Pubertal boys with short stature who were treated with GH and letrozole were followed up at outpatient clinics in our hospital. Twenty subjects who reached AH are reported here.

Results
Baseline chronological age was 12.12 ± 1.14 yr and bone age was 13.00 ± 0.93 yr. The period of GH/letrozole treatment was 1.94 ± 0.67 yr. Height standard deviation score for bone age was increased from -1.46 ± 0.51 before treatment to -0.12 ± 0.57 after treatment (P < 0.001). The predicted AH before treatment, predicted AH after treatment, AH, and genetic target height were 161.02 ± 4.12 cm, 172.11 ± 4.20 cm, 172.67 ± 2.72 cm, and 167.67 ± 3.56 cm, respectively. There was a significant predicted AH difference before and after treatment (P < 0.001). There was a significant difference between predicted AH before treatment and genetic target height (P < 0.001). Predicted AH after therapy was higher than that of gene target height (P < 0.001), as well as AH and genetic target height (P < 0.001). There was no significant side effect.

Conclusions
GH and letrozole combination can enhance AH in pubertal boys with short stature.
Development of a natural language processing algorithm to detect chronic cough in electronic health records
Authors: Bali Vishal , Weaver Jessica , Turzhitsky Vladimir , Schelfhout Jonathan , Paudel Misti L. , Hulbert Erin , Peterson-Brandt Jesse , Currie Anne-Marie Guerra , Bakka Dylan 
Published: June 2022

AbstractBackgroundChronic cough (CC) is difficult to identify in electronic health records (EHRs) due to the lack of specific diagnostic codes. We developed a natural language processing (NLP) model to identify cough in free-text provider notes in EHRs from multiple health care providers with the objective of using the model in a rules-based CC algorithm to identify individuals with CC from EHRs and to describe the demographic and clinical characteristics of individuals with CC.MethodsThis was a retrospective observational study of enrollees in Optum’s Integrated Clinical + Claims Database. Participants were 18–85 years of age with medical and pharmacy health insurance coverage between January 2016 and March 2017. A labeled reference standard data set was constructed by manually annotating 1000 randomly selected provider notes from the EHRs of enrollees with ≥ 1 cough mention. An NLP model was developed to extract positive or negated cough contexts. NLP, cough diagnosis and medications identified cough encounters. Patients with ≥ 3 encounters spanning at least 56 days within 120 days were defined as having CC.ResultsThe positive predictive value and sensitivity of the NLP algorithm were 0.96 and 0.68, respectively, for positive cough contexts, and 0.96 and 0.84, respectively, for negated cough contexts. Among the 4818 individuals identified as having CC, 37% were identified using NLP-identified cough mentions in provider notes alone, 16% by diagnosis codes and/or written medication orders, and 47% through a combination of provider notes and diagnosis codes/medications. Chronic cough patients were, on average, 61.0 years and 67.0% were female. The most prevalent comorbidities were respiratory infections (75%) and other lower respiratory disease (82%).ConclusionsOur EHR-based algorithm integrating NLP methodology with structured fields was able to identify a CC population. Machine learning based approaches can therefore aid in patient selection for future CC research studies.
Profiles of facial soft tissue changes during and after orthodontic treatment in female adults
Authors: Gao Jie , Wang Xian , Qin Zaixiu , Zhang Hao , Guo Donghui , Xu Yuerong , Jin Zuolin 
Published: June 2022

Abstract
Background
Some female adults who received orthodontic treatment often complain about thinner faces, protruding cheekbones and sunken temples, even at the beginning of treatment. The present research aimed to explore facial soft tissue changes during and after orthodontic treatment, as well as the related factors affecting facial soft tissue changes.

Methods
This study used 3dMD stereo photography technology to compare facial soft tissue changes among adult females who received orthodontics. A total of 52 adult females (24 teeth extraction, 28 non-teeth extraction cases) were included and potential correlations between related factors (facial morphology features, the change of occlusal height and dental arch width) were evaluated during different treatment periods.

Results
Overall, 3D-negative soft tissue changes of the buccal region moderately correlated with distances of nasion-menton and subnasale-menton (both rs = 0.30, P < 0.05) as well as the ratio of subnasale-menton/right gonion-left gonion (rs = 0.33, P < 0.05) and nasion-menton/right zygomatic point-left zygomatic point (rs = 0.30, P < 0.05). Among the 3D angle measurements, the right chelion-median upper lip point-left chelion angle was found to have a moderate correlation with 3D negative changes of the upper cheilion region (rs = 0.31, P < 0.01). Analysis of occlusal height changes revealed that an increase in the posterior facial height (nasion-gonial distance) may be a risk factor for negative changes in the zygomatic arch area. In addition, a moderate positive correlation between the maxillary first molar width changes and 3D-negative changes of the lower cheek region was found (rs = 0.41, P < 0.05).

Conclusions
After orthodontic treatment, adult females with wide and short faces may be prone to negative soft tissue changes. Changes of posterior facial height and arch width between the first molars were also risk factors for negative changes of facial soft tissues. Extraction is not a major factor producing facial soft tissue changes.