bluuebunny/crossref_metadata_2025 huggingface dataset:
Preserving conceptual model semantics in the forward engineering of relational schemas
Authors: Guidoni Gustavo L. , Almeida João Paulo A. , Guizzardi Giancarlo
Published: December 2022

Forward engineering relational schemas based on conceptual models (in languages such as UML and ER) is an established practice, with several automated transformation approaches discussed in the literature and implemented in production tools. These transformations must bridge the gap between the primitives offered by conceptual modeling languages on the one hand and the relational model on the other. As a result, it is often the case that some of the semantics of the source conceptual model is lost in the transformation process. In this paper, we address this problem by forward engineering additional constraints along with the transformed schema (ultimately implemented as triggers). We formulate our approach in terms of the operations of “flattening” and “lifting” of classes to make our approach largely independent of the particular transformation strategy (one table per hierarchy, one table per class, one table per concrete class, one table per leaf class, etc.). An automated transformation tool is provided that traces the cumulative consequences of the operations as they are applied throughout the transformation process. We report on tests of this tool using models published in an open model repository.
Risk factors, prediction model, and prognosis analysis of myocardial injury after acute upper gastrointestinal bleeding
Authors: Hao Junjun , Dang Peizhu , Quan Xingpu , Chen Zexuan , Zhang Guiyun , Liu Hui , Shi Tao , Yan Yang
Published: December 2022

Background

Cardiovascular complications in patients with acute upper gastrointestinal bleeding (AUGIB) have been associated with a high-risk of subsequent adverse consequences. This study aimed to analyze the risk factors for myocardial injury in AUGIB patients, predict the risk of myocardial injury, and explore the clinical prognosis and influencing factors in AUGIB patients with myocardial injury.

Materials and methods

A retrospective case-control study based on AUGIB patients in the First Affiliated Hospital of Xi’an Jiaotong University from 2016 to 2020 was performed. We divided the enrolled patients into a myocardial injury group and a control group according to whether they developed myocardial injury. The variables significant in the univariate analysis were subjected to binary logistic regression for risk factor analysis and were used to establish a nomogram for predicting myocardial injury. In addition, logistic regression analysis was performed to better understand the risk factors for in-hospital mortality after myocardial injury.

Result

Of the 989 AUGIB patients enrolled, 10.2% (101/989) developed myocardial injury. Logistic regression analysis showed that the strong predictors of myocardial injury were a history of hypertension (OR: 4.252, 95% CI: 1.149–15.730, P = 0.030), blood urea nitrogen (BUN) (OR: 1.159, 95% CI: 1.026–1.309, P = 0.018) and left ventricular ejection fraction (LVEF) <68% (OR: 3.667, 95% CI: 1.085–12.398, P = 0.037). The patients with a tumor history (digestive system tumors and non-digestive system tumors) had no significant difference between the myocardial injury group and the control group (P = 0.246). A prognostic nomogram model was established based on these factors with an area under the receiver operator characteristic curve of 0.823 (95% CI: 0.730–0.916). The patients with myocardial injury had a much higher in-hospital mortality rate (10.9% vs. 2.0%, P < 0.001), and an elevated D-dimer level was related to in-hospital mortality among the AUGIB patients with myocardial injury (OR: 1.273, 95% CI: 1.085–1.494, P = 0.003).

Conclusion

A history of hypertension, renal dysfunction, and cardiac function with LVEF <68% were strong predictors of myocardial injury. Coagulopathy was found to be associated with poor prognosis in AUGIB patients with myocardial injury.
How can landslide risk maps be validated? Potential solutions with open-source databases
Authors: Caleca Francesco , Tofani Veronica , Segoni Samuele , Raspini Federico , Franceschini Rachele , Rosi Ascanio
Published: December 2022

Landslides are a worldwide natural hazard that cause more damage and casualties than other hazards. Therefore, social and economic losses can be reduced through a landslide quantitative risk assessment (QRA). In the last two decades, many attempts of quantitative analysis on various scales have been performed; nevertheless, the major difficulty of QRA lies in how precise and reliable the assessment should have to be useful. For this reason, in this paper, we analyzed different freely available datasets and some products of previous research to assess the soundness of the outcomes performed by a recent QRA of slow-moving landslides in the Arno River basin (Central Italy). The validation process was carried out by comparing the abovementioned datasets and two components of the selected QRA (hazard and risk). The obtained results showed a robust correlation between most of the testing dataset and risk components, highlighting the accuracy of the selected QRA.
Investigating student approaches to scenario-based assessments of systems thinking
Authors: Norris Matthew B. , Grohs Jacob R. , Knight David B.
Published: December 2022

The development of systems thinking is considered a critical skill set for addressing interdisciplinary problems. This skill set is particularly important in the field of engineering, where engineers are often tasked with solving socio-technical problems that often require knowledge beyond their original discipline and practice in unfamiliar contexts. However, existing assessments often fail to accurately measure teachable knowledge or skills that constitute systems thinking. To investigate this issue, we compared students’ performance on two previously and independently peer-reviewed scenario-based assessments for systems thinking: The Village of Abeesee and the Lake Urmia Vignette. Twenty undergraduate engineering students participated in a multi-phase case study utilizing think aloud protocols and semi-structured interview methods to elicit the approaches students took thinking across the two instruments and past experiences that they felt prepared them to solve these ill-structured problems. We found that the way a scenario is presented to students impacts their subsequent problem-solving approach, which complicates assessment of systems thinking. Additionally, students identified only limited opportunities for the development of ill-structured problem-solving skills necessary for systems thinking. Our findings inform future work on improving systems thinking assessments and emphasize the importance of more intentionally supplying opportunities for students to practice solving ill-structured problems throughout the curriculum.
Uterine cytokine profiles after low-molecular-weight heparin administration are associated with pregnancy outcomes of patients with repeated implantation failure
Authors: Niu Zhihong , Zhou Mingjuan , Xia Lan , Zhao Shen , Zhang Aijun
Published: December 2022

Introduction

Low molecular-weight heparin (LMWH) plays a role in repeated implantation failure (RIF), but outcomes are controversial. LMWH can potentially modulate local immune responses associated with the establishment and maintenance of pregnancy. The study aimed to explore the effects of LWMH in uterine inflammatory cytokine profiles and pregnancy outcomes of patients with repeated implantation failure (RIF) but without thrombophilia.

Methods

We compared clinical characteristics and reproductive outcomes among 326 patients with RIF, but not thrombophilia, undergoing frozen embryo transfer (FET) cycle with or without LMWH treatment. Endometrium secretions were aspirated from both groups after 3 days of progesterone administration before and after LMWH treatment. Cytokine mRNA expression was analyzed in primary endometrial cells in vitro.

Results

The clinical and ongoing pregnancy rates did not significantly differ between the groups (31.5% vs. 24.4%, p = 0.15; 29.6% vs. 20.7%, p = 0.06). Concentrations of IL-6 and granulocyte-colony stimulating factor (G-CSF) in uterine secretions were significantly increased in the LWMH group, regardless of pregnancy outcomes (P < 0.05). And, in all patients treated with LWMH, those of secreted IL-6, IL-15 and G-CSF were significantly increased in pregnant group (P < 0.05). The expression of mRNA for G-CSF and IL-6 was significantly increased in human endometrial stromal cells in vitro (P < 0.05) after stimulation with LWMH (10 IU/mL).

Conclusions

Uterine cytokine profiles after LMWH administration are associated with pregnancy outcomes and LMWH may be beneficial for patients with three implantation failures who do not have coagulation disorders.
Biodynamic lighting conditions preserve nocturnal melatonin production in pregnant women during hospitalization: A randomized prospective pilot study
Authors: Bagci Soyhan , Wieduwilt Astrid , Alsat Ebru Aileen , Blickwedel Jana , Strizek Brigitte , Di Battista Christian , Lachner Agnes , Plischke Herbert , Melaku Tamene , Müller Andreas
Published: December 2022

Background and purpose

Maternal circadian rhythms are important for maintaining maternal and fetal homeostasis. The maternal circadian system coordinates the internal clock of the fetus with environmental lighting conditions via the melatonin signal. The intensity and wavelength of daylight influence nocturnal melatonin production. This study aims to evaluate the effect of environmental lighting conditions on melatonin production in pregnant women with reduced mobility during hospitalization.

Methods

We installed a human-centric lighting system with biodynamic effects (BDL, biodynamic lighting) in the patient rooms. The pregnant women in the patient rooms with standard indoor conditions served as a control group. The illuminance (lux) and dose of effective circadian irradiation (Hec) were recorded every 10 seconds by light dosimeters (Lucerne University, Switzerland) attached to the patients` clothing.

Results

We analyzed the illuminance status of 47 pregnant women with a median (IQR) gestational age of 29.9 (25.4-32.3) weeks of gestation. The median illuminance in the control group was significantly lower (p<0.05) than in the BDL group in the morning and afternoon from day 1 to 5. BDL patients had a significantly higher effective circadian irradiation in the morning. The effective circadian irradiation showed a significant daily rhythm only in the BDL group. The BDL group had a significantly higher melatonin production on day 3 (p=0.006) and day 5 (p=0.012) than the control group median (IQR) nocturnal 6-Sulfatoxymelatonin excretion 15840 (10140-22160) ng/12h vs. 6141 (2080-11328) ng/12h on day 3 and 18780 (11320-23562) ng/12h vs. 6380 (3500-17600) ng/12h on day 5).

Conclusion

We have demonstrated that dramatically altered lighting conditions of hospitalized pregnant women may be optimized by installing biodynamic lighting systems in the patient rooms resulting in the maintenance of nocturnal melatonin production in pregnant women.
Emerging mechanisms progress of colorectal cancer liver metastasis
Authors: Zhao Wenhu , Dai Shipeng , Yue Lei , Xu Fan , Gu Jian , Dai Xinzheng , Qian Xiaofeng
Published: December 2022

Colorectal cancer (CRC) is the third most common malignancy and the second most common cause of cancer-related mortality worldwide. A total of 20% of CRC patients present with distant metastasis. The hepatic portal venous system, responsible for collecting most intestinal blood, makes the liver the most common site of CRC metastasis. The formation of liver metastases from colorectal cancer is a long and complex process. It involves the maintenance of primary tumors, vasculature invasion, distant colonization, and metastasis formation. In this review, we serve on how the CRC cells acquire stemness, invade the vascular, and colonize the liver. In addition, we highlight how the resident cells of the liver and immune cells interact with CRC cells. We also discuss the current immunotherapy approaches and challenges we face, and finally, we look forward to finding new therapeutic targets based on novel sequencing technologies.
Case report: Clinical characteristics and treatment of secondary osteoporosis induced by X-linked congenital adrenal dysplasia
Authors: Tao Xiaohui , Xu Tian , Liu Li , Lin Xiaoyun , Zhang Zhenlin , Yue Hua
Published: December 2022

Objective

To summarize the clinical features and bone complications in a patient from a large family with X-linked congenital adrenocortical hypoplasia (AHC) and evaluate the efficacy of different treatment regimens on the prognosis of secondary osteoporosis caused by AHC at a 5-year follow-up.

Methods

A large family with AHC was recruited, and the causative gene mutation was identified by Sanger sequencing in the proband. Clinical features as well as radiological examinations and laboratory indices of osteoporosis secondary to AHC were analyzed in this study. Meanwhile, the proband was treated with classical antiresorptive drugs (bisphosphonates) for 2 years and switched to a vitamin K2 analogue for another 3 years, during which the efficacy of the drugs was evaluated.

Results

The proband was identified as carrying a homozygous insertion mutation (p. Thr193GlyfsX13) in the NR0B1 (nuclear receptor subfamily 0, group B, member 1) gene, resulting in a premature stop codon due to a frameshift mutation. During treatment and follow-up, the proband did not respond well to bisphosphonate and developed atypical femoral fractures. Vitamin K2 improved clinical symptoms. In terms of bone mineral density (BMD), there is no evidence of any effect of vitamin K2 on the neck of femur, though some minor effects on spinal BMD cannot be excluded.

Conclusions

Secondary osteoporosis induced by AHC deserves clinical attention. Unlike in primary osteoporosis, the curative effect of bisphosphonates was unsatisfactory and was more likely to cause atypical femoral fractures in long-term treatment. It is suggested that bone anabolic drugs may be better alternatives.
Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae)
Authors: Zhao Yaqi , Zhang Liangzhi , Tang Xianjiang , Ren Shien , Zhang Yanming
Published: December 2022

The prevalence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose a great threat to public health. The importance of pollution in determining the occurrence of ARGs and VFs in wildlife is poorly understood. Using a metagenomic approach, this study investigates the composition and functional pathways of bacteria, ARGs, and VFs in the gut microbiome of Plateau pikas in regions of medical pollution (MPR), heavy tourist traffic (HTR), and no contamination (NCR). We found that the abundance of probiotic genera (Clostridium, Eubacterium, Faecalibacterium, and Roseburia) were significantly lower in the HTR. The metabolic pathways of replication and repair in the endocrine and nervous systems were significantly enriched in the MPR, whereas endocrine and metabolic diseases were significantly enriched in the NCR. The Shannon and Gini–Simpson α-diversity indices of ARGs were highest in the HTR, and there were significant differences in β-diversity among the three regions. The resistance of ARGs to glycopeptide antibiotics increased significantly in the MPR, whereas the ARGs for aminocoumarins increased significantly in the HTR. The diversity of mobile genetic elements (MGEs) was significantly higher in the MPR than in other regions. We observed a strong positive correlation between ARGs and pathogenic bacteria, and the network structure was the most complex in the MPR. There were significant differences in the β-diversity of VFs among the three regions. Medical pollution led to significant enrichment of fibronectin-binding protein and PhoP, whereas tourism-related pollution (in the HTR) led to significant enrichment of LPS and LplA1. Our study indicates that environmental pollution can affect the structure and function of gut microbes and disseminate ARGs and VFs via horizontal transmission, thereby posing a threat to the health of wild animals.
Comparative chloroplast genomics provides insights into the genealogical relationships of endangered Tetraena mongolica and the chloroplast genome evolution of related Zygophyllaceae species
Authors: Yang Yanci , Jia Yun , Zhao Yanling , Wang Yonglong , Zhou Tao
Published: December 2022

A comprehensive understanding of genetic background for rare species will provide an important theoretical basis for the future species management, monitoring and conservation. Tetraena mongolica is restrictedly distributed in the western Ordos plateau of China and has been listed as a national protected plant. We generated 13 chloroplast (cp) genomes of T. mongolica (size range of 106,062–106,230 bp) and conducted a series of comparative analyses of six Zygophyllaceae cp genomes. T. mongolica cp genome exhibited a quadripartite structure with drastically reduced inverted repeats (IRs, 4,315 bp) and undergone the loss of a suit of ndh genes and a copy of rRNAs. Furthermore, all the T. mongolica populations were divided into two genetic groups based on complete cp phylogenomics. In addition, notably variable genome size, gene order and structural changes had been observed among the six Zygophyllaceae cp genomes. Overall, our findings provide insights into the cp genome evolution mode and intraspecific relationships of T. mongolica, and provide a molecular basis for scientific conservation of this endangered plant.
Involvement of the STING signaling in COVID-19
Authors: Xiao Ruoxuan , Zhang Ao
Published: December 2022

The coronavirus disease 2019 (COVID-19) pandemic caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has cast a notorious damage to the public health and global economy. The Stimulator of Interferon Genes (STING) is a crucial element of the host antiviral pathway and plays a pivotal but complex role in the infection and development of COVID-19. Herein, we discussed the antagonistic mechanism of viral proteins to the STING pathway as well as its activation induced by host cells. Specifically, we highlighted that the persistent activation of STING by SARS-CoV-2 led to abnormal inflammation, and STING inhibitors could reduce the excessive inflammation. In addition, we also emphasized that STING agonists possessed antiviral potency against diverse coronavirus and showed adjuvant efficacy in SARS-CoV-2 vaccines by inducing IFN responses.
Integrative transcriptomic analysis in human and mouse model of anaphylaxis identifies gene signatures associated with cell movement, migration and neuroinflammatory signalling
Authors: Rijavec Matija , Maver Aleš , Turner Paul J. , Hočevar Keli , Košnik Mitja , Yamani Amnah , Hogan Simon P. , Custovic Adnan , Peterlin Borut , Korošec Peter
Published: December 2022

Background

Anaphylaxis is an acute life-threatening allergic reaction and a concern at a global level; therefore, further progress in understanding the underlying mechanisms and more effective strategies for diagnosis, prevention and management are needed.

Objective

We sought to identify the global architecture of blood transcriptomic features of anaphylaxis by integrating expression data from human patients and mouse model of anaphylaxis.

Methods

Bulk RNA-sequencings of peripheral whole blood were performed in: i) 14 emergency department (ED) patients with acute anaphylaxis, predominantly to Hymenoptera venom, ii) 11 patients with peanut allergy undergoing double-blind, placebo-controlled food challenge (DBPCFC) to peanut, iii) murine model of IgE-mediated anaphylaxis. Integrative characterisation of differential gene expression, immune cell-type-specific gene expression profiles, and functional and pathway analysis was undertaken.

Results

1023 genes were commonly and significantly dysregulated during anaphylaxis in ED and DBPCFC patients; of those genes, 29 were also dysregulated in the mouse model. Cell-type-specific gene expression profiles showed a rapid downregulation of blood basophil and upregulation of neutrophil signature in ED and DBPCFC patients and the mouse model, but no consistent and/or significant differences were found for other blood cells. Functional and pathway analysis demonstrated that human and mouse blood transcriptomic signatures of anaphylaxis follow trajectories of upregulation of cell movement, migration and neuroinflammatory signalling, and downregulation of lipid activating nuclear receptors signalling.

Conclusion

Our study highlights the matched and extensive blood transcriptomic changes and suggests the involvement of discrete cellular components and upregulation of migration and neuroinflammatory pathways during anaphylaxis.
Vaginal neutrophil infiltration is contingent on ovarian cycle phase and independent of pathogen infection
Authors: Latorre M. C. , Gómez‐Oro C. , Olivera‐Valle I. , Blazquez‐Lopez E. , Gallego‐Valle J. , Ibañez‐Escribano A. , Casesnoves P. , González‐Cucharero C. , Muñoz‐Fernandez M. A. , Sanz L. , Vaquero J. , Martín‐Rabadań P. , Perez‐Milan F. , Relloso M.
Published: December 2022

The mucosa of the female reproductive tract must reconcile the presence of commensal microbiota and the transit of exogenous spermatozoa with the elimination of sexually transmitted pathogens. In the vagina, neutrophils are the principal cellular arm of innate immunity and constitute the first line of protection in response to infections or injury. Neutrophils are absent from the vaginal lumen during the ovulatory phase, probably to allow sperm to fertilize; however, the mechanisms that regulate neutrophil influx to the vagina in response to aggressions remain controversial. We have used mouse inseminations and infections of Neisseria gonorrhoeae, Candida albicans, Trichomonas vaginalis, and HSV-2 models. We demonstrate that neutrophil infiltration of the vaginal mucosa is distinctively contingent on the ovarian cycle phase and independent of the sperm and pathogen challenge, probably to prevent sperm from being attacked by neutrophils. Neutrophils extravasation is a multi-step cascade of events, which includes their adhesion through selectins (E, P and L) and integrins of the endothelial cells. We have discovered that cervical endothelial cells expressed selectin-E (SELE, CD62E) to favor neutrophils recruitment and estradiol down-regulated SELE expression during ovulation, which impaired neutrophil transendothelial migration and orchestrated sperm tolerance. Progesterone up-regulated SELE to restore surveillance after ovulation.
Intraepithelial lymphocytes in the pig intestine: T cell and innate lymphoid cell contributions to intestinal barrier immunity
Authors: Wiarda Jayne E. , Loving Crystal L.
Published: December 2022

Intraepithelial lymphocytes (IELs) include T cells and innate lymphoid cells that are important mediators of intestinal immunity and barrier defense, yet most knowledge of IELs is derived from the study of humans and rodent models. Pigs are an important global food source and promising biomedical model, yet relatively little is known about IELs in the porcine intestine, especially during formative ages of intestinal development. Due to the biological significance of IELs, global importance of pig health, and potential of early life events to influence IELs, we collate current knowledge of porcine IEL functional and phenotypic maturation in the context of the developing intestinal tract and outline areas where further research is needed. Based on available findings, we formulate probable implications of IELs on intestinal and overall health outcomes and highlight key findings in relation to human IELs to emphasize potential applicability of pigs as a biomedical model for intestinal IEL research. Review of current literature suggests the study of porcine intestinal IELs as an exciting research frontier with dual application for betterment of animal and human health.
Body composition parameters for predicting the efficacy of neoadjuvant chemotherapy with immunotherapy for gastric cancer
Authors: Lin Guang-Tan , Huang Jiao-Bao , Lin Ju-Li , Lin Jian-Xian , Xie Jian-Wei , Wang Jia-Bin , Lu Jun , Zheng Chao-Hui , Huang Chang-Ming , Li Ping
Published: December 2022

Background

Immune checkpoint inhibitors are increasingly used in neoadjuvant therapy for locally advanced gastric cancer. However, the effect of body composition on the efficacy of neoadjuvant therapy has not been reported.

Methods

The computed tomography (CT) images and clinicopathological data of 101 patients with locally advanced gastric cancer who received neoadjuvant chemotherapy combined with immunotherapy (NCI) from 2019 to 2021 were collected. The CT image of L3 vertebral body section was selected, and the body composition before and after the neoadjuvant treatment was calculated using the SliceOmatic software, mainly including skeletal muscle index (SMI), subcutaneous adipose index (SAI), and visceral adipose index (VAI). The relationship between body composition and the efficacy and adverse events of NCI was analyzed.

Results

Of the 101 patients, 81 with evaluable data were included in the analysis. Of the included patients, 77.8% were male; the median age of all the patients was 62 years, and the median neoadjuvant therapy cycle was three. After the neoadjuvant therapy, 62.9% of the tumors were in remission (residual tumor cells ≤ 50%), and 37.1% of the tumors had no remission (residual tumor cells>50%). Moreover, 61.7% of the patients had treatment-related adverse events (TRAEs), and 18.5% had immune-related adverse events (irAEs). After neoadjuvant therapy, the body mass index (from 23 to 22.6 cm2/m2, p=0.042), SAI (from 34.7 to 32.9 cm2/m2, p=0.01) and VAI (from 32.4 to 26.8 cm2/m2, p=0.005) were significantly lower than those before treatment, while the SMI had no significant change (44.7 vs 42.5 cm2/m2, p=0.278). The multivariate logistics regression analysis revealed that low SMI (odds ratio [OR]: 3.23,95% confidence interval [CI]: 1.06–9.81, p=0.047), SMI attenuation (△SMI) ≥ 1.8(OR: 1.45,95%CI: 1.20–3.48, p=0.048), and clinical node positivity (OR: 6.99,95%CI: 2.35–20.82, p=0.001) were independent risk factors for non-remission. Additionally, high SAI is an independent risk factor for irAEs (OR: 14, 95%CI: 1.73–112.7, p=0.013).

Conclusion

Low SMI and △SMI≥1.8 are independent risk factors for poor tumor regression in patients with advanced gastric cancer receiving NCI. Patients with a high SAI are more likely to develop irAEs.
JAK–STAT signaling pathway in the pathogenesis of atopic dermatitis: An updated review
Authors: Huang I-Hsin , Chung Wen-Hung , Wu Po-Chien , Chen Chun-Bing
Published: December 2022

Atopic dermatitis (AD) is a chronic, inflammatory, pruritic form of dermatosis with heterogeneous manifestations that can substantially affect patients' quality of life. AD has a complex pathogenesis, making treatment challenging for dermatologists. The Janus kinase (JAK)–signal transducer and activator of transcription (STAT) pathway plays a central role in modulating multiple immune axes involved in the immunopathogenesis of AD. In particular, Th2 cytokines, including interleukin (IL)-4, IL-5, IL-13, IL-31, and thymic stromal lymphopoietin, which contribute to the symptoms of chronic inflammation and pruritus in AD, are mediated by JAK–STAT signal transduction. Furthermore, JAK–STAT is involved in the regulation of the epidermal barrier and the modulation of peripheral nerves related to the transduction of pruritus. Targeting the JAK–STAT pathway may attenuate these signals and show clinical efficacy through the suppression of various immune pathways associated with AD. Topical and oral JAK inhibitors with variable selectivity have emerged as promising therapeutic options for AD. Notably, topical ruxolitinib, oral upadacitinib, and oral abrocitinib were approved by the U.S. Food and Drug Administration for treating patients with AD. Accordingly, the present study reviewed the role of JAK–STAT pathways in the pathogenesis of AD and explored updated applications of JAK inhibitors in treating AD.
Case report: Persistent shedding of a live vaccine-derived rubella virus in a young man with severe combined immunodeficiency and cutaneous granuloma
Authors: Bonner Kimberly E. , Sukerman Ellie , Liko Juventila , Lanzieri Tatiana M. , Sutton Melissa , DeBess Emilio , Leesman Christopher , Icenogle Joseph , Hao LiJuan , Chen Min-hsin , Faisthalab Raeesa , Leman Richard F. , Cieslak Paul R. , DeRavin Suk See , Perelygina Ludmila
Published: December 2022

A young man with X-linked severe combined immunodeficiency developed a persistent vaccine-derived rubella virus (VDRV) infection, with the emergence of cutaneous granulomas more than fifteen years after receipt of two doses of measles-mumps-rubella (MMR) vaccine. Following nasopharyngeal swab (NP) collection, VDRV was detected by real-time polymerase chain reaction (RT-qPCR) and sequencing, and live, replication-competent VDRV was isolated in cell culture. To assess duration and intensity of viral shedding, sequential respiratory samples, one cerebrospinal fluid sample, and two urine samples were collected over 15 months, and VDRV RNA was detected in all samples by RT-qPCR. Live VDRV was cultured from nine of the eleven respiratory specimens and from one urine specimen. To our knowledge, this was the first reported instance of VDRV cultured from respiratory specimens or from urine. To assess potential transmission to close contacts, NP specimens and sera were collected from all household contacts, all of whom were immunocompetent and previously vaccinated with MMR. VDRV RNA was not detected in any NP swabs from the contacts, nor did serologic investigations suggest VDRV transmission to any contacts. This report highlights the need to understand the prevalence and duration of VDRV shedding in granuloma patients and to estimate the risk of VDRV transmission to immune and non-immune contacts.
Assessment of CO2 and O2 spatial variability in an indigenous aquaculture system for restoration impacts
Authors: Lechner Evan , Rii Yoshimi M. , Ruttenberg Kathleen , Kotubetey Keli‘iahonui , Sabine Christopher L.
Published: December 2022

Spatial variability in carbon dioxide (CO2) and oxygen (O2) was assessed within an Indigenous Hawaiian fishpond undergoing active ecosystem restoration. The brackish, tidal fishpond is located within Kāne‘ohe Bay, Hawai‘i. Following a year of monthly discrete sampling, a significant shift in DIC and percent O2 saturation was observed along the North-South axis within the pond. The south end of the pond was higher in DIC (+35 μmol·kg⁻¹) and lower in percent O2 saturation (-19%) than the north end, which exhibited values similar to those observed in water entering the fishpond from the bay. Water quality parameters and inequal proximity to water flux sites suggested that a difference in residence time may exist along the north-south axis. In addition, ΔTA/ΔDIC relationships revealed a respiration signal in south end of the pond, which was enhanced at depth. While physical processes strongly affect CO2 and O2 across various temporal scales, spatial patterns in biological processes may also affect variability within the fishpond. These findings demonstrate that changes in water chemistry within the fishpond are the result of ecosystem restoration efforts. In turn, future management decisions at the fishpond will play an important role in preserving its viability as a healthy habitat for the intended marine species.
Turbulence affects larval vertical swimming in the cold-water coral Lophelia pertusa
Authors: Fagerström Vilhelm , Broström Göran , Larsson Ann I.
Published: December 2022

Vertical migration of marine larvae may drastically affect their dispersal, especially if they are spawned in the deep sea. Previous studies have shown that the planktonic larvae of the cold-water coral Lophelia pertusa in still water swim upwards at a speed of ca. 0.5 mm s-1 during a pre-competency period of 3–5 weeks. This behavioral trait is thought to benefit dispersion of larvae as it promotes near surface drift in relatively strong currents. In the ocean however, larvae regularly encounter turbulent water movements potentially impeding their swimming ability. With no apparent stabilizing mechanism, it may be expected that the body orientation of these larvae, and consequently their directed swimming, is sensitive to perturbation by external forces. We investigated the effects of turbulence on vertical swimming of pre-competent L. pertusa larvae by exposing them to relevant turbulence intensities within a grid-stirred tank. Larval movement and water flow were simultaneously recorded, allowing for analysis of individual larval swimming velocities. We showed that the upwards directed swimming speed generally decreased with increasing turbulence, dropping to non-significant in turbulence levels occurring near ocean boundaries. Our results do however suggest that L. pertusa larvae maintain their upwards directed swimming, albeit at reduced speed, in a major part of the water column, thus allowing them to spend part of their planktonic phase in the uppermost ocean layer. This new insight into the behavior of L. pertusa larvae in their natural environment strengthens the notion of the species as one with strong potential for long-distance dispersal. Such information is important for the understanding of L. pertusa population connectivity, and vital when developing tools for modelling of larval transport.
Settlement experiment of spat using three different collectors in two contrasting coastal sites from Chile (SE Pacific Ocean)
Authors: Díaz Christian , Sobenes Catterina , Cruz Motta Juan José , Riera Rodrigo
Published: December 2022

Most of the marine bivalve production comes from aquaculture and only 11% comes from the wild fishery. For example, mussel aquaculture still strongly relies on spat - the recently settled juveniles. Gaps of information on the recruitment and settlement of spat are important drawbacks for the development of mussel aquaculture in several geographic regions. We here study these processes using three collectors (Anchovy mesh, Rope and Raschel mesh) throughout one year in two coastal sites of Central Chile (Coliumo and Punta Lobería) at three depths (2, 4 and 6 m). Five spat species were settled in the collectors, i.e. Aulacomya atra, Choromytilus chorus, Mytilus chilensis, Mytilus galloprovincialis and Semimytilus algosus. Recruitment was consistently higher during summer and autumn at both sites. Different seasonal recruitment patterns were observed regarding the spat species. Spat collection of the former mytilid species occurs from spring to autumn with the exception of M. galloprovincialis in Coliumo and M. chilensis in Punta Lobería. M. galloprovincialis is settled mostly in autumn and summer, and M. chilensis during winter. There were also differences when considering the collector type, mostly due to A. atra and S. algosus which peaked in nylon rope. Spat collection of the commercial species M. chilensis should be preferentially carried out in nylon rope during autumn in Coliumo and summer and autumn in Punta Lobería. During summer and autumn, also S. algosus will be settled. These results will enable the implementation of management measures to promote mytilid culture on the coastal zone of the Biobío region.
Multiscale attention-based detection of tiny targets in aerial beach images
Authors: Gao Shurun , Liu Chang , Zhang Haimiao , Zhou Zhehai , Qiu Jun
Published: December 2022

Tiny target detection in marine scenes is of practical importance in marine vision applications such as personnel search and rescue, navigation safety, and marine management. In the past few years, methods based on deep convolutional neural networks (CNN) have performed well for targets of common sizes. However, the accurate detection of tiny targets in marine scene images is affected by three difficulties: perspective multiscale, tiny target pixel ratios, and complex backgrounds. We proposed the feature pyramid network model based on multiscale attention to address the problem of tiny target detection in aerial beach images with large field-of-view, which forms the basis for the tiny target recognition and counting. To improve the ability of the tiny targets’ feature extraction, the proposed model focuses on different scales of the images to the target regions based on the multiscale attention enhancement module. To improve the effectiveness of tiny targets’ feature fusion, the pyramid structure is guided by the feature fusion module in order to give further semantic information to the low-level feature maps and prevent the tiny targets from being overwhelmed by the information at the high-level. Experimental results show that the proposed model generally outperforms existing models, improves accuracy by 8.56 percent compared to the baseline model, and achieves significant performance gains on the TinyPerson dataset. The code is publicly available via Github.
A novel statistical approach to predict seasonal high tide flooding
Authors: Dusek Gregory , Sweet William V. , Widlansky Matthew J. , Thompson Philip R. , Marra John J.
Published: December 2022

Sea level rise is increasing the frequency of high tide flooding in coastal communities across the United States. Although the occurrence and severity of high-tide flooding will continue to increase, skillful prediction of high tide flooding on monthly-to-annual time horizons is lacking in most regions. Here, we present an approach to predict the daily likelihood of high tide flooding at coastal locations throughout the U.S. using a novel probabilistic modeling approach that relies on relative sea-level rise, tide predictions, and climatological non-tidal residuals as measured by NOAA tide gauges. A retrospective skill assessment using the climatological sea level information indicates that this approach is skillful at 61 out of 92 NOAA tide gauges where at least 10 high tide flood days occurred from 1997–2019. In this case, a flood day occurs when the observed water level exceeds the gauge-specific high tide flood threshold. For these 61 gauges, on average 35% of all floods are accurately predicted using this model, with over half of the floods accurately predicted at 18 gauges. The corresponding False-Alarm-Rate is less than 10% for all 61 gauges. Including mean sea level anomaly persistence at leads of 1 and 3 months further improves model skill in many locations, especially the U.S. Pacific Islands and West Coast. Model skill is shown to increase substantially with increasing sea level at nearly all locations as high tides more frequently exceed the high tide flooding threshold. Assuming an intermediate amount of relative sea level rise, the model will likely be skillful at 93 out of the 94 gauges projected to have regular flooding by 2040. These results demonstrate that this approach is viable to be incorporated into NOAA decision-support products to provide guidance on likely high tide flooding days. Further, the structure of the model will enable future incorporation of mean sea level anomaly predictions from numerical, statistical, andmachine learning forecast systems.
Carbonate system data tracing freshwater inflow into the Ross Sea through the eastern gate and along the Ross Ice Shelf (Antarctica)
Authors: Rivaro Paola , Vivado Davide , Castagno Pasquale , Falco Pierpaolo , Zambianchi Enrico , Ianni Carmela
Published: December 2022

The eastern Ross Sea is a key area to understand the role of the Amundsen Sea inflow of freshwater that can influence the Ross Sea water properties and salt budget. A survey was carried out in the eastern Ross Sea during the austral summer 2019–20 to evaluate the contribution of the Amundsen Sea Water (ASW) to the salinity variability. A total of 248 seawater samples were collected f\or the analysis of total alkalinity (AT) and pH. The data collected were used together with temperature and salinity to obtain a full description of the carbonate system properties including total inorganic carbon (CT), CO2 partial pressure (pCO2), calcium carbonate saturation state of aragonite and calcite (Ω), and Revelle factor. Moreover, we estimated the anthropogenic carbon (Cant) throughout the TrOCA method to better understand the carbon cycle, also considering the effect of atmospheric CO2 uptake on ocean acidification. We used principal component analysis (PCA) to investigate the major controls on the carbonate system parameters with the aim of defining their sensitivity as chemical tracers. The changes in carbonate chemistry in surface waters were mainly due to the physical properties. AT and pH traced the entry of the ASW showing limited mixing between water masses on the shelf area. Shelf waters were enriched in Cant, which resulted lower than the estimated value for shelf waters produced in western Ross Sea.
The efficacy of adding oral sodium cromoglycate to stable treatment for controlling bullous pemphigoid-related pruritus: A retrospective study
Authors: Keller Rosenthal Noy , Boucher Darby , Murrell Dedee F.
Published: December 2022

Introduction

Bullous pemphigoid (BP) is the most common autoimmune subepidermal blistering disease which mainly affects the elderly. It manifests as severe pruritus, urticarial plaques, and tense bullae and is associated with significant mortality. Therapy options for itch in BP patients are limited, mainly because the pathogenesis of itch in BP remains unclear. Sodium cromoglycate was commonly used in the past as an inhaled drug for the management of bronchial asthma and as an oral treatment for children with urticaria pigmentosa. In this study we sought to assess its efficacy in reducing BP associated itch.

Objective

Assessing the efficacy of oral sodium cromoglycate in reducing BP-related pruritus after stabilization of disease activity.

Methods

We retrospectively reviewed the medical records of patients with a confirmed diagnosis of BP who were treated with sodium cromoglycate. Patient reported outcome measures (PROM) including: BPDAI pruritus, ABQOL and TABQOL, and BPDAI activity score were compared at two points in time: before commencing treatment with sodium cromoglycate or before commencing maximal dose of this treatment, and at least 4 weeks after treatment commencement.

Results

A total of 21 patients met the inclusion criteria. After at least 4 weeks of treatment with oral sodium cromoglycate BPDAI pruritus, ABQOL and TABQOL scores were statistically significantly decreased compared to the scores prior to treatment commencement, P < 0.000, P < 0.008, and P < 0.004, respectively.

Discussion

Oral treatment with sodium cromoglycate for the management of pruritus in BP patients may be beneficial, however, further prospective studies are required to better assess its efficacy.
A rare case of Pseudomonas putida ventriculitis in intensive care unit: A case report
Authors: Mokhtar Mohammad Nizam , Azaharuddin Izzuddin , Abdullah Farah Hanim , Izaham Azarinah , Abdul Rahman Raha
Published: December 2022

Pseudomonas putida is a rare pathogen leading to nosocomial and central nervous system infections. Despite having a low virulence and being a rare organism to cause bacteremia, it can evolve into a multidrug-resistant organism and lead to mortality and morbidity in the intensive care setting. A 64-year-old male gardener was presented with extensive acute subarachnoid hemorrhage with intraventricular extension causing hydrocephalus requiring embolization and coiling following a cerebral angiogram, which showed bilateral posterior circulation aneurysm and left anterior circulation aneurysm. External ventricular drain (EVD) was inserted given the worsening hydrocephalus. During his stay in the intensive care unit (ICU), he was becoming more septic and a full septic workup including a cerebral spinal fluid culture taken from the indwelling catheter of the EVD and was found to be positive for a ceftazidime-sensitive strain of P. putida. Following the treatment with intravenous ceftazidime for 1 week and a revision of the EVD on day 32 of admission, he continued to recover well and showed an improvement in his Glasgow Coma Scale (GCS) and septic parameters. Eventually, he was able to wean off mechanical ventilation. He was discharged from ICU care to the neurosurgical ward with supplemental oxygen on day 42 of admission. It is necessary to be aware of the possibility of nosocomial P. putida infection, especially in patients with indwelling catheters, and to consider the early initiation of appropriate antibiotic regimens once detected as well as strict precautions in hygiene during the management of these patients to avoid further development of multi-drug resistant (MDR) strains.
Pregnancy outcomes in a malaria-exposed Malian cohort of women of child-bearing age
Authors: Gaoussou Santara , Attaher Oumar , Swihart Bruce , Traore Moussa , Diarra Soumaila , Soumbounou Ibrahim H. , Ndiaye Oulematou , Issiaka Djibrilla , Morrison Robert , Mahamar Almahamoudou , Duffy Patrick E. , Dicko Alassane , Fried Michal
Published: December 2022

In Sub-Saharan Africa, malaria continues to be associated with adverse pregnancy outcomes including stillbirth, early neonatal death, preterm delivery, and low birth weight. Current preventive measures are insufficient and new interventions are urgently needed. However, before such interventions can be tested in pregnant women, background information on pregnancy outcomes in this target population must be collected. We conducted an observational study in Ouélessébougou, Mali, a malaria-endemic area where first antenatal visit commonly occurs during the second trimester of pregnancy, hindering calculation of miscarriage rate in the population. To accurately determine the rate of miscarriage, 799 non-pregnant women of child-bearing age were enrolled and surveyed via monthly follow up visits that included pregnancy tests. Out of 505 women that completed the study, 364 became pregnant and 358 pregnancies were analyzed: 43 (12%) resulted in miscarriage, 28 (65.1%) occurred during the first trimester of pregnancy. We also determined rates of stillbirth, neonatal death, preterm delivery, and small for gestational age. The results showed high rate of miscarriage during the first trimester and established a basis to evaluate new interventions to prevent pregnancy malaria. This survey design enabled identification of first trimester miscarriages that are often missed by studies conducted in antenatal clinics.

Clinical trial registration

[https://clinicaltrials.gov/], identifier [NCT0297 4608].
Fungus Pichia kudriavzevii XTY1 and heterotrophic nitrifying bacterium Enterobacter asburiae GS2 cannot efficiently transform organic nitrogen via hydroxylamine and nitrite
Authors: Xu Tianyue , Song Simeng , Ren Baihui , Li Jiahuan , Yang Jiyun , Bai Long , Piao Zhongyun
Published: December 2022

Heterotrophic nitrification is a process of organic nitrogen degradation completed by the participation of heterotrophic nitrifying microorganisms, which can accelerate the nitrogen transformation process. However, the current research mainly focuses on heterotrophic nitrifying bacteria and their ammonium degradation capacities. And there is little accumulation of research on fungi, the main force of heterotrophic nitrification, and their capacities to transform organic nitrogen. In this study, novel heterotrophic nitrifying fungus (XTY1) and bacterium (GS2) were screened and isolated from upland soil, and the strains were identified and registered through GenBank comparison. After 24 h single nitrogen source tests and 15N labeling tests, we compared and preliminarily determined the heterotrophic nitrification capacities and pathways of the two strains. The results showed that XTY1 and GS2 had different transformation capacities to different nitrogen substrates and could efficiently transform organic nitrogen. However, the transformation capacity of XTY1 to ammonium was much lower than that of GS2. The two strains did not pass through NH2OH and NO2− during the heterotrophic nitrification of organic nitrogen, and mainly generated intracellular nitrogen and low N2O. Other novel organic nitrogen metabolism pathways may be existed, but they remain to be further validated.