bluuebunny/crossref_metadata_2025 huggingface dataset:
The Evolutionary Pattern of Language in English Fiction Over the Last Two Centuries: Insights From Linguistic Concreteness and Imageability
Authors: Sun Kun , Wang Rong
Published: January 2022

Fiction has come to play an essential part in human culture and life in recent centuries. Because of its importance, the language or discourse of fiction has been widely studied. Discerning the evolutionary pattern of language in fiction is greatly helpful in understanding the changes in human culture and society. However, most previous studies on literary language that made use of quantitative or computational methods restricted themselves to a few authors or groups and only took into account a relative short span of time. Furthermore, most of the quantitative analysis therein was based on a primary and rather primitive algorithm that summarizes the frequencies of linguistic units in corpora. To overcome these limitations, this study uses semantic similarity as computed by semi-supervised methods to examine diachronic changes. In this study, the three large-scale corpora representing the English language and English fiction were used to investigate the evolutionary patterns concerning diachronic concreteness/imageability. The data from the two measures are well mapped and shown to support the argument that English fiction, as a special genre, exhibits an evolutionary tendency toward increasing concreteness/imageability. This indicates that modern fiction may have become increasingly important in human society, but easier to read and process in words than 19th century English fiction. This study proposed that learnability, genre difference, the changes of population size, and the other factors might have caused the systemic change. The current study is thus an important contribution to understanding the evolutionary trend of language in fiction as well as understanding the development of the English language as a whole. This study creates a novel quantitative methodology and applies this to the examination of diachronic changes of language in literary works.
A Genetic Toolkit for Simultaneous Generation of LexA- and QF-Expressing Clones in Selected Cell Types in Drosophila
Authors: Banzai Kota , Shen Ping , Kamiyama Daichi
Published: January 2022

Visualization and manipulation of defined motoneurons have provided significant insights into how motor circuits are assembled in Drosophila. A conventional approach for molecular and cellular analyses of subsets of motoneurons involves the expression of a wide range of UAS transgenes using available GAL4 drivers (eg, eve promoter-fused GAL4). However, a more powerful toolkit could be one that enables a single-cell characterization of interactions between neurites from neurons of interest. Here we show the development of a UAS > LexA > QF expression system to generate randomly selected neurons expressing one of the 2 binary expression systems. As a demonstration, we apply it to visualize dendrite-dendrite interactions by genetically labeling eve+ neurons with distinct fluorescent reporters.
Nomenclature of wöhlerite-group minerals
Authors: Dal Bo Fabrice , Friis Henrik , Mills Stuart J.
Published: January 2022

A nomenclature and classification scheme for wöhlerite-group minerals has been established. The general formula of minerals belonging to this group is given by X8(Si2O7)2W4, where X = Na+, Ca2+, Mn2+, Ti4+, Zr4+ and Nb5+; and W = F– and O2–. In addition, they may incorporate significant amounts of Mg2+, Fe2+, Y3+ and REE3+, where REE are the lanthanides. The main structural feature of these minerals is the four-columns-wide octahedral walls, which are interconnected through corner sharing and via the disilicate groups. The wöhlerite-group minerals crystallise in different unit-cell settings and symmetries, depending on the cationic ordering in the octahedral walls and the relative position of the disilicate groups. Different combinations of X and W constituents should be regarded as separate mineral species. In the case of coupled heterovalent substitutions at different crystallographic sites, it is advised to use the site-total charge approach to determine the correct end-member composition. Due to their structural and chemical features, wöhlerite-group minerals can easily form crystals with several micro domains, showing different crystal structures and chemical compositions. In addition, the crystallisation of polytypes is relatively common, although they should not be regarded as distinct mineral species. To date, ten minerals belonging to the wöhlerite group are considered as valid species: baghdadite, burpalite, cuspidine, hiortdahlite, janhaugite, låvenite, moxuanxueite, niocalite, normandite and wöhlerite. Låvenite and normandite are isostructural and are respectively the Zr and Ti end-members of a solid-solution series. Marianoite is discredited, as it is corresponds to wöhlerite. The ideal formula of hiortdahlite is revised as Na2Ca4(Ca0.5Zr0.5)Zr(Si2O7)2OF3, with one cationic site characterised by a valency-imposed double site-occupancy. These changes have been approved by the IMA–CNMNC (Proposal 20–D).
Construction and investigation of β3GNT2-associated regulatory network in esophageal carcinoma
Authors: Luo Zhiguo , Hu Qing , Tang Yuanhui , Leng Yahui , Tian Tian , Tian Shuangyue , Huang Chengyang , Liu Ao , Deng Xinzhou , Shen Li
Published: January 2022

Background

Glycosyltransferases play a crucial role in various cancers. β1, 3-N-acetylglucosaminyltransferase 2, a polylactosamine synthase, is an important member of the glycosyltransferase family. However, the biological function and regulatory mechanism of β3GNT2 in esophageal carcinoma (ESCA) is still poorly understood.

Methods

The Cancer Genome Atlas and Genotype-Tissue Expression databases were used for gene expression and prognosis analysis. Quantitative real-time PCR, Western blot, and immunohistochemistry were performed to detect the expression of β3GNT2 in ESCA cell lines and tissues. In vitro assays and xenograft tumor models were utilized to evaluate the impact of β3GNT2 on ESCA progression. The downstream effectors and upstream regulators of β3GNT2 were predicted by online software and verified by functional experiments.

Results

We found that β3GNT2 was highly expressed in ESCA tissues and positively correlated with poor prognosis in ESCA patients. β3GNT2 expression was closely associated with the tumor size, TNM stage, and overall survival of ESCA patients. Functionally, β3GNT2 promoted ESCA cell growth, migration, and invasion in vitro, as well as tumorigenesis in vivo. Mechanistically, β3GNT2 knockdown decreased the expression of the polylactosamine on EGFR. Knockdown of β3GNT2 also inhibited the JAK/STAT signaling pathway. Meanwhile, the JAK/STAT inhibitor could partly reverse the biological effects caused by β3GNT2 overexpression. Moreover, β3GNT2 expression was positively regulated by CREB1 and negatively regulated by miR-133b. Both CREB1 and miR-133b was involved in the β3GNT2-mediated ESCA progression.

Conclusions

Our study, for the first time, reveals the importance of β3GNT2 in ESCA progression and offers a potential therapeutic target for ESCA.
Iam hiQ—a novel pair of accuracy indices for imputed genotypes
Authors: Rosenberger Albert , Tozzi Viola , Bickeböller Heike ,   the INTEGRAL-ILCCO consortium, Hung Rayjean J. , Christiani David C. , Caporaso Neil E. , Liu Geoffrey , Bojesen Stig E. , Le Marchand Loic , Albanes Demetrios , Aldrich Melinda C. , Tardon Adonina , Fernández-Tardón Guillermo , Rennert Gad , Field John K. , Davies Mike , Liloglou Triantafillos , Kiemeney Lambertus A. , Lazarus Philip , Haugen Aage , Zienolddiny Shanbeh , Lam Stephen , Schabath Matthew B. , Andrew Angeline S. , Duell Eric J. , Arnold Susanne M. , Brunnström Hans , Melander Olle , Goodman Gary E. , Chen Chu , Doherty Jennifer A. , Teare Marion Dawn , Cox Angela , Woll Penella J. , Risch Angela , Muley Thomas R. , Johansson Mikael , Brennan Paul , Landi Maria Teresa , Shete Sanjay S. , Amos Christopher I.
Published: January 2022

Background

Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imputed is fundamental. Several accuracy measures have been proposed and some are implemented in imputation software, unfortunately diversely across platforms. In the present paper, we introduce Iam hiQ, an independent pair of accuracy measures that can be applied to dosage files, the output of all imputation software. Iam (imputation accuracy measure) quantifies the average amount of individual-specific versus population-specific genotype information in a linear manner. hiQ (heterogeneity in quantities of dosages) addresses the inter-individual heterogeneity between dosages of a marker across the sample at hand.

Results

Applying both measures to a large case–control sample of the International Lung Cancer Consortium (ILCCO), comprising 27,065 individuals, we found meaningful thresholds for Iam and hiQ suitable to classify markers of poor accuracy. We demonstrate how Manhattan-like plots and moving averages of Iam and hiQ can be useful to identify regions enriched with less accurate imputed markers, whereas these regions would by missed when applying the accuracy measure info (implemented in IMPUTE2).

Conclusion

We recommend using Iam hiQ additional to other accuracy scores for variant filtering before stepping into the analysis of imputed GWAS data.
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses
Authors: Zou Zhaonan , Iwata Michio , Yamanishi Yoshihiro , Oki Shinya
Published: January 2022

Background

Elucidating the modes of action (MoAs) of drugs and drug candidate compounds is critical for guiding translation from drug discovery to clinical application. Despite the development of several data-driven approaches for predicting chemical–disease associations, the molecular cues that organize the epigenetic landscape of drug responses remain poorly understood.

Results

With the use of a computational method, we attempted to elucidate the epigenetic landscape of drug responses, in terms of transcription factors (TFs), through large-scale ChIP-seq data analyses. In the algorithm, we systematically identified TFs that regulate the expression of chemically induced genes by integrating transcriptome data from chemical induction experiments and almost all publicly available ChIP-seq data (consisting of 13,558 experiments). By relating the resultant chemical–TF associations to a repository of associated proteins for a wide range of diseases, we made a comprehensive prediction of chemical–TF–disease associations, which could then be used to account for drug MoAs. Using this approach, we predicted that: (1) cisplatin promotes the anti-tumor activity of TP53 family members but suppresses the cancer-inducing function of MYCs; (2) inhibition of RELA and E2F1 is pivotal for leflunomide to exhibit antiproliferative activity; and (3) CHD8 mediates valproic acid-induced autism.

Conclusions

Our proposed approach has the potential to elucidate the MoAs for both approved drugs and candidate compounds from an epigenetic perspective, thereby revealing new therapeutic targets, and to guide the discovery of unexpected therapeutic effects, side effects, and novel targets and actions.
Varia: a tool for prediction, analysis and visualisation of variable genes
Authors: Mackenzie Gavin , Jensen Rasmus W. , Lavstsen Thomas , Otto Thomas D.
Published: January 2022

Background

Parasites use polymorphic gene families to evade the immune system or interact with the host. Assessing the diversity and expression of such gene families in pathogens can inform on the repertoire or host interaction phenotypes of clinical relevance. However, obtaining the sequences and quantifying their expression is a challenge. In Plasmodium falciparum, the highly polymorphic var genes encode the major virulence protein, PfEMP1, which bind a range of human receptors through varying combinations of DBL and CIDR domains. Here we present a tool, Varia, to predict near full-length gene sequences and domain compositions of query genes from database genes sharing short sequence tags. Varia generates output through two complementary pipelines. Varia_VIP returns all putative gene sequences and domain compositions of the query gene from any partial sequence provided, thereby enabling experimental validation of specific genes of interest and detailed assessment of their putative domain structure. Varia_GEM accommodates rapid profiling of var gene expression in complex patient samples from DBLα expression sequence tags (EST), by computing a sample overall transcript profile stratified by PfEMP1 domain types.

Results

Varia_VIP was tested querying sequence tags from all DBL domain types using different search criteria. On average 92% of query tags had one or more 99% identical database hits, resulting in the full-length query gene sequence being identified (> 99% identical DNA > 80% of query gene) among the five most prominent database hits, for ~ 33% of the query genes. Optimized Varia_GEM settings allowed correct prediction of > 90% of domains placed among the four most N-terminal domains, including the DBLα domain, and > 70% of C-terminal domains. With this accuracy, N-terminal domains could be predicted for > 80% of queries, whereas prediction rates of C-terminal domains dropped with the distance from the DBLα from 70 to 40%.

Conclusion

Prediction of var sequence and domain composition is possible from short sequence tags. Varia can be used to guide experimental validation of PfEMP1 sequences of interest and conduct high-throughput analysis of var type expression in patient samples.
Longitudinal SARS-CoV-2 seroepidemiological investigation among healthcare workers at a tertiary care hospital in Germany
Authors: Tomczyk Sara , Hönning Alexander , Hermes Julia , Grossegesse Marica , Hofmann Natalie , Michel Janine , Neumann Markus , Nitsche Andreas , Hoppe Berthold , Eckmanns Tim , Schmidt-Traub Hajo , Zappel Kristina
Published: January 2022

Background

SARS-CoV-2 cases in Germany increased in early March 2020. By April 2020, cases among health care workers (HCW) were detected across departments at a tertiary care hospital in Berlin, prompting a longitudinal investigation to assess HCW SARS-CoV-2 serostatus with an improved testing strategy and associated risk factors.

Methods

In May/June and December 2020, HCWs voluntarily provided blood for serology and nasopharyngeal/oropharyngeal (NP/OP) samples for real-time polymerase chain reaction (PCR) and completed a questionnaire. A four-tiered SARS-CoV-2 serological testing strategy including two different enzyme-linked immunosorbent assays (ELISA) and biological neutralization test (NT) was used. ELISA-NT correlation was assessed using Pearson’s correlation coefficient. Sociodemographic and occupational factors associated with seropositivity were assessed with multivariate logistic regression.

Results

In May/June, 18/1477 (1.2%) HCWs were SARS-CoV-2 seropositive, followed by 56/1223 (4.6%) in December. Among those tested in both, all seropositive in May/June remained seropositive by ELISA and positive by NT after 6 months. ELISA ratios correlated well with NT titres in May/June (R = 0.79) but less so in December (R = 0.41). Those seropositive reporting a past SARS-CoV-2 positive PCR result increased from 44.4% in May/June to 85.7% in December. HCWs with higher occupational risk (based on profession and working site), nurses, males, and those self-reporting COVID-19-like symptoms had significantly higher odds of seropositivity.

Conclusions

This investigation provides insight into the burden of HCW infection in this local outbreak context and the antibody dynamics over time with an improved robust testing strategy. It also highlights the continued need for effective infection control measures particularly among HCWs with higher occupational risk.
Replacing vaccine paper package inserts: a multi-country questionnaire study on the acceptability of an electronic replacement in different target groups
Authors: Bamberger Martina , De Loof Hans , Marstboom Charlotte , Oury Stéphanie , Bonanni Paolo , Launay Odile , Kojouharova Mira , Van Damme Pierre
Published: January 2022

Background

In the European Union it is mandatory to include paper package leaflets (PPL) with all medicines, including vaccines, to inform the recipient. However, it is difficult to meet the necessity for localized PPLs in each of the 24 official European languages. Replacing PPLs with electronic versions offers many advantages including redistribution across nations, reduced storage space, accessibility by the visually impaired, easily updated information or the addition of video content. We wanted to assess the attitudes of patients (vaccine recipients or their parents) to the potential of replacing PPL with electronic versions.

Methods

We surveyed vaccinees or their parents in four European countries—Belgium, Italy, Bulgaria and France—for their actual use of vaccine PPLs and their opinions about switching to an electronic package leaflet. Our survey was conducted online because of the COVID-19 pandemic and resulted in 2518 responses to a questionnaire targeted at three specific groups with particular information needs: parents of young children, pregnant women and the elderly (≥ 60 years).

Results

Our main findings are that currently vaccine PPLs are rarely used and frequently unavailable for the vaccinee. Across the four countries surveyed 55–82% of vaccinees would accept an electronic version, as did 64% when there was an option to request a printout of the leaflet.

Conclusions

We found that switching to electronic versions of vaccine PPLs is an acceptable alternative for the public, potentially increasing the quality and amount of information reaching vaccinees while eliminating some barriers to redistribution of vaccines between countries.
Reproductive and hormonal risk factors for sarcoidosis: a nested case–control study
Authors: Dehara Marina , Sachs Michael C. , Kullberg Susanna , Grunewald Johan , Blomberg Anders , Arkema Elizabeth V.
Published: January 2022

Background

Sarcoidosis incidence peaks in females around the fifth decade of life, which coincides with menopause, suggesting hormonal factors play a role in disease development. We investigated whether longer exposure to reproductive and hormonal factors is associated with reduced sarcoidosis risk.

Methods

We conducted a matched case–control study nested within the Mammography Screening Project. Incident sarcoidosis cases were identified via medical records and matched to controls on birth and questionnaire date (1:4). Information on hormonal factors was obtained through questionnaires prior to sarcoidosis diagnosis. Multilevel modelling was used to estimate adjusted odds ratios with 95% credible intervals (OR; 95% CI).

Results

In total, 32 sarcoidosis cases and 124 controls were included. Higher sarcoidosis odds were associated with older age at menarche (OR 1.19: 95% CI 0.92–1.55), natural menopause versus non-natural (OR 1.53: 95% CI 0.80–2.93), later age at first pregnancy (OR 1.11: 95% CI 0.76–1.63) and ever hormone replacement therapy (HRT) use (OR 1.40: 95% CI 0.76–2.59). Lower odds were associated with older age at menopause (OR 0.90: 95% CI 0.52–1.55), longer duration of oral contraceptive use (OR 0.70: 95% CI 0.45–1.07), longer duration of HRT use (OR 0.61: 95% CI 0.22–1.70), ever local estrogen therapy (LET) use (OR 0.83: 95% CI 0.34–2.04) and longer duration of LET use (OR 0.78: 95% CI 0.21–2.81). However, the CIs could not rule out null associations.

Conclusion

Given the inconsistency and modest magnitude in our estimates, and that the 95% credible intervals included one, it still remains unclear whether longer estrogen exposure is associated with reduced sarcoidosis risk.
Identifying palliative care needs of patients with non-communicable diseases in Indonesia using the SPICT tool: a descriptive cross-sectional study
Authors: Effendy Christantie , Silva Jony Francisco Dos Santos , Padmawati Retna Siwi
Published: January 2022

Background

In Indonesia, Non-Communicable Diseases (NCD) are a contributing factor to mortality with most cases involving heart disease, cancer, chronic lung disease and diabetes. Accordingly, the identification of palliative care needs is very important as a first step in providing palliative care for these patients with NCD. However, currently there is no national standardized tool nor guidance system for identifying palliative care needs of NCD patients in Indonesia. The Supportive and Palliative Care Indicators Tool (SPICT) has been used worldwide for screening palliative care needs. This study aimed to identify palliative care needs in NCD patients using the SPICT tool.

Methods

This descriptive study used a cross-sectional design. Sampling technique used convenience sampling with a total sample of 124 adult patients with NCD in Dr. Sardjito Hospital Yogyakarta. Data collection used the Indonesian version of the SPICT. Data analyses used descriptive statistics and chi-square tests withp < 0,05 set as significant. Additionally, the prevalence of patients requiring palliative care was also calculated.

Results

The patients with NCD requiring palliative care who were screened using the SPICT tool were 61.3%. The nurses identified only 17.7%, while the physicians identified only 9.7%. The overall agreement of the clinician’s assessments to the researchers was < 32%. Meanwhile, agreement with nurses was 31 and 25% with the physicians.

Conclusions

These results highlight that by using the SPICT tool, recognition of hospitalized patients with NCD needing palliative care increased from 10 to 18% to > 61%. The Indonesian version of the SPICT tool can help the clinicians to reach meet agreement in identifying hospitalized patients who need palliative care as the first step in addressing palliative interventions for patients with NCD. It can provide several benefits in screening patients with NCD from the beginning of diagnosis.
Remote interpreting in primary care settings: a feasibility trial in Germany
Authors: Fiedler Jonas , Pruskil Susanne , Wiessner Christian , Zimmermann Thomas , Scherer Martin
Published: January 2022

Background

Global migration trends have led to a more diverse population in health care services everywhere, which in turn has set off a paradigm shift away from medical paternalism toward more patient autonomy. Consequently, physicians need to provide a more precise patient-centred healthcare. Professional interpreting appears to play a crucial part in tackling the challenges of language barriers adequately. The aim of this study was to conduct process evaluation through the implementing of video remote interpreting (VR) and telephone remote interpreting (TR) within primary care facilities in the northern German metropolis of Hamburg.

Methods

We conducted a three-armed exploratory pilot trial, which compared VR to TR and to a control group (CG) in different primary care settings. We assessed feasibility of implementation, as well as the acceptance of interpreting tools among their users. In addition, we compared the quality of communication as perceived by patients and physicians, as well as the enabling of patient-centred medicine over all three study groups using quantitative questionnaires.

Results

13 practices (7 GPs, 3 Gynaecologists, 3 Paediatricians) took part in this trial. 183 interpreting calls were documented, 178 physicians as well as 127 patients answered their respective questionnaires. The implementation of the VR- und TR-tools went smoothly and they were broadly accepted by their users. However, the tools were used significantly less often than we had anticipated. With regards to quantitative questionnaires, VR scored significantly better than the control group in terms of the perceived quality of communication by both, patients and physicians and enabled of patient-centred medicine.

Conclusion

Our main findings were the discrepancy between the assumed high demand of professional interpreting solutions on the one hand and the low willingness of practices to participate on the other. The rather low utilisation rates were also noteworthy. This discrepancy indicates a lack of awareness concerning the adverse effects of using informal or no interpreter in medical settings, which needs to be rectified. Due to the small sample size, all statistical results must be viewed with caution. However, our results show that remote interpreting represents a promising approach to tackling language barriers in primary care settings.
Equal access to healthcare in national legislations: how do Croatia, Germany, Poland, and Slovenia counteract discrimination in healthcare?
Authors: Bielińska Katarzyna , Chowaniec Anna , Doričić Robert , Nowak Marianne , Orzechowski Marcin , Ramšak Mojca , Łuków Paweł , Muzur Amir , Zupanič-Slavec Zvonka , Steger Florian
Published: January 2022

Background

The aim of the study was a comparative analysis of legislative measures against discrimination in healthcare on the grounds of a) race and ethnicity, b) religion and belief, and c) gender identity and sexual orientation in Croatia, Germany, Poland and Slovenia.

Methods

We conducted a search for documents in national legal databases and reviewed legal commentaries, scientific literature and official reports of equality bodies. We integrated a comparative method with text analysis and the critical interpretive approach. The documents were examined in their original languages: Croatian, German, Polish, and Slovenian.

Results

All examined states prohibit discrimination and guarantee the right to healthcare on the constitutional level. However, there are significant differences among them on the statutory level, regarding both anti-discriminatory legal measures and other legislation affecting access to healthcare for groups of diverse race or ethnicity, religion or belief, sexual orientation or gender identity. Croatia and Slovenia show the most comprehensive legislation concerning non-discrimination in healthcare in comparison to Germany and even more Poland. Except for Slovenia, explicit provisions protecting equal access for members of the abovementioned groups are insufficiently represented in healthcare legislation.

Conclusions

The study identified legislative barriers to access to healthcare for persons of diverse race or ethnicity, religion or belief, sexual orientation or gender identity in Croatia, Germany, Poland and Slovenia. The discrepancies in the level of implementation of anti-discriminatory measures among these states show that there is a need for comprehensive EU-wide regulations, which would implement the principle of equal treatment in the specific context of healthcare. General anti-discrimination regulations should be strengthened by inclusion of anti-discrimination provisions directly into national legislation relating specifically to the area of healthcare.
Genotyping of Chlamydia abortus using multiple loci variable number of tandem repeats analysis technique
Authors: Barati Sara , Bakhtiari Naghmeh Moori , Shokoohizadeh Leili , Ghorbanpoor Masoud , Momtaz Hassan
Published: January 2022

Background

The correlation between various factors (geographical region, clinical incidence, and host type) and the genomic heterogeneity has been shown in several bacterial strains includingChlamydia abortus.

Methods

The aim of this study was to survey the predominant types ofC. abortusstrains isolated from ruminants in Iran by the multiple loci variable number of tandem repeats (VNTR) analysis (MLVA) method.C. abortusinfection was evaluated in a total of 117 aborted fetuses by real-time PCR. The isolation was done via the inoculation of the positive samples in chicken embryo and the L929 cell line. Genotyping was carried out by MLVA typing technique.

Results

Forty samples (34.2%) were detected withC. abortusinfection; however, chlamydial infection in ruminants of Charmahal/Bakhtiari (3 bovines and 35 sheep) was higher than that of Khuzestan (2 sheep). All MLVA types (MT1-MT8) were detected in the collected samples from Charmahal/Bakhtiari but only 2 types (MT1 and MT3) were reported in samples from Khuzestan. The main MT type was MT1 (32% of aborted fetuses). Although in this study only 9 cow samples were investigated, they possessed similar clusters to those obtained from sheep (MT1 and MT6).

Variation of type in sheep samples (MT1 to MT8) was more than that of bovine samples (MT1, and MT6).

Conclusion

By this research revealed thatC.abortuswas responsible for a significant percentage of ruminant abortion in two studied regions. The main MT type was MT1 (32% of aborted fetuses) and also 7 different genotypes were involved in infections. So it is concluded that diversity inC.abortusgenotyping is high in two regions.
Case–control study on TP73 rs1801173 C > T gene polymorphism and susceptibility to gastric cancer in a Chinese Han population
Authors: Pan Huiwen , Gu Xuyu , Wang Xiaoyan , Gao Zhenjun , Ding Guowen , Zou Chen , Fan Yu
Published: January 2022

Background

This study investigated the role of TP73 gene polymorphism, rs1801173on risk of gastric cancer.

Methods

We conducted a case-controlled study including 577 primary gastric cancer and 678 normal control cases. The target gene fragment was amplified using PCR using blood samples collected from patients. Allele analysis and genotyping were performed using snapshot method.

Results

The findings showed that the control group had consistent genotype frequency distribution and presented Hardy–Weinberg equilibrium. The results showed no significant differences in sex, drinking history and age distributions between subjects with the polymorphism and subjects in the control group. Smoking status was correlated with incidence of gastric cancer (P = 0.006). The rs1801173 locus of TP73 gene contained 3 genotypes including: TT, CT, and CT. Logistic regression analysis showed that distribution of recessive model and dominant model was comparable between the two groups before (P = 0.688; 0.937) or after (P = 0.703; 0.990) adjusting for confounders. The distribution frequency in case group was not significantly different relative to that of the control group (P = 0.763).

Conclusion

Smoking can independently influence the risk of gastric cancer. TP73 gene rs1801173 polymorphism was not significantly correlated with risk of gastric cancer.
Addition of chemoradiotherapy to palliative chemotherapy in de novo metastatic nasopharyngeal carcinoma: a real-world study
Authors: Zheng Shuo-Han , Wang Yu-Tong , Liu Song-Ran , Huang Zi-Lu , Wang Guan-Nan , Lin Jin-Tao , Ding Shi-Rong , Chen Chen , Xia Yun-Fei
Published: January 2022

Background

To determine whether concurrent chemotherapy is necessary during locoregional radiotherapy (RT) after palliative chemotherapy (PCT) in patients with de novo metastatic nasopharyngeal carcinoma (mNPC).

Methods

A total of 746 patients with mNPC from 2000 to 2017 at our hospital were retrospectively reviewed. Among them, 355 patients received PCT followed by RT. Overall survival (OS) and progression-free survival (PFS), including locoregional progression-free survival (LRPFS) and distant progression-free survival (DPFS) were estimated with the Kaplan–Meier method and log-rank test. Cox proportional-hazards models, landmark analyses, propensity score matching, and subgroup analyses were used to address confounding.

Results

Of the patients included in our study, 192 received radiotherapy alone after PCT (PCT + RT), and 163 received concurrent chemoradiotherapy after PCT (PCT + CCRT). The prognosis of PCT + CCRT was significantly better than that of PCT + RT (5 year OS, 53.0 vs 36.2%; P = 0.004). After matching, the 5 year OS rates of the two groups were 55.7 and 39.0%, respectively (P = 0.034) and the median DPFS were 29.4 and 18.7 months, respectively (P = 0.052). Multivariate Cox regression analysis indicated that PCT + CCRT was an independent favorable prognostic factor (P = 0.009). In addition, conducting concurrent chemoradiotherapy after 4–6 cycles of PCT or conducting concurrent chemotherapy with single-agent platinum was associated with significant survival benefit in the matched cohort (5 year OS rate, 60.4 or 57.4%, respectively). The survival difference between groups remained significant when evaluating patients who survived for ≥ 1 year (P = 0.028).

Conclusions

The optimal treatment strategy of mNPC is the combination of PCT followed by concurrent chemoradiotherapy. More specifically, concurrent chemoradiotherapy with single-agent platinum after 4–6 cycles of PCT is suggested.
HIV-2/SIV Vpx antagonises NF-κB activation by targeting p65
Authors: Fink Douglas L. , Cai James , Whelan Matthew V. X. , Monit Christopher , Maluquer de Motes Carlos , Towers Greg J. , Sumner Rebecca P.
Published: January 2022

Background

The NF-κB family of transcription factors and associated signalling pathways are abundant and ubiquitous in human immune responses. Activation of NF-κB transcription factors by viral pathogen-associated molecular patterns, such as viral RNA and DNA, is fundamental to anti-viral innate immune defences and pro-inflammatory cytokine production that steers adaptive immune responses. Diverse non-viral stimuli, such as lipopolysaccharide and cytokines, also activate NF-κB and the same anti-pathogen gene networks. Viruses adapted to human cells often encode multiple proteins targeting the NF-κB pathway to mitigate the anti-viral effects of NF-κB-dependent host immunity.

Results

In this study we have demonstrated using a variety of assays, in a number of different cell types including primary cells, that plasmid-encoded or virus-delivered simian immunodeficiency virus (SIV) accessory protein Vpx is a broad antagonist of NF-κB signalling active against diverse innate NF-κB agonists. Using targeted Vpx mutagenesis, we showed that this novel Vpx phenotype is independent of known Vpx cofactor DCAF1 and other cellular binding partners, including SAMHD1, STING and the HUSH complex. We found that Vpx co-immunoprecipitated with canonical NF-κB transcription factor p65, but not NF-κB family members p50 or p100, preventing nuclear translocation of p65. We found that broad antagonism of NF-κB activation by Vpx was conserved across distantly related lentiviruses as well as for Vpr from SIV Mona monkey (SIVmon), which has Vpx-like SAMHD1-degradation activity.

Conclusions

We have discovered a novel mechanism by which lentiviruses antagonise NF-κB activation by targeting p65. These findings extend our knowledge of how lentiviruses manipulate universal regulators of immunity to avoid the anti-viral sequelae of pro-inflammatory gene expression stimulated by both viral and extra-viral agonists. Importantly our findings are also relevant to the gene therapy field where virus-like particle associated Vpx is routinely used to enhance vector transduction through antagonism of SAMHD1, and perhaps also through manipulation of NF-κB.

Graphical Abstract
BioRssay: an R package for analyses of bioassays and probit graphs
Authors: Karunarathne Piyal , Pocquet Nicolas , Labbé Pierrick , Milesi Pascal
Published: January 2022

Dose–response relationships reflect the effects of a substance on organisms, and are widely used in broad research areas, from medicine and physiology, to vector control and pest management in agronomy. Furthermore, reporting on the response of organisms to stressors is an essential component of many public policies (e.g. public health, environment), and assessment of xenobiotic responses is an integral part of World Health Organization recommendations. Building upon an R script that we previously made available, and considering its popularity, we have now developed a software package in the R environment,BioRssay, to efficiently analyze dose–response relationships. It has more user-friendly functions and more flexibility, and proposes an easy interpretation of the results. The functions in theBioRssaypackage are built on robust statistical analyses to compare the dose/exposure–response of various bioassays and effectively visualize them in probit-graphs.

Graphical Abstract
Spatiotemporal distribution, abundance, and host interactions of two invasive vectors of arboviruses, Aedes albopictus and Aedes japonicus, in Pennsylvania, USA
Authors: Little Eliza A. H. , Hutchinson Michael L. , Price Keith J. , Marini Alyssa , Shepard John J. , Molaei Goudarz
Published: January 2022

Background

Aedes albopictus and Aedes japonicus, two invasive mosquito species in the United States, are implicated in the transmission of arboviruses. Studies have shown interactions of these two mosquito species with a variety of vertebrate hosts; however, regional differences exist and may influence their contribution to arbovirus transmission.

Methods

We investigated the distribution, abundance, host interactions, and West Nile virus infection prevalence of Ae. albopictus and Ae. japonicus by examining Pennsylvania mosquito and arbovirus surveillance data for the period between 2010 and 2018. Mosquitoes were primarily collected using gravid traps and BG-Sentinel traps, and sources of blood meals were determined by analyzing mitochondrial cytochrome b gene sequences amplified in PCR assays.

Results

A total of 10,878,727 female mosquitoes representing 51 species were collected in Pennsylvania over the 9-year study period, with Ae. albopictus and Ae. japonicus representing 4.06% and 3.02% of all collected mosquitoes, respectively. Aedes albopictus was distributed in 39 counties and Ae. japonicus in all 67 counties, and the abundance of these species increased between 2010 and 2018. Models suggested an increase in the spatial extent of Ae. albopictus during the study period, while that of Ae. japonicus remained unchanged. We found a differential association between the abundance of the two mosquito species and environmental conditions, percent development, and median household income. Of 110 Ae. albopictus and 97 Ae. japonicus blood meals successfully identified to species level, 98% and 100% were derived from mammalian hosts, respectively. Among 12 mammalian species, domestic cats, humans, and white-tailed deer served as the most frequent hosts for the two mosquito species. A limited number of Ae. albopictus acquired blood meals from avian hosts solely or in mixed blood meals. West Nile virus was detected in 31 pools (n = 3582 total number of pools) of Ae. albopictus and 12 pools (n = 977 total pools) of Ae. japonicus.

Conclusions

Extensive distribution, high abundance, and frequent interactions with mammalian hosts suggest potential involvement of Ae. albopictus and Ae. japonicus in the transmission of human arboviruses including Cache Valley, Jamestown Canyon, La Crosse, dengue, chikungunya, and Zika should any of these viruses become prevalent in Pennsylvania. Limited interaction with avian hosts suggests that Ae. albopictus might occasionally be involved in transmission of arboviruses such as West Nile in the region.

Graphical Abstract
Social life-cycle assessment (S-LCA) of residential rooftop solar panels using challenge-derived framework
Authors: Bonilla-Alicea Ricardo J. , Fu Katherine
Published: January 2022

Background

Social life-cycle assessment (S-LCA) provides a framework to evaluate the social impacts of decisions made during the design phases of a product. Rooftop solar panels are considered an environmentally friendly renewable energy technology due to their ability to generate electricity without producing greenhouse gases while generating electricity. This study presents the application of a challenge-derived S-LCA framework to assess the social impacts of rooftop solar panels in the southeast region of the United States (U.S.) during the use and end-of-life phases.

Methods

The challenge-derived S-LCA framework was developed based on a set of challenges to performing social assessments. The challenges were identified through a systematic mapping process and verified using expert feedback. Additional feedback is gathered through users from mechanical engineering capstone design students. The case study application shown in this paper aims to identify the potential social impacts at a pre-implementation stage of the rooftop solar panel in residential applications. The framework follows the ISO 14040 LCA structure, and the analysis was performed based on impact indicators (Type-I framework) and performance reference points (PRP).

Results

The framework implements existing social impact assessment methodologies, and guides each of the assessment stages based on the type of analysis performed. The results highlight the workers as the stakeholder group with the highest social impacts. The results also highlight the need for regulation to make rooftop solar panels accessible to low-income community members.

Conclusions

An S-LCA framework to assess the social impacts of product systems and technologies is implemented to evaluate the potential social impacts of residential rooftop solar panels. The framework presented applies to product systems and technologies at a pre- or post-implementation state, and it aims to guide novice and expert users alike. Nonetheless, further research is still needed to improve the methodology presented, and additional case studies should be performed to test the applicability of the framework across a broad set of fields.
Multi-temporal analysis of past and future land cover change in the highly urbanized state of Selangor, Malaysia
Authors: Azari Majid , Billa Lawal , Chan Andy
Published: January 2022

Background

This study analysed the multi-temporal trend in land cover, and modelled a future scenario of land cover for the year 2030 in the highly urbanized state of Selangor, Malaysia. The study used a Decision Forest-Markov chain model in the land change modeller (LCM) tool of TerrSet software. Land cover maps of 1999, 2006 and 2017 were classified into 5 classes, namely water, natural vegetation, agriculture, built-up land and cleared land. A simulated land cover map of 2017 was validated against the actual land cover map 2017. The Area Under the Curve (AUC) value of 0.84 of Total Operating Characteristics (TOC) and higher percentage of components of agreement (Hits + Correct rejection) compared to components of disagreement (Misses + False alarm + Wrong hits) indicated successful validation of the model.

Results

The results showed between the years 1999 to 2017 there was an increase in built-up land cover of 608.8 km2 (7.5%), and agricultural land 285.5 km2 (3.5%), whereas natural vegetation decreased by 831.8 km2 (10.2%). The simulated land cover map of 2030 showed a continuation of this trend, where built-up area is estimated to increase by 723 km2 (8.9%), and agricultural land is estimated to increase by 57.2 km2 (0.7%), leading to a decrease of natural vegetation by 663.9 km2 (8.1%) for the period 2017 to 2030. The spatial trend of land cover change shows built-up areas mostly located in central Selangor where the highly urbanized and populated cities of Kuala Lumpur and Putrajaya and the Klang valley are located.

Conclusion

The future land cover modelling indicates that built-up expansion mostly takes place at edges of existing urban boundaries. The results of this study can be used by policy makers, urban planners and other stakeholders for future decision making and city planning.
Systematic review on factors influencing the effectiveness of alcohol-based hand rubbing in healthcare
Authors: Price Lesley , Gozdzielewska Lucyna , Alejandre Julius Cesar , Jorgenson Annelysse , Stewart Emma , Pittet Didier , Reilly Jacqui
Published: January 2022

Background

The effectiveness of hand rubbing with alcohol-based handrub (ABHR) is impacted by several factors. To investigate these, World Health Organization (WHO) commissioned a systematic review.

Aim

To evaluate the impact of ABHR volume, application time, rubbing friction and hand size on microbiological load reduction, hand surface coverage or drying time.

Methods

Medline, CINAHL, Web of Science and ScienceDirect databases were searched for healthcare or laboratory-based primary studies, published in English, (1980- February 2021), investigating the impact of ABHR volume, application time, rubbing friction or hand size on bacterial load reduction, hand coverage or drying time. Two reviewers independently performed data extraction and quality assessment. The results are presented narratively.

Findings

Twenty studies were included in the review. Categories included: ABHR volume, application time and rubbing friction. Sub-categories: bacterial load reduction, hand size, drying time or hand surface coverage. All used experimental or quasi-experimental designs. Findings showed as ABHR volume increased, bacterial load reduced, and drying times increased. Furthermore, one study showed that the application of sprayed ABHR without hand rubbing resulted in significantly lower bacterial load reduction than poured or sprayed ABHR with hand rubbing (− 0.70; 95%CI: − 1.13 to − 0.28). Evidence was heterogeneous in application time, volume, technique, and product. All studies were assessed as high risk of bias.

Conclusions

There is insufficient evidence to change WHO recommendation of a palmful of ABHR in a cupped hand applied for 20–30 s or manufacturer-recommended volume applied for about 20 s (Centers for Disease Control and Prevention). Future hand hygiene research should standardise volume, application time, and consider hand size.
Dimensions of poverty as risk factors for antimicrobial resistant organisms in Canada: a structured narrative review
Authors: King Teagan , Schindler Richelle , Chavda Swati , Conly John
Published: January 2022

Background

Few studies have assessed the relationship between poverty and the risk of infection with antimicrobial resistant organisms (AROs). We sought to identify, appraise, and synthesize the available published Canadian literature that analyzes living in poverty and risk of AROs.

Methods

A structured narrative review methodology was used, including a systematic search of three databases: MedLINE, EMBASE and Web of Science for articles pertaining to poverty, and infection with AROs in Canada between 1990 and 2020. Poverty was broadly defined to include economic measures and associated social determinants of health. Based on inclusion and exclusion criteria, there were 889 initial articles, and 43 included in the final review. The final articles were extracted using a standard format and appraised using the Joanna Briggs Institute Levels of Evidence framework.

Results

Of 43 studies, 15 (35%) related to methicillin-resistant Staphylococcus aureus (MRSA). One study found a 73% risk reduction (RR 0.27, 95%CI 0.19–0.39, p =  < 0.0001) in community-acquired MRSA (CA-MRSA) infection for each $100,000 income increase. Results pertaining to homelessness and MRSA suggested transmission was related to patterns of frequent drug use, skin-to-skin contact and sexual contact more than shelter contact. Indigenous persons have high rates of CA-MRSA, with more rooms in the house being a significant protective factor (OR 0.86, p = 0.023). One study found household income over $60,000 (OR 0.83, p = 0.039) in univariate analysis and higher maternal education (OR 0.76, 95%CI 0.63–0.92, p = 0.005) in multivariate analysis were protective for otitis media due to an ARO among children. Twenty of 43 (46.5%) articles pertained to tuberculosis (TB). Foreign-born persons were four times more likely to have resistant TB compared to Canadian-born persons. None of the 20 studies used income in their analyses.

Conclusions

There is an association between higher income and protection from CA-MRSA. Mixed results exist regarding the impact of homelessness and MRSA, demonstrating a nuanced relationship with behavioural risk factors. Higher income and maternal education were associated with reduced ARO-associated acute otitis media in children in one study. We do not have a robust understanding of the social measures of marginalization related to being foreign-born that contribute to higher rates of resistant TB infection.