bluuebunny/crossref_metadata_2025 huggingface dataset:
Vegetation community dynamics during naturalized developmental restoration ofPinus tabulaeformisplantation in North warm temperate zone
Authors: Qiu Zhenlu , Zhang Mei , Wang Kefan , Shi Fuchen
Published: December 2022

The study is to explore the dynamics of community structure, diversity, interspecific relationships and stability during naturalized developmental vegetation restoration which realized by natural interaction between plantation and native trees without human’s involvement. The naturalized developmental restored forests in Baxianshan National Reserve were divided into three typical stages (i.e. Pinus tabulaeformis forest stage, mixed forest stage and near-natural forest stage) according to the ratio of P. tabulaeformis coverage to arbor layer, and the zonal natural secondary forests for control. According to the data of each wood gauge, we focused on the dynamics of community in terms of structure, diversity and stability. We found that, (i) The composition of dominant populations kept stable since the mixed forests stage and the α-diversity increased with restoration; (ii) The diameter class structure of tree layer exhibited a tendency of bell-shaped type toward inverted J-type, indicating an active regenerating and developmental status; (iii) Niche width of dominant populations such as Juglans mandshurica, Quercus mongolica, Quercus variabilis and Tilia amurensis increased during restoration, while that of Quercus dentata population decreased after playing a pioneer role; (iv) The proportion of negative association and high niche overlapped population pairs (>0.5) both decreased with restoration. In summary, naturalized developmental restoration has promoted the actively developing and regenerating of populations and improved the healthy restoration of plantation community. The status and interrelationships of populations were still being adjusted. The results provide a reference for revealing the dynamic characteristics of vegetation community development in naturalized developmental restoration of plantations.
Review of meteorite irradiation tests to support next C-type asteroid missions
Authors: Kereszturi Á , Gyollai I , Juhász Z , Pál B D , Rácz R , Rezes D , Sulik B
Published: December 2022

Effect of space weathering of airless asteroids could be better understood by artificial irradiation tests on meteorites in laboratories. This work surveys the infrared and Raman analysis based interpretation of simulated charged particle irradiation tests in order to better understand near-future observational possibilities of asteroid visiting missions and also to support the planning of next missions and directions of detector improvement. Recent works properly targeted different meteors and meteor relevant minerals, evaluating bulk meteorite spectra, during the irradiation tests. He+, (Ne+, Kr+), and Ar+ ions were used with fluxes characteristic for inner planetary system solar wind, considering 1–10 million yr exposure durations. Although main meteorite minerals were irradiated and analysed, one missing aspect is that only bulk analysis have been done, not minerals separately in their original embedded context. Some Earth based mineral references were also analysed; however, they might not necessarily behave similar to the same type of reference minerals and irradiation effect is poorly known for feldspar, troilite, and magnetite. Darkening should be also further analysed for separate minerals too, together with the record of peak shape and position changes. Infrared ATR analysis might still provide such data in the future using the recently emerged technology, as well as Raman analysis – however for flyby missions’ infrared is the useful method while Raman can be used only at in situ missions. The overview including the tables to support the identification of specific missing information related gaps in our current knowledge and directions for future research.
Quantifying the dust in SN 2012aw and iPTF14hls with ORBYTS
Authors: Niculescu-Duvaz Maria , Barlow M J , Dunn William , Bevan Antonia , Ahmed Omar , Arkless David , Barker Jon , Bartolotta Sidney , Brockway Liam , Browne Daniel , Esmail Ubaid , Garner Max , Guz Wiktoria , King Scarlett , Kose Hayri , Lampstaes-Capes Madeline , Magen Joseph , Morrison Nicole , Oo Kyaw , Paik Balvinder , Primrose Joanne , Quick Danny , Radeka Anais , Rodney Anthony , Sandeman Eleanor , Sheikh Fawad , Stansfield Camron , Symister Delayne , Taylor Joshua , Wilshere William , Wesson R , De Looze I , Clayton G C , Krafton K , Matsuura M
Published: December 2022

Core-collapse supernovae (CCSNe) are capable of producing large quantities of dust, with strong evidence that ejecta dust masses can grow significantly over extended periods of time. Red–blue asymmetries in the broad emission lines of CCSNe can be modelled using the Monte Carlo radiative transfer code damocles, to determine ejecta dust masses. To facilitate easier use of damocles, we present a Tkinter graphical user interface (GUI) running damocles. The GUI was tested by high school students through the Original Research By Young Twinkle Students programme, who used it to measure the dust masses formed at two epochs in Type IIP CCSNe, SN 2012aw and iPTF14hls, demonstrating that a wide range of people can contribute to scientific advancement. Bayesian methods quantified uncertainties on our model parameters. From the red scattering wing in the day 1863 Hα profile of SN 2012aw, we constrained the dust composition to large (radius >0.1 μm) silicate grains, with a dust mass of $6.0^{+21.9}_{-3.6}\times 10^{-4}~\mathrm{ M}_\odot$. From the day 1158 Hα profile of SN 2012aw, we found a dust mass of $3.0^{+14}_{-2.5}\times 10^{-4}$ M⊙. For iPTF14hls, we found a day 1170 dust mass of 8.1$^{+81}_{-7.6}\times 10^{-5}$ M⊙ for a dust composition consisting of 50 per cent amorphous carbon and 50 per cent astronomical silicate. At 1000 d post-explosion, SN 2012aw and iPTF14hls have formed less dust than the peculiar Type II SN 1987A, suggesting that SN 1987A may have formed a larger dust mass than typical Type IIP’s.
Total electron content depression in the nightside Martian ionosphere: statistical results from Mars Express MARSIS measurements and implications
Authors: Cao Yutian , Niu Dandan , Liang Wenjun , Cui Jun , Wu Xiaoshu , Wan Xin , Zhong Jiahao , Li Lei , Rong Zhaojin , Wei Yong
Published: December 2022

Thermal electron depression and energetic electron depletion are two well-known features of the nightside Martian ionosphere. While the latter has been extensively studied in the past, there is no report of systematic and firm identification of the former and hence the correlation between them is unknown. Applying an automatic procedure to the Mars Express total electron content (TEC) measurements, we identify a large number of TEC depression features that amount to one-third of the available nightside measurements. Similar to the observation of energetic electron depletion, large amplitude TEC depression is more frequently observed near strong magnetic fields, as an expected result of the established solar-wind-driven scenario that the shielding of precipitating electrons by closed magnetic loops is responsible for the observed reduction in thermal electron density. However, small amplitude depression appears to be uniformly distributed across the Martian surface, implying an alternative origin yet to be determined. Contrary to our expectation, TEC depression and energetic electron depletion are not usually collocated, but this dilemma may simply reflect the complexity of the magnetic field topology with respect to the spacecraft trajectory.
Assessing university policies for enhancing societal impact of academic research: A multicriteria mapping approach
Authors: Kuipers-Dirven Rosa , Janssen Matthijs , Hoekman Jarno
Published: December 2022

While there is a prolific debate on evaluating the societal impact of academic research, so far little attention has been paid to assessing the design and implementation of suitable organizational strategies. This article argues that evaluation methods are needed which are both formative and sensitive to diverging views on what defines and constitutes societal impact. We use a participatory deliberation method, the Multicriteria Mapping (MCM) approach, to examine how stakeholders appraise the use of university policy options for enhancing societal impact, and understand on what basis they judge the performance of these options. Focusing on a large Dutch research-based university, we conduct 22 interviews with academics, management, and support staff as well as strategic policy officers to examine how they rank and discuss the expected performance of university policy options identified in previous literature. Our results show that interviewees base their scores on criteria related to policy options’ expected organizational output and external outcomes, as well as their practical and, to a lesser degree, cultural, and financial feasibility. The resulting rankings also point at contrasts in the perceived potential of policy options, with interviewees assigning priority to providing researchers with recognition and rewards for impact-based activities. We conclude by discussing how MCM can be used as a formative evaluation method to assess and select policies and inform decision-making that fit a university’s particular situation. Besides drawing lessons for the context of our illustrative case, we also reflect on the relevance of the evaluation method and our findings for other universities.
Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks
Authors: Ji Jiayi , Jackson Donavan J , Leaché Adam D , Yang Ziheng
Published: December 2022

In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.]
A combined clinical and genetic model for predicting risk of ovarian cancer
Authors: Dite Gillian S. , Spaeth Erika , Murphy Nicholas M. , Allman Richard
Published: December 2022

Objective

Women with a family history of ovarian cancer or a pathogenic or likely pathogenic gene variant are at high risk of the disease, but very few women have these risk factors. We assessed whether a combined polygenic and clinical risk score could predict risk of ovarian cancer in population-based women who would otherwise be considered as being at average risk.

Methods

We used the UK Biobank to conduct a prospective cohort study assessing the performance of 10-year ovarian cancer risks based on a polygenic risk score, a clinical risk score and a combined risk score. We used Cox regression to assess association, Harrell’s C-index to assess discrimination and Poisson regression to assess calibration.

Results

The combined risk model performed best and problems with calibration were overcome by recalibrating the model, which then had a hazard ratio per quintile of risk of 1.338 [95% confidence interval (CI), 1.152–1.553], a Harrell’s C-index of 0.663 (95% CI, 0.629–0.698) and overall calibration of 1.000 (95% CI, 0.874–1.145). In the refined model with estimates based on the entire dataset, women in the top quintile of 10-year risk were at 1.387 (95% CI, 1.086–1.688) times increased risk, while women in the top quintile of full-lifetime risk were at 1.527 (95% CI, 1.187–1.866) times increased risk compared with the population.

Conclusion

Identification of women who are at high risk of ovarian cancer can allow healthcare providers and patients to engage in joint decision-making discussions around the risks and benefits of screening options or risk-reducing surgery.
Antidepressant-like effect of acute dose of Naringin involves suppression of NR1 and activation of protein kinase A/cyclic adenosine monophosphate response element-binding protein/brain-derived neurotrophic factor signaling in hippocampus
Authors: Wang Guangyao , Yang Haixia , Zuo Wenren , Mei Xiaoyun
Published: December 2022

Naringin (Nr) has been identified to have antidepressant-like effects through repeated treatment. However, the underlying mechanism of the rapid antidepressant-like effects of Nr was still unclear. The present study used behavioral tests, classic depressive model and pharmacological methods to reveal the rapid antidepressant-like potential of Nr. We found that a single dose of Nr (20 mg/kg) produced antidepressant-like action after 2 h in the tail suspension test (TST) and forced swimming test (FST). Moreover, ketamine-like effects were also demonstrated by using the chronic mild stress model (CMS) and learned helplessness (LH), and the results showed that Nr reversed all behavioral defects, TST, FST, source preference test (SPT) in CMS, and LH testing, TST, FST in LH model, at 2 h after a single administration. In addition, Nr (20 mg/kg) could improve the abnormal expressions of NMDA receptor NR1 and PKA/CREB/BDNF pathway in hippocampus 2 h after a single administration in CMS mice. Further investigation revealed that activation of NMDA receptors by NMDA (750 mg/kg) could block the antidepressant effects of acute administration of Nr (20 mg/kg). However, the inhibition of NMDA receptors by MK-801 (0.05 mg/kg) promoted the subdose of Nr (10 mg/kg) to have antidepressant effect, which was similar to the effective dose Nr (20 mg/kg). Taken together, acute dose of Nr produces rapid antidepressant-like action, and the underlying mechanism could be through inhibiting NMDA receptors in the hippocampus.
Huntington-associated protein 1 inhibition contributes to neuropathic pain by suppressing Cav1.2 activity and attenuating inflammation
Authors: Pan JingYing , Zhao YaYu , Sang Rui , Yang RiYun , Bao JingYin , Wu YongJiang , Fei Ying , Wu Jian , Chen Gang
Published: December 2022

Although pain dysfunction is increasingly observed in Huntington disease, the underlying mechanisms still unknown. As a crucial Huntington-associated protein, Huntington-associated protein 1 (HAP1) is enriched in normal spinal dorsal horn and dorsal root ganglia (DRG) which are regarded as “primary sensory center,” indicating its potential functions in pain process. Here, we discovered that HAP1 level was greatly increased in the dorsal horn and DRG under acute and chronic pain conditions. Lack of HAP1 obviously suppressed mechanical allodynia and hyperalgesia in spared nerve injury (SNI)-induced and chronic constriction injury-induced pain. Its deficiency also greatly inhibited the excitability of nociceptive neurons. Interestingly, we found that suppressing HAP1 level diminished the membrane expression of the L-type calcium channel (Cav1.2), which can regulate Ca2+ influx and then influence brain-derived neurotrophic factor (BDNF) synthesis and release. Furthermore, SNI-induced activation of astrocytes and microglia notably decreased in HAP1-deficient mice. These results indicate that HAP1 deficiency might attenuate pain responses. Collectively, our results suggest that HAP1 in dorsal horn and DRG neurons regulates Cav1.2 surface expression, which in turn reduces neuronal excitability, BDNF secretion, and inflammatory responses and ultimately influences neuropathic pain progression.
Management of Opioid-induced Constipation in Older Adults
Authors: Horrigan Jamie , Bhumi Sriya , Miller David , Jafri Mikram , Tadros Micheal
Published: December 2022

Opioid-induced constipation (OIC) is a common condition in older adults who may not be responsive to traditional laxative therapy. OIC is defined as new or worsening constipation symptoms that occur with initiation of or altering the dose of opioid analgesia. For adult patients with OIC and noncancer pain, we recommend considering nonpharmacologic interventions (eg, dietary measures, increased physical activity, and biofeedback training) and over-the-counter laxatives, followed by prescription opioid receptor antagonists (methylnaltrexone, naloxegol, and naldemedine) if traditional over-the-counter laxatives fail. Other options may include lubiprostone, linaclotide, plecanatide, and prucalopride; however, these are not indicated for OIC specifically or studied in older adults. Because of the complex nature of absorption, distribution, metabolism, and excretion in the aging population, all agents used to treat OIC must be evaluated individually and reevaluated as patients continue to age. This review will serve as a guide to managing OIC in older adults.
Effect of Premedication With Pronase Before Upper Gastrointestinal Endoscopy
Authors: Li Jun , Wang Lan , Hu Weiling , Wu Jiaguo , Chen Hongtan , Wang Liangjing , Lv Bin , Zhang Xiaofeng , Dai Yiyang , Huang Zhiming , Cai Zhenzhai , Ding Xiaoyun , Ye Liping , Ding Jin , Xiang Lijuan , Ye Bin , Chen Shujie , Si Jianmin
Published: December 2022

Objectives:

This study aimed to confirm whether premedication with pronase before endoscopy improves mucosal visualization and increases precancerous lesion and cancer lesion detection rates.

Materials and Methods:

From June 2018 to April 2019, out-patients scheduled for endoscopy from 13 hospitals were screened to be randomly allocated in a 2:1 ratio to premedication with pronase (group A) and water (group B). The primary endpoint was mucosal visibility scores, and the secondary endpoint was precancerous and cancer lesion detection rates. This trial was registered at Chinese Clinical Trial Registry, and the registration number was ChiCTR1800016853.

Results:

Group A showed significantly lower mucosal visibility scores (better mucosal visibility) of esophagus, stomach, and duodenum than group B, with all P-values <0.001. The overall cancer detection rates between group A and group B were 0.83 and 1.08%, and overall detection rates of precancerous and cancer lesion were 4.4 and 4.9%, both without significant difference (P=1.000 and 0.824). In addition, the flushing volume (milliliter) of group A (10.52±23.41) was less than group B (36.30±52.11) (P<0.001), and the flushing frequency of group A (0.46±1.01) was fewer than group B (1.62±2.12) (P<0.001).

Conclusions:

Premedication with pronase could achieve better mucosal visibility and decrease flushing frequency and volume, but may not increase lesion detection rates.
Hepatocellular Adenoma: A Case Report, Current Updates on Subtyping, and Diagnostic Pitfalls
Authors: Jung Geunyoung , Liu Yongjun
Published: December 2022

Hepatocellular adenoma (HCA) is a benign liver neoplasm that typically arises in the noncirrhotic liver. Based on molecular findings, HCA can be subclassified into the following subtypes: hepatocyte nuclear factor 1α–inactivated HCA, inflammatory HCA, β-catenin–activated HCA, sonic hedgehog-activated HCA, and unclassified HCA. Mixed β-catenin–activated inflammatory HCA may rarely occur. We report a case of HCA that was initially diagnosed as inflammatory HCA on a biopsy but finally was confirmed to be β-catenin–activated inflammatory HCA on the resection specimen. Most recent updates on molecular classification, key histologic features of each subtype, and common diagnostic pitfalls are discussed.
Histomorphological Subtypes of Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma: Review and Update
Authors: Hwang Yoon Jung , Kim Haeryoung
Published: December 2022

Primary liver cancers comprise a heterogeneous group of neoplasms, with the 2 main entities being hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). Over the past decades, HCC and iCCA have been recognized to be heterogeneous in morphology, molecular features, and biological behavior, and the most recent World Health Organization classification of digestive system tumors describes various histomorphological subtypes of HCC and iCCA, some of which also have characteristic molecular features, clinical correlates, and prognostic implications. In this review, we discuss 4 recently described subtypes of HCC and iCCA—macrotrabecular HCC, steatohepatitic HCC, scirrhous HCC, and small duct iCCA—based on a series of cases.
A Case Review on Combined Hepatocellular Cholangiocarcinoma
Authors: Kondo Reiichiro , Akiba Jun , Yano Hirohisa
Published: December 2022

Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) is a rare primary liver tumor with neoplastic components of both hepatocytic and cholangiocytic differentiation within the same tumor, such as the case reported herein. There is a need to standardize the pathological diagnosis of cHCC-CCA and to improve the concordance of diagnosis among pathologists based on consensus paper because of its histological and phenotypic diversity that leads to confusion in terminology and classification. This case review addresses the terminology, classification, and clinical and pathological characteristics of cHCC-CCA and its differential diagnosis.
SNHG1 alleviates the oxidative stress and inflammatory response in traumatic brain injury through regulating miR-377-3p/DUSP1 axis
Authors: Jiao Wei , Jiang Lili , Zhang Yulei
Published: December 2022

Objectives

To investigate the role of short nucleolar RNA host gene 1 (SNHG1) in regulating inflammation and brain injury in traumatic brain injury (TBI).

Methods

The Feeney’s free-falling method was used to induce moderate TBI model in mice. Lipopolysaccharide (LPS) was employed to construct the microglia in vitro. Reverse transcription-PCR (RT-PCR) was conducted to monitor expression of SNHG1, microRNAs (miR)-377-3p, oxidative and inflammatory factors. TdT-mediated dUTP nick end labeling and immunohistochemistry were adopted to determine neuronal cell apoptosis. Flow cytometry was conducted to measure apoptosis. Moreover, Bax, Bcl2, Caspase3, dual-specific phosphatase-1 (DUSP1)/mitogen-activated protein kinase/NF-KB were tested by western blot. Furthermore, bioinformatics, dual-luciferase assay and RNA-binding protein immunoprecipitation experiment were implemented to verify the targeting relationship among SNHG1, miR-377-3p and DUSP1.

Results

SNHG1 was knocked down, while miR-377-3p was overexpressed in TBI mice and lipopolysaccharide-induced microglia. Meanwhile, overexpressing SNHG1 reduced neuronal damage and weakened the oxidative stress and inflammation in TBI on matter in vivo or in vitro. Additionally, overexpressing SNHG1 attenuated miR-377-3p-mediated inflammatory factors, oxidative stress and neuronal damage. Moreover, miR-377-3p was the target of SNHG1 and DUSP1.

Conclusions

This study provides a better understanding of the SNHG1/miR-377-3p/DUSP1 axis in regulating the development of TBI, which is helpful to formulate a treatment plan for TBI.
Effects of the genetic knockout of the β-1,3-galactosyltransferase 2 on spatial learning and neurons in the adult mouse hippocampus and somatosensory cortex
Authors: Chen Xiaojie , Wang Pan , Ren Lili , Deng Xinyang , Yin Xuechen , Zhang Luyun , Li Qingyu , Bai Lina , Li Xiaojia , Wang Peng , Bi Jing
Published: December 2022

Objective

Glycosyltransferases contribute to the biosynthesis of glycoproteins, proteoglycans and glycolipids and play essential roles in various processes in the brain, such as learning and memory, brain development, neuronal survival and neurodegeneration. β-1,3-galactosyltransferase 2 (B3galt2) belongs to the β-1,3-galactosyltransferase gene family and is highly expressed in the brain. Recent studies have indicated that B3galt2 plays a vital role in ischemic stroke through several signaling pathways in a mouse model. However, the function of B3galt2 in the brain remains poorly understood.

Methods

The genotypes of mice were determined by PCR. To verify B3galt2 expression in an adult mouse brain, X-gal staining was performed in 6-month-old B3galt2 heterozygous (B3galt2+/−
) mice. Using adult B3galt2 homozygous (B3galt2−/−
), heterozygous and wild-type (WT) littermates, spatial learning and memory were determined by the Morris Water Maze test, and neurotoxicity and synaptic plasticity were examined by immunofluorescence.

Results

B3galt2 was highly expressed in the adult mouse hippocampus and cortex, especially in the hippocampal dentate gyrus. Compared to that of WT mice, the spatial learning ability of adult B3galt2−/−
mice was impaired. B3galt2 mutations also caused neuronal loss and synaptic dysfunction in the hippocampus and somatosensory cortex, and these changes were more obvious in B3galt2−/−
mice than in B3galt2+/−
mice.

Conclusions

The findings indicate that B3galt2 plays an important role in cognitive function, neuronal maintenance and synaptic plasticity in the adult mouse brain. This study suggests that genetic and/or pharmacological manipulation of glycosyltransferases may be a novel strategy for elucidating the mechanism of and managing various brain disorders.
Exploring B and T-cell epitopes for constructing a Novel Multiepitope vaccine to combat emerging Monkeypox infection: A Reverse Vaccinology approach
Authors: Yousaf Hassan , Naz Anam
Published: December 2022

Background

While the whole mankind is resurrecting from the recent Covid-19 pandemic, new cases of the monkeypox virus have been reported inflicting serious threats to the public health. Monkeypox is a newly emerging, zoonotic orthopoxvirus having similar symptoms as that of the smallpox. So far, no approved treatment and therapeutics are in line to fight the infection.

Methodology

Therefore, in the present study, we have deployed a computational pipeline. We have retrieved the helper T-cell lymphocytes, cytotoxic T-cell and B-cell inducing epitopes by targeting the cell surface binding protein of the virus and further filtered the high-quality peptides based on their immunogenicity, antigenicity and allergenicity. After subsequent steps, we constructed and validated the tertiary structure of vaccine and analyzed its molecular interactions with toll like receptor-2 (TLR-2) and toll like receptor-4 (TLR-4) through molecular docking and the atomic movements and stability through molecular dynamics simulation approach. Moreover, C-IMMSIM server was used to evaluate the immune response triggering capacity of the chimeric vaccine through the immunoglobin profile.

Conclusion

The conductedin silicostudy concludes that the surface protein of monkeypox virus is one of the major culprit antigens in mediating the disease. Hence, our study will aid in the better formulation of vaccines in future by targeting the suitable drug or vaccine candidates.
Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
Authors: Moesslacher Christina S. , Woodsmith Jonathan , Auernig Elisabeth , Feichtner Andreas , Jany-Luig Evelyne , Jehle Stefanie , Worseck Josephine M. , Heine Christian L. , Stefan Eduard , Stelzl Ulrich
Published: December 2022

NF2 (Neurofibromine 2, merlin) is frequently inactivated in cancer, where its NF2 tumor suppressor functionality is tightly coupled to protein conformation. How NF2 conformation is regulated and how NF2 conformation influences tumor suppressor activity is a largely open question. Here we systematically characterized three NF2 conformation-dependent protein interactions utilizing deep mutational scanning interaction perturbation analyses. We identified two regions in NF2 with clustered mutations which affected conformation dependent protein interactions. NF2 variants in the F3 subdomain and the α3H helix region substantially modulated NF2 conformation and homomerization. Mutations in the F3 subdomain altered proliferation in three cell lines and matched patterns of disease mutations in neurofibromatosis. This study highlights the power of systematic mutational interaction perturbation analysis to identify missense variants impacting NF2 conformation and provides insight into NF2 tumor suppressor function.
Directed evolution of generalist biosensors for single ring aromatics
Authors: Cole Hannah O. , Kosonocky Clayton W. , Schechter Mason , Gollihar Jimmy , Ellington Andrew D. , d’Oelsnitz Simon
Published: December 2022

Biosensors can accelerate the engineering of new biosynthetic pathways. Phloroglucinol is a platform chemical of wide utility that can be produced at limited titers inEscherichia coli. Starting from the TetR family repressor RolR that is responsive to the related compound resorcinol, we were able to employ a combined selection and screen to identify variants that had greatly improved activities with phloroglucinol (EC50 for phloroglucinol of 131 uM, relative to an estimated 42 mM for wild-type RolR). The variants obtained were further screened with a panel of similar single ring aromatics, and several were found to be generalists, consistent with the hypothesis that both natural and directed evolution tend to first create semi-specific pockets prior to further optimization for new function
A deep active learning-based and crowdsourcing-assisted solution for named entity recognition in Chinese historical corpora
Authors: Yan Chengxi , Tang Xuemei , Yang Hao , Wang Jun
Published: December 2022

Purpose

The majority of existing studies about named entity recognition (NER) concentrate on the prediction enhancement of deep neural network (DNN)-based models themselves, but the issues about the scarcity of training corpus and the difficulty of annotation quality control are not fully solved, especially for Chinese ancient corpora. Therefore, designing a new integrated solution for Chinese historical NER, including automatic entity extraction and man-machine cooperative annotation, is quite valuable for improving the effectiveness of Chinese historical NER and fostering the development of low-resource information extraction.

Design/methodology/approach

The research provides a systematic approach for Chinese historical NER with a three-stage framework. In addition to the stage of basic preprocessing, the authors create, retrain and yield a high-performance NER model only using limited labeled resources during the stage of augmented deep active learning (ADAL), which entails three steps—DNN-based NER modeling, hybrid pool-based sampling (HPS) based on the active learning (AL), and NER-oriented data augmentation (DA). ADAL is thought to have the capacity to maintain the performance of DNN as high as possible under the few-shot constraint. Then, to realize machine-aided quality control in crowdsourcing settings, the authors design a stage of globally-optimized automatic label consolidation (GALC). The core of GALC is a newly-designed label consolidation model called simulated annealing-based automatic label aggregation (“SA-ALC”), which incorporates the factors of worker reliability and global label estimation. The model can assure the annotation quality of those data from a crowdsourcing annotation system.

Findings

Extensive experiments on two types of Chinese classical historical datasets show that the authors’ solution can effectively reduce the corpus dependency of a DNN-based NER model and alleviate the problem of label quality. Moreover, the results also show the superior performance of the authors’ pipeline approaches (i.e. HPS + DA and SA-ALC) compared to equivalent baselines in each stage.

Originality/value

The study sheds new light on the automatic extraction of Chinese historical entities in an all-technological-process integration. The solution is helpful to effectively reducing the annotation cost and controlling the labeling quality for the NER task. It can be further applied to similar tasks of information extraction and other low-resource fields in theoretical and practical ways.
Exploring the perspectives of engineering undergraduates on employability and employability building activities
Authors: Howell Simon , Hall Wayne , Geelan David
Published: December 2022

Purpose

This study was conducted to gain a better understanding of engineering students' perceptions of the meaning of employability and the activities that contribute to employability development.

Design/methodology/approach

A survey was used to take a cross-section of student perspectives at key stages in the degree, and was followed by a series of focus groups to further explore student opinions on employability. Responses to selected open-ended questions and relevant sections of focus group transcripts were analysed using a thematic analysis approach.

Findings

It was found that students have different perspectives on the meaning of employability, with the majority describing employability as having the right skills, attributes or competencies. Employability development activities were integrated into three broad categories: developing engineering knowledge, skills and industry experience; career building and industry awareness; and degree progression and completion. Participants also identified barriers to employability development and suggested areas for improvement.

Practical implications

The study recommends university staff ensure there is a shared understanding of employability within the student cohort by explicitly reframing employability as being about becoming a professional and that students are repeatedly exposed to the relevant set of industry competencies or standards. The study also outlines a range of activities that students connect to their employability development.

Originality/value

The findings of this study will assist university staff across the sector to make decisions about how they can best support employability development in their undergraduate students.
Ties that bind: leveraging horizontal and vertical ties within an entrepreneurial community in cross-promotional social media marketing
Authors: Dowin Kennedy Elena , Horky Alisha Blakeney , Kaufmann Ethan
Published: December 2022

Purpose

The purpose of this paper is to examine how small and medium enterprises (SMEs) within an entrepreneurial community engage in cross-promotion on social media via Facebook. This paper specifically examines how SME community members leverage their horizontal and vertical ties to generate publicity, improve brand perceptions and drive traffic to themselves or community events.

Design/methodology/approach

This paper uses a qualitative approach, examining 1,025 Facebook posts from 27 members of an entrepreneurial community in the southeast USA to develop typologies of posting strategies, post purposes and post functions.

Findings

This paper finds that in the entrepreneurial community of interest, many members engage in cross-promotion via social media at various frequencies and with distinctive purposes. This paper identifies five distinct patterns of cross-promotion – quality signaling, traffic driving, community amplifying, hybrid cross-promotion and infrequent engagement. This paper also notes differences between cross-promotional strategies of vertical and horizontal partners.

Originality/value

This paper advances understanding of social media marketing and identifies key patterns of SME social media behavior. Although previous research has noted the importance of social media for SMEs, there has been little research regarding posting strategies being used by these firms. Further, to this point, there has not been a framework to understand how firms can use social media to cross-promote one another. This paper seeks to begin filling these gaps by providing a useful framework that can be used by SMEs in coordinating their social media posting strategies as well as by researchers studying SME cross-promotion.
An architecture for a net zero world: Global climate governance beyond the epoch of failure
Authors: Burke Anthony
Published: December 2022

In the wake of the 2021 Glasgow meeting of the Paris Agreement, where states embedded a 2050 pathway to net zero that will overshoot the Earth's remaining carbon budget for 1.5°C, attention is turning to the flaws of the UN Framework Convention on Climate Change. This article highlights ways in which it blocks effective climate action, which has been acknowledged by states who are now pursuing voluntary and nonbinding initiatives on coal, forests, and oil and gas. The article assesses new proposals for treaties on deforestation, the elimination of coal, and a fossil fuel nonproliferation treaty. It argues that states should take these proposals to the UN General Assembly and adopt them as binding treaties consistent with holding global heating at 1.5°C. Following the model of the Nuclear Weapons Convention it further argues that these treaties should be folded into a full Greenhouse Convention, supported by a powerful International Climate Agency, to secure a net zero world. Drawing upon new proposals for an Earth‐centric law that takes in the totality of social‐natural processes at the planetary scale, these proposals could form part of a reformed international legal architecture that could be equal to the diabolical governance challenges of the Anthropocene.
Towards a transformative governance of the Amazon
Authors: Pereira Joana Castro , Terrenas João
Published: December 2022

The crises of the Anthropocene can neither be confronted incrementally nor through short‐term, reductionist strategies. As the risk of severe, irreversible socioecological damage increases, transformative change towards achieving long‐term sustainability becomes ever‐pressing. Against this backdrop, we explore how transformative governance can help strengthen ecosystem resilience, empower vulnerable communities and ensure sustainable development in the Amazon. The article starts by briefly reviewing the concept of transformative governance, arguing that it provides an adequate framework for thinking about and responding to the challenges of the Anthropocene. It then looks at how extant governance practices are destroying and fragmenting the Amazon, eroding the resilience of regional ecosystems. It proceeds by investigating how the Andes–Amazon–Atlantic Corridor, a transnational project aligned with the normative commitments and operational principles of transformative governance, aimed at protecting, restoring and building socioecological connectivity in the region, can offer an alternative pathway for Amazonian development in the new geological epoch.
Identification of a novel anoikis‐related gene signature to predict prognosis and tumor microenvironment in lung adenocarcinoma
Authors: Diao Xiayao , Guo Chao , Li Shanqing
Published: December 2022

Background

Lung adenocarcinoma (LUAD) is the most prevalent histotype of non‐small cell lung cancer. Anoikis, an alternative form of programmed cell death, plays a pivotal role in cancer invasion and metastasis, preventing the detached cancer cells from readhering to other substrates for abnormal proliferation. The aim of this study was to conduct a comprehensive analyses of the prognostic implications of anoikis‐related genes (ARGs) in LUAD.

Methods

ARGs were selected from The Cancer Genome Atlas (TCGA) database and Genecards dataset using differential expression analysis. The signature incorporating ARGs was identified using univariate Cox regression analysis and LASSO regression analysis. Furthermore, a nomogram containing the signature and clinical information was developed through univariate and multivariate Cox regression analysis. Kaplan–Meier survival analysis and receiver operating characteristic (ROC) curves were applied to evaluate the predictive validity of these risk models. Finally, functional analysis of the selected ARGs in signature and analysis of immune landscape were also conducted.

Results

A 16‐gene signature was integrated to stratify LUAD patients into different survival risk groups. The prognostic risk score generated from the signature and TNM stage were identified as independent prognostic factors and utilized to develop a nomogram. Both the signature and the nomogram showed satisfactory prediction performance in predicting overall survival (OS) of LUAD patients. The ARGs were enriched in several biological functions and signaling pathways. Finally, differences of immune landscape were investigated among the high‐ and low‐risk groups stratified by the signature.

Conclusions

This study revealed potential relationships between ARGs and prognosis of LUAD. The prognostic predictors identified in present study could be utilized as potential biomarkers for clinical applications.
Standardized nuclear markers improve and homogenize species delimitation in Metazoa
Authors: Dietz Lars , Eberle Jonas , Mayer Christoph , Kukowka Sandra , Bohacz Claudia , Baur Hannes , Espeland Marianne , Huber Bernhard A. , Hutter Carl , Mengual Ximo , Peters Ralph S. , Vences Miguel , Wesener Thomas , Willmott Keith , Misof Bernhard , Niehuis Oliver , Ahrens Dirk
Published: December 2022

Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly used for the identification of animal species, despite several challenges.

Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan‐level universal single‐copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and use coalescent‐based species inference as well as population admixture analyses and phenetic methods.

We demonstrate that metazoan USCOs distinguish well closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa, as judged by comparison with morphospecies delimitations. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels.

Metazoan USCOs provide a powerful and unifying framework for DNA‐based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources.
Using the LSAT as a labor market thermometer for lawyers
Authors: Koch James V. , Blake‐Gonzalez Barbara
Published: December 2022

We rely upon a 50‐state, 20‐year panel to find that the number of Law School Admissions Test (LSAT) takers is only loosely related to economic conditions—although slightly more for men than for women, who in 2020 accounted for 58% of all LSAT takers. The number of test takers rose more than 35% between 2014 and 2020. This wave accentuated an already existing downtrend in the median real income of lawyers, and thus provides support for the hypothesis that most states have more lawyers than they need.
Preference for rural living environment improvement initiatives in China
Authors: Zhang Zhaohui , Paudel Krishna P. , Upadhyaya Kamal
Published: December 2022

The Chinese government has launched the Rural Living Environment Improvement Initiative (RLEII) to solve the poor living conditions in rural areas. The initiative enhances rural greenery; provides sanitary toilets; and promotes proper disposal of animal manure, sewage, and household waste in rural areas. We collected data using in‐person interviews with 938 rural residents in Xinjiang, China, to elicit their preference, preference intensity, and preference heterogeneity for RLEII. Results indicated that rural residents prefer to see shortcomings of the RLEII addressed. Rural greening construction is identified with the highest preference intensity. We also find significant heterogeneity in rural residents' preferences for each attribute of RLEII. The preference heterogeneity is rooted in the region's economic condition (poor vs. nonpoor region). It is essential to understand rural residents' choice for rural public goods supply and to respect their preference intensity, sequence, and heterogeneity for RLEII to enhance the implementation performance. We discuss the implications of these findings.
Individual identification of dairy cows based on deep learning and feature fusion
Authors: Du Yongxing , Kou Yan , Li Baoshan , Qin Ling , Gao Di
Published: December 2022

Individual identification of dairy cows is one of the most important prerequisites for an intelligent dairy farming. Herein, a new method of individual identification of dairy cows based on the fusion of deep and shallow features of dairy cow's trunk image is proposed. Our aim is to obtain low‐cost, touch‐free, and high‐accuracy individual identification of dairy cows. First, the model of VGG‐16 is improved. Second, the multiple overlapping pooling layer in the improved VGG‐16 model is used as a feature extractor to extract the features of dairy cow's trunk image, and the global average pooling (GAP) layer was used to replace the traditional flatten layer to reduce the dimensions of the extracted shallow and deep features. Finally, the features after the dimensionality reduction are fused using the Concat method and input the fusion of new features into the support vector machine (SVM) classifier for classification. The proposed method was trained and tested on the dataset of 3151 cow trunk images captured by us. Experimental results showed that this method not only has better recognition accuracy of 99.48% than the VGG‐16, AlexNet, and ResNet‐50 models but also has fewer model parameters, faster convergence speed, and stronger generalization ability.