bluuebunny/crossref_metadata_2025 huggingface dataset:
Disempowering Women and Constructing Muslims as ‘Other’: A Study of India’s Anti-Conversion Legislations
Authors: Jamshed Mohammad , Karim Mohammad Rezaul , Banu Sameena
Published: March 2023

As a constitutional democracy, India remains committed to the cherished values of individual liberty and freedom of conscience which form the core of the fundamental rights enshrined in our constitution. However, in the last few years, we have witnessed a marked departure and foundational shift in the pursuit of these values. What we see in terms of the curtailment of women’s freedom, dictating personal relationship choices and maligning Muslims as a danger to Hindu women’s honour, delivers a severe blow to our pluralistic ethos and the cherished values of coexistence. The recently enacted legislations dressed up as anti-conversion laws to criminalise love choices bear a clear reflection of Nazi Germany’s Nuremberg Laws in many ways. Against the background of the state making intrusions into private spaces, denying the right to choose partners and acting as an oppressive surveillance agency, this study argues that these laws subvert the vision of our constitutional democracy and defy various judicial orders. It examines the literature on Hindu rights for women, analyses the contents of the legislation considering the contemporary discourse, to argue that these laws amount to undoing our achievements as a secular modern nation in the last seven decades.
An Unjust Mercy: Locating the Illegalities in the Release of the Convicts in the Bilkis Bano Case
Authors: Kanjilal Amartya
Published: March 2023

The Gujarat government’s decision on 15 August 2022, to release all 11 prisoners sentenced to life imprisonment in the Bilkis Bano case has serious implications, both for the rights of Bilkis Bano herself and the policy landscape around reformative prison measures like remission and premature release. Here I attempt to locate the release within a larger national context wherein carceral notions of justice, typified by longer and harsher prison sentences, are gaining currency both within the government and judiciary. I examine the deeply flawed process by which the prisoners came to be released, highlighting the arbitrariness and legal infirmities that render the government’s decision illegal.
The Importance of the Authentic Virtuous Employee in the Search for Meaningfulness in Work
Authors: Smith Raymond D. , Kulkarni Subodh P.
Published: March 2023

The article focuses on the ‘meaningfulness in work’ concept and addresses three theoretical gaps by investigating ‘meaningfulness in work’ from the perspective of Heidegger’s ‘authenticity’ and ‘Dasein’ constructs as well as virtue ethics. First, it adapts Heideggerian phenomenology and argues that meaningfulness in work may be revealed to an ‘authentic’ employee, while they performs everyday activities by ‘existing’ in their world and discovers their Dasein. Second, it emphasizes the normative, as opposed to instrumental implications of meaningfulness and invokes virtue ethics towards this end. Third, it integrates the Heideggerian approach with virtue ethics to describe how an ‘authentic’ and ‘virtuous’ employee may achieve meaningfulness in work (conceptualized as ‘eudaimonia’). An ‘authentic virtuous employee’ ‘exists in their world’ and discovers what is truly meaningful in work to them. They also displays temperance and courage in terms of closing the gaps between current and desired levels of meaningfulness in work, and continually contemplates it. We describe a ‘professional’ as an example of an ‘authentic virtuous employee’.
The Network Structures and Characteristics of Global Hubs of STI in Big Data Analysis and Mining Technology
Authors: He Peng , Bai Xu , Cao Di , Wu Jinxi
Published: March 2023

Global hubs of STI are strategic nodes in the global science network and will lead the future of global scientific progress. This paper takes big data analysis and mining technology as an example, exploring the structures and characteristics of global science network of 15 representative global hubs of STI from 2000 to 2019. Based on the data of highly cited papers and methods of social network analysis, we find that the global science network has the structure of hierarchy, with an obvious characteristic of regionality. Based on the structures and characteristics of global science network, the knowledge flow and management model of global hubs has been proposed, which may be conducive to strengthening the knowledge management and network collaboration among global hubs of STI in other frontier technologies.
Network Characteristics of Innovation Ecosystem: Knowledge Collaboration and Enterprise Innovation
Authors: Zhang Yanli , Wang Dantong , Xiao Xun
Published: March 2023

This paper investigates the linkage between network characteristics of the innovation ecosystem, knowledge collaboration and enterprise innovation in the case of China. The results demonstrate that knowledge collaboration plays a part in the mediating role between network characteristics of the innovation ecosystem and enterprise innovation. The resource integration capability could regulate the mediating role of knowledge collaboration, which means the stronger the resource integration capability, the stronger the mediating effect.
Empirical Analysis of Global Markets Herding on COVID-19 Effect
Authors: Loang Ooi Kok , Ahmad Zamri
Published: March 2023

This article investigates the presence of herding on global stock markets during COVID-19. Cross-Sectional Absolute Deviation developed by Chiang and Zheng (2010) and Chang et al. (2000) examine market-wide herding. Results show that herding is prevalent in Brazil, Germany, India, Italy, Korea, China-Shanghai, China-Shenzhen and Turkey. During the epidemic, no evidence of herding was detected in France, Hong Kong, Indonesia, Japan, Malaysia, Poland, the United Kingdom and the United States. It has been shown that the United States and Chinese cross-market herding substantially influences all markets. The impact of analyst information (target price, EPS forecasts and revenue predictions) on herding is shown before the pandemic and weakening during the pandemic. It indicates that investors disregard expert recommendations and liquidate equities during the pandemic. The findings shed light on the occurrence and determinants of herding that causes investors’ to behave irrationally during COVID-19. Policymakers, government and regulators should formulate a more robust policy to monitor, control and oversee the naïve herding that drives fundamentals away from stock prices.
Automation and AI-Enabled Customer Journey: A Bibliometric Analysis
Authors: Rana Jyoti , Jain Ruchi , Santosh KC
Published: March 2023

This article aims to scrutinize the dynamics of scientific publications devoted to optimizing the customer journey in the retail sector through the application of artificial intelligence (AI) and determines the status of existing research on the role of AI in the retail sector. The research objective was to analyse the pool of scientific publications from the Scopus database to analyse how emerging technologies have improved customer journey (pre-purchase, purchase, post-purchase). The research employed a publication search by article title, abstract and keywords to collect the data set from the Scopus database. The selected publications were visualized using the software VOSviewer 1.6.16.0, and Biblioshiny to perform bibliometric analyses. An initial sample of 356 research articles was collected. After reading the abstract and full article, a final corpus of 149 scientific publications over two decades (1989–2021) was analysed in the study. Our findings suggest the prominence of authors and journal publishing in implementing AI in retail to automate customer journey. The results highlight how the application of AI fosters in improving the different phases of customer journey among the retailing sectors. Banking and fashion are the retailing sectors that have major applications of AI in the customer journey. Further studies should be conducted to gain deeper insights into the emerging use of AI in other sectors of the economy. It was also found from the intensive literature review that in the purchasing and decision-making phase of the customer journey, the deployment of AI is the most. This study analysed the incorporation of AI into the customer journey to highlight its impact on retailing. This study contributes to the literature by adding the lenses of AI in key management areas in retailing.
A Bibliometric Study on Corporate Transparency and Disclosures
Authors: Bhimavarapu Venkata Mrudula , Rastogi Shailesh , Mulay Preeti
Published: March 2023

Corporate transparency is a critical requirement for effective governance. Through a thorough financial regulation, it has the potential to influence investors’ investment decisions in a company. The global financial crisis, in the past, has prompted a high level of openness worldwide since it frequently implies the quality of information disclosure. To make investment decisions, investors rely on the information provided by the firms. Hence it is crucial to have an encyclopaedic understanding of corporate disclosures. This research employs bibliometric analysis from a multi-industry approach to systematically synthesize and improve corporate transparency and disclosures. For 23 years, 410 journal articles were collected from the Scopus database between 1998 and 2021. This article highlights the publication trend and identifies the most influential work, authors, countries and journals. Finally, the Author, Journal and keyword co-occurrence have expressed the article’s research themes through thematic progression. Lastly, the article highlights the gaps in the literature and makes recommendations for further research.
Pursuit of Autonomy: An Assessment of Japan’s Latent Counterspace Capabilities
Authors: Vijayakumar Anupama , Krishnan Vineeth
Published: March 2023

Pacifism has been the cornerstone of Japan’s identity in the post-1945 era. In the light of its changing threat perception in the post-Cold War period, Japan has been increasingly pursuing autonomy in the security domain while stretching the limits of its pacifist identity. It has hence sought to build a strong technological base to support its latent military capabilities. This article attempts to contextualise Japan’s pursuit of autonomy in outer space amid growing security competition in the domain. It discusses the legal and organisational changes that have allowed for a growing involvement of Japan’s Self-Defense Forces in operating space assets. The potential counterspace applications of major technological capabilities shown by Japan in the civilian and commercial space sectors are assessed. The article surmises that Japan, which has a global reputation as a benign space power, can continue to refine its latent counterspace capabilities amidst a pursuit of autonomy, without straying much from its pacifist traditions.
Disrupting the Saviour Politics in the Women, Peace and Security Agenda in the Global South: Grassroots Women Creating Gender Norms in Nepal and Sri Lanka
Authors: Whetstone Crystal , Luna K. C.
Published: March 2023

Saviour politics permeates some understandings of global gender norms by those who construct the Global North as the origin of global gender norms, and less attention is given to how saviour politics functions within the Global South, wielded by some privileged women against grassroots women. We argue that grassroots Global South women, despite their marginalisation, are global gender norms actors and deserve greater decision-making power on the local and international stages. We show how the United Nations Security Council Resolution 1325 on Women, Peace, and Security (WPS) and the broader WPS agenda focus on global gender norms construction in Nepal and Sri Lanka. We rely on qualitative methods. We highlight work done by grassroots women from diverse castes, ethnicities, religious backgrounds, abilities, education and social locations that construct global gender norms. This article adds to the WPS, Global South-Global North relations and global gender norms building.
Cooling and Crack Suppression of Bone Material Drilling Based on Microtextured Bit Modeled on Dung Beetle
Authors: Lian Yunsong , Chen Xiande , Xie Chaoping , Long Yangyang , Lin Fengtian , Zhou Wei , Chu Xuyang
Published: March 2023

In recent years, the number of patients with orthopedic diseases such as cervical spondylosis has increased, resulting in an increase in the demand for orthopedic surgery. However, thermal necrosis and bone cracks caused by surgery severely restrict the development and progression of orthopedic surgery. For the material of cutting tool processing bone in bone surgery of drilling high temperature lead to cell death, easy to produce the problem such as crack cause secondary damage effects to restore, in this paper, a bionic drill was designed based on the micro-structure of the dung beetle’s head and back. The microstructure configuration parameters were optimized by numerical analysis, and making use of the optical fiber laser marking machine preparation of bionic bit; through drilling test, the mathematical model of drilling temperature and crack generation based on micro-structure characteristic parameters was established by infrared thermal imaging technology and acoustic emission signal technology, and the cooling mechanism and crack suppression strategy were studied. The experimental results show that when the speed is 60 m/min, the cooling effects of the bionic bit T1 and T2 are 15.31% and 19.78%, respectively, and both kinds of bits show obvious crack suppression effect. The research in this paper provides a new idea for precision and efficient machining of bone materials, and the research results will help to improve the design and manufacturing technology and theoretical research level in the field of bone drilling tools.
The appropriacy of the analytical models for calculating the shear capacity of cross-laminated timber (CLT) under out-of-plane bending
Authors: Huang Zirui , Jiang Lingyun , Ni Chun , Chen Zhongfan
Published: March 2023

Rolling shear, an inherent property of cross-laminated timber (CLT) due to the weak shear strength of cross layers, is always the determinant of load-bearing capacity for short-span CLT members subjected to out-of-plane bending. Many analytical models were developed to calculate the shear capacity of CLT members. Because of the difficulty to precisely model the complicated shear failure mechanisms, however, no model was universally accepted. This paper aims to study the appropriacy of the commonly used analytical models, namely, composite beam theory, shear analogy method, Gamma method, and simple beam theory, by tests and analytical calculations. A composite beam theory-based simplified method was proposed. Three-point loading tests for the short-span CLT panels with 3 and 5 layers were conducted, and the shear capacities of the test specimens were calculated using the above-mentioned analytical methods. Shear strength and modulus of cross layers of the test specimens, which were used as the inputs for calculating the shear capacities, were tested by modified planar shear method. By comparing the calculation results obtained from different analytical models and the test results as well, it can be concluded that: (1) composite beam theory, shear analogy method, and the proposed simplified method give almost the same calculation results, therefore, the proposed simplified method can be used as the replacement for the other models; (2) Gamma method is more appropriate for calculating the shear capacity in case the input shear strength is determined by planar shear test; (3) the simple beam theory that is used in CSA O86 provides significantly lower shear capacity predictions than those obtained by the other methods.
Galcanezumab effects on incidence of headache after occurrence of triggers, premonitory symptoms, and aura in responders, non-responders, super-responders, and super non-responders
Authors: Ashina Sait , Melo-Carrillo Agustin , Toluwanimi Ajayi , Bolo Nicolas , Szabo Edina , Borsook David , Burstein Rami
Published: March 2023

Background

The goal of this observational, open-label, cohort study was to determine whether prophylactic migraine treatment with galcanezumab, a peripherally acting drug, alters the incidence of premonitory symptoms, and/or occurrence of headache after exposure to triggers or aura episodes in treatment-responders (≥ 50% reduction in monthly migraine days [MMD]), super-responders (≥ 70%), non-responders (< 50%) and super non-responders (< 30%).

Methods

Participants were administered electronic daily headache diaries to document migraine days and associated symptoms one month before and during the three months of treatment. Questionnaires were used to identify conscious prodromal and trigger events that were followed by headache prior to vs. after 3 months of treatment.

Results

After 3 months of galcanezumab treatment, (a) the incidence of premonitory symptoms that were followed by headache decreased by 48% in the 27 responders vs. 28% in the 19 non-responders, and by 50% in the 11 super-responders vs. 12% in the 8 super non-responders; (b) the incidence of visual and sensory aura that were followed by headache was reduced in responders, non-responders, and super-responders, but not in super non-responders; (c) the number of triggers followed by headache decreased by 38% in responders vs. 13% in non-responders, and by 31% in super-responders vs. 4% in super non-responders; and (d) some premonitory symptoms (e.g., cognitive impairment, irritability, fatigue) and triggers (e.g., stress, sleeping too little, bright light, aura) were followed by headache only in super non-responders.

Conclusions

Mechanistically, these findings suggest that even a mild decrease in migraine frequency is sufficient to partially reverse the excitability and responsivity of neurons involved in the generation of certain triggers and potentially premonitory symptoms of migraine.

Trial registration

ClinicalTrials.gov: NCT04271202. Registration date: February 10, 2020.
Disease burden of migraine and tension-type headache in non-high-income East and Southeast Asia from 1990 to 2019
Authors: Ge Rongguang , Chang Jie
Published: March 2023

Background

The world faces severe challenges from migraine and tension-type headache (TTH), which cause grave disability to patients and place a heavy burden on their caregivers. However, headaches in specific individual regions have rarely been investigated. Therefore, we aimed to fully analyse and describe the current status and changing trends in migraine and TTH in non-high-income East and Southeast Asia to provide more detailed real-world information for policy-making.

Methods

The migraine and TTH data used for analysis were all extracted from the Global Burden of Disease (GBD) database. We adopted three major indicators of disease burden, including prevalence, incidence, and years lived with disability (YLD), and two major metrics, including the absolute number and the age-standardized rate, in our present study for further evaluation by age and sex. The results are presented in the form of mean values and 95% uncertainty intervals (UIs). In addition, the differences between non-high-income East and Southeast Asia and other regions, as well as the potential associations between headache burden and socioeconomic background, were explored.

Results

In 2019, approximately 195,702,169 migraine patients and 291,924,564 TTH patients lived in non-high-income East Asia, and 113,401,792 migraine patients and 179,938,449 TTH patients lived in non-high-income Southeast Asia. In terms of specific countries and regions, the highest age-standardized YLD rate (ASYR) of migraine was in Thailand [645 (95% UI: 64 to 1,554)]. The highest ASYR of TTH was in Indonesia [54 (95% UI: 15 to 197)]. Furthermore, people between the ages of 40 and 44, especially females, were identified as the main population that suffered from migraine and TTH. Unfortunately, we did not observe a significant association between headache burden and socioeconomic background.

Conclusions

To date, the threats from migraine and TTH in non-high-income East and Southeast Asia are still serious and ongoing, leading to prominently negative impacts on the daily life and work of local residents. Therefore, full attention and sound guidelines are urgently needed to obtain greater advantages in fighting against the burden of headache disorders in the future.
Evidence-based yet still challenging! Research on physical activity in old age
Authors: Brach Michael , de Bruin Eling D. , Levin Oron , Hinrichs Timo , Zijlstra Wiebren , Netz Yael
Published: March 2023

Preserving functional health and quality-of-life in old age is a major goal and global challenge in public health. The high rate of sedentary behavior that is characteristic of the older adult population exacerbates impairments of physiological and structural systems that are typically seen in the aging process. Achieving an understanding of the profound influence of physical activity on all aspects of health in old age is the driving force behind the emergence of "physical activity in old age" as a growing area of research. Accumulated evidence implies that being physically active and exercising is far superior to other optimal aging facilitators. Yet this area of research faces numerous constraints and obstacles. This commentary addresses some of these challenges, primarily the heterogeneity of the aging process, which induces both inter- and intra-individual differences among aged individuals, heterogeneity in assessment tools, unjustified inclusion/exclusion criteria and insufficient recruitment strategies, difficulties in implementing research results in real-world conditions, and rudimentary exploitation of innovative technology. We explain the importance of establishing a network of multidisciplinary scientists and stakeholders to propose consensus-based goals and scientifically evidenced wide-ranging plans for dealing with these challenges. In addition, we suggest work directions for this network.
Oscillatory shear stress modulates Notch-mediated endothelial mesenchymal plasticity in cerebral arteriovenous malformations
Authors: Karthika C. L. , Venugopal Vani , Sreelakshmi B. J. , Krithika S. , Thomas Jaya Mary , Abraham Mathew , Kartha C. C. , Rajavelu Arumugam , Sumi S.
Published: March 2023

Background

Cerebral arteriovenous malformations (cAVM) are a significant cause of intracranial hemorrhagic stroke and brain damage. The arteriovenous junctions in AVM nidus are known to have hemodynamic disturbances such as altered shear stress, which could lead to endothelial dysfunction. The molecular mechanisms coupling shear stress and endothelial dysfunction in cAVMs are poorly understood. We speculated that disturbed blood flow in artery–vein junctions activates Notch receptors and promotes endothelial mesenchymal plasticity during cAVM formation.

Methods

We investigated the expression profile of endothelial mesenchymal transition (EndMT) and cell adhesion markers, as well as activated Notch receptors, in 18 human cAVM samples and 15 control brain tissues, by quantitative real-time PCR (qRT-PCR) and immunohistochemical evaluation. Employing a combination of a microfluidic system, qRT-PCR, immunofluorescence, as well as invasion and inhibitor assays, the effects of various shear stress conditions on Notch-induced EndMT and invasive potential of human cerebral microvascular endothelial cells (hCMEC/d3) were analyzed.

Results

We found evidence for EndMT and enhanced expression of activated Notch intracellular domain (NICD3 and NICD4) in human AVM nidus samples. The expression of transmembrane adhesion receptor integrin α9/β1 is significantly reduced in cAVM nidal vessels. Cell–cell adhesion proteins such as VE-cadherin and N-cadherin were differentially expressed in AVM nidus compared with control brain tissues. Using well-characterized hCMECs, we show that altered fluid shear stress steers Notch3 nuclear translocation and promotes SNAI1/2 expression and nuclear localization. Oscillatory flow downregulates integrin α9/β1 and VE-cadherin expression, while N-cadherin expression and endothelial cell invasiveness are augmented. Gamma-secretase inhibitor RO4929097, and to a lesser level DAPT, prevent the mesenchymal transition and invasiveness of cerebral microvascular endothelial cells exposed to oscillatory fluid flow.

Conclusions

Our study provides, for the first time, evidence for the role of oscillatory shear stress in mediating the EndMT process and dysregulated expression of cell adhesion molecules, especially multifunctional integrin α9/β1 in human cAVM nidus. Concomitantly, our findings indicate the potential use of small-molecular inhibitors such as RO4929097 in the less-invasive therapeutic management of cAVMs.

Graphical Abstract
What’s effective and ineffective in preparing high school biology educators to teach evolution? Evidence from a representative national U.S. survey
Authors: Branch Glenn , Plutzer Eric , Reid Ann
Published: March 2023

Background

What types of coursework prepare biology teachers to teach evolution effectively? The present study provides answers to that question based on evidence from a nationally representative sample of public high school biology teachers in the U.S. Data about their pre-service coursework (in seven categories) and their attitudes and practices relevant to teaching evolution (in five categories relating to personal acceptance of evolution, perception of scientific consensus on evolution, instructional time devoted to evolution, classroom characterization of evolution and creationism, and emphasis on specific topics in teaching evolution) were collected.

Results

Coursework focused on evolution was significantly associated with positive outcomes: more class hours devoted to evolution, not presenting creationism as scientifically credible, and prioritizing common ancestry, human evolution, and the origin of life as topics of instruction, while shunning Biblical perspectives on the history of life. Similarly, coursework with some evolution content was significantly associated with positive outcomes: awareness of the scientific consensus on evolution, presenting evolution but not creationism as scientifically credible, and prioritizing common ancestry as a topic of instruction. But surprisingly, methods coursework on problem-based learning was significantly associated with negative outcomes: presenting creationism as well as evolution as scientifically credible and prioritizing Biblical perspectives on the history of life as a topic of instruction. Similarly, and likewise surprisingly, methods coursework on teaching controversial topics was associated with a negative outcome: presenting creationism as scientifically credible.

Conclusion

Consistent with previous work, the results of the present study suggest that pre-service coursework in evolution is important in preparing educators to teach evolution effectively. But they also suggest, surprisingly, that pre-service methods coursework aimed at preparing educators to teach evolution effectively tends, at present, to be counterproductive, leading to the presentation of creationism as scientifically credible.
Correlation and agreement between arterial and venous blood gas analysis in patients with hypotension—an emergency department-based cross-sectional study
Authors: Prasad Hari , Vempalli Nagasubramanyam , Agrawal Naman , Ajun U. N. , Salam Ajmal , Subhra Datta Soumya , Singhal Ashutosh , Ranjan Nishant , Shabeeba Sherin P. P. , Sundareshan G.
Published: March 2023

Background

Blood gas analysis is integral to assessing emergency department (ED) patients with acute respiratory or metabolic disease. Arterial blood gas (ABG) is the gold standard for oxygenation, ventilation, and acid–base status but is painful to obtain. Peripheral venous blood gas (VBG) is a valuable alternative as it is less painful and easy to collect. The comparability of ABG and VBG was studied in various conditions. But in hypotension, previous findings were inconsistent. So, we studied the correlation and agreement between ABG and VBG in hypotensive patients.

Methodology

The study was conducted at the emergency department of a tertiary healthcare center in Northern India. Patients with hypotension above 18 years who satisfied the inclusion criteria were clinically evaluated. Patients who require ABG as a part of routine care were sampled. ABG was collected from the radial artery. VBG was obtained from the cubital or dorsal hand veins. Both samples were collected within 10 min and were analyzed. All ABG and VBG variables were entered in premade proforma. The patient was then treated and disposed of according to institutional protocol.

Results

A total of 250 patients were enrolled. The mean age was 53.25 ± 15.71 years. 56.8% were male. The study included 45.6% septic, 34.4% hypovolemic, 18% cardiogenic, and 2% obstructive shock patients. The study found a strong correlation and agreement for ABG and VBG pH, pCO2, HCO3, lactate, sodium, potassium, chloride, ionized calcium, blood urea nitrogen, base excess, and arterial/alveolar oxygen ratio. Hence, regression equations were made for the aforementioned. There was no correlation observed between ABG and VBG pO2 and SpO2. Our study concluded that VBG could be a reasonable alternative for ABG in hypotensive patients. We can also mathematically predict values of ABG from VBG using regression equations derived.

Conclusions

ABG sampling causes most unpleasant experiences to patients and is associated with complications like arterial injury, thrombosis, air or clotted-blood embolism, arterial occlusion, hematoma, aneurysm formation, and reflex sympathetic dystrophy. The study has shown strong correlations and agreements for most ABG and VBG parameters and can predict ABG mathematically using regression formulas formulated from VBG. This will decrease needle stick injury, consume less time, and make blood gas evaluation easy in hypotensive settings.
Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication?
Authors: Tong Shuai , Ashikari Motoyuki , Nagai Keisuke , Pedersen Ole
Published: March 2023

As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
Retrograde Intrarenal Surgery for Partial Staghorn Calculus in Thoracic Kidney: Case Report
Authors: Venkatachalapathy Vigneswara Srinivasan Sockkalingam , Palathullil Datson George , Sam Dempsey Mohan , Abraham George Palathullil
Published: March 2023

Background

Thoracic kidney (TK) presenting with symptomatic urolithiasis is a rare case scenario. Retrograde intrarenal surgery (RIRS) for calculus in TK is not reported in the literature. We report a case of partial staghorn calculus in TK managed by RIRS.

Case presentation

A young adult male presented with back pain and was found to have right TK and bilateral partial staghorn calculus. He also had right cryptorchidism with intraabdominally located testis. He underwent staged bilateral RIRS and laparoscopic right orchiectomy. Follow-up ultrasound imaging showed complete stone clearance in both kidneys.

Conclusions

RIRS is safe and effective treatment option, in the management of urolithiasis in TK. The anatomical abnormalities in TK did not play any hindrance role in the ureteral access, renal maneuverability of the flexible ureterorenoscope and subsequent drainage of the stone dust after RIRS.
Evaluation of macroscopic fundamental diagram characteristics for a quantified penetration rate of autonomous vehicles
Authors: Bilal Muhammad Tabish , Giglio Davide
Published: March 2023

Background

The availability of private vehicles with autonomous features is widespread nowadays. Various car manufacturers are providing attributes like collision warning, city automatic emergency braking, adaptive cruise control, pedestrian detection, lane-keeping assistance and lane departure warning, rear cross-traffic and blind-spot warning in their high-end models.

Purpose

Such features can automatically manage the macroscopic fundamental traffic parameters such as speed, headway, etc adaptively. Consequently leading to a heterogeneous traffic stream with diverse car-following behaviour comprising completely manual/traditional (TVs) and autonomous vehicles (AVs). This questions the applicability of classic traffic flow theory relationships on such heterogeneous traffic streams.

Methodology

This paper focuses on developing the macroscopic fundamental diagram for such heterogeneous traffic streams based on the quantified penetration rate (QPR) for autonomous vehicles. The penetration rate is devised by taking into account user demographics, land usage and road network properties. QPR is used as an input for heterogeneous urban traffic stream scenarios to calculate the aggregated urban traffic network dynamics of flow and density for the same network. Travel time versus flow characteristics is evaluated based on calibrated hyperbolic urban link travel time function for both interrupted and uninterrupted flows following the aggregated speed and density output from MFDs for heterogeneous traffic streams. Also, two scenarios are generated for comparison to explain the improvement in the network characteristics together with a sensitivity analysis.

Results

Compared to the base scenario there could be 25-35% of AVs on the road networks based on the analysis in coming fifteen years. This increment in usage impacts the capacity of road networks positively by increasing it up to 59%.

Conclusions

Results obtained after the application of the suggested model approach to the real network can be used to define a realistic method for multi-vehicle equilibrium assignment models for heterogeneous traffic streams including autonomous vehicles instead of approximating the penetration rates.
A correction procedure for the working hours variable in the IAB employee history
Authors: vom Berge Philipp , Umkehrer Matthias , Wanger Susanne
Published: March 2023

Administrative labour market data for Germany do not contain detailed information on working hours. This poses a serious challenge for many empirical research questions. Between 2010 and 2014, however, it is possible to merge a supplementary data source containing information on working hours reported by employers for each job to the German Social Accident Insurances. One complicating factor is that employers were allowed to report actual working hours, contractual working hours or a full-time worker reference value, and it is not obvious from the data which re-porting scheme was actually used. In this report, we describe this supplementary data source and propose a correction procedure that maps all data entries so that they uniformly reflect contractual working time. After this correction, the distribution of contractual weekly working hours in the combined administrative labour market data closely resembles the distribution from the German Structural Earnings Survey.
nPoRe: n-polymer realigner for improved pileup-based variant calling
Authors: Dunn Tim , Blaauw David , Das Reetuparna , Narayanasamy Satish
Published: March 2023

Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers ($$n=1$$

n
=
1

) and tandem repeats ($$2 \le n \le 6$$

2
≤
n
≤
6

). At the same precision, haplotype phasing improves INDEL recall from 63.76 to $$70.66\%$$

70.66
%

and nPoRe realignment improves it further to $$73.04\%$$

73.04
%

.
Seven bacterial response-related genes are biomarkers for colon cancer
Authors: Xiong Zuming , Li Wenxin , Luo Xiangrong , Lin Yirong , Huang Wei , Zhang Sen
Published: March 2023

Background

Colon cancer (CC) is a common tumor that causes significant harm to human health. Bacteria play a vital role in cancer biology, particularly the biology of CC. Genes related to bacterial response were seldom used to construct prognosis models. We constructed a bacterial response-related risk model based on three Molecular Signatures Database gene sets to explore new markers for predicting CC prognosis.

Methods

The Cancer Genome Atlas (TCGA) colon adenocarcinoma samples were used as the training set, and Gene Expression Omnibus (GEO) databases were used as the test set. Differentially expressed bacterial response-related genes were identified for prognostic gene selection. Univariate Cox regression analysis, least absolute shrinkage and selection operator-penalized Cox regression analysis, and multivariate Cox regression analysis were performed to construct a prognostic risk model. The individual diagnostic effects of genes in the prognostic model were also evaluated. Moreover, differentially expressed long noncoding RNAs (lncRNAs) were identified. Finally, the expression of these genes was validated using quantitative polymerase chain reaction (qPCR) in cell lines and tissues.

Results

A prognostic signature was constructed based on seven bacterial response genes: LGALS4, RORC, DDIT3, NSUN5, RBCK1, RGL2, and SERPINE1. Patients were assigned a risk score based on the prognostic model, and patients in the TCGA cohort with a high risk score had a poorer prognosis than those with a low risk score; a similar finding was observed in the GEO cohort. These seven prognostic model genes were also independent diagnostic factors. Finally, qPCR validated the differential expression of the seven model genes and two coexpressed lncRNAs (C6orf223 and SLC12A9-AS1) in 27 pairs of CC and normal tissues. Differential expression of LGALS4 and NSUN5 was also verified in cell lines (FHC, COLO320DM, SW480).

Conclusions

We created a seven-gene bacterial response‐related gene signature that can accurately predict the outcomes of patients with CC. This model can provide valuable insights for personalized treatment.
FDC-SP as a diagnostic and prognostic biomarker and modulates immune infiltrates in renal cell carcinoma
Authors: Chang Fan , Zhang Jiang-Hui , Wu Wen-Song , Tang Shuai , lv Zheng , Chen Fang-Min
Published: March 2023

Background

Renal cell carcinoma (RCC), one of the top 10 causes of cancer death, is responsible for more than 90% of all cases of primary renal cancer worldwide. Follicular dendritic cell-secreted protein (FDC-SP) specifically binds to activated B cells and regulates the generation of antibodies. It is also thought to promote cancer cell invasion and migration, which could help with tumor metastases. This study aimed to assess the efficacy of FDC-SP in the diagnosis and prognosis of RCC and to investigate the relationship between immune infiltration in RCC and these outcomes.

Results

RCC tissues had significantly higher levels of FDC-SP protein and mRNA than normal tissues. The high level of FDC-SP expression was linked to the T stage, histological grade, pathological stage, N stage, M stage, and OS event. Functional enrichment analysis identified the major pathways that were enriched as immune response regulation, complement, and coagulation. Immunological checkpoints and immune cell infiltration were observed to substantially correlate with the levels of FDC-SP expression. FDC-SP expression levels showed the ability to precisely distinguish high-grade or high-stage renal cancer (area under the curve (AUC) = 0.830, 0.722), and RCC patients with higher FDC-SP expression levels had worse prognoses. The AUC values for one-, two-, and five-year survival rates were all greater than 0.600. Moreover, the FDC-SP expression is an independent predictive biomarker of OS in RCC patients.

Conclusion

FDC-SP may be a prospective therapeutic target in RCC as well as a possible diagnostic and prognostic biomarker associated with immune infiltration.
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution
Authors: Ascolani Gianluca , Angaroni Fabrizio , Maspero Davide , Craighero Francesco , Bhavesh Narra Lakshmi Sai , Piazza Rocco , Damiani Chiara , Ramazzotti Daniele , Antoniotti Marco , Graudenzi Alex
Published: March 2023

Background

Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit the mutational profiles of single cells generated via variant calling, in order to reconstruct the evolutionary history of a tumor and characterize the impact of therapeutic strategies, such as the administration of drugs. To this end, we have recently developed the LACE framework for the Longitudinal Analysis of Cancer Evolution.

Results

The LACE 2.0 release aimed at inferring longitudinal clonal trees enhances the original framework with new key functionalities: an improved data management for preprocessing of standard variant calling data, a reworked inference engine, and direct connection to public databases.

Conclusions

All of this is accessible through a new and interactive Shiny R graphical interface offering the possibility to apply filters helpful in discriminating relevant or potential driver mutations, set up inferential parameters, and visualize the results. The software is available at: .
PWN: enhanced random walk on a warped network for disease target prioritization
Authors: Han Seokjin , Hong Jinhee , Yun So Jeong , Koo Hee Jung , Kim Tae Yong
Published: March 2023

Background

Extracting meaningful information from unbiased high-throughput data has been a challenge in diverse areas. Specifically, in the early stages of drug discovery, a considerable amount of data was generated to understand disease biology when identifying disease targets. Several random walk-based approaches have been applied to solve this problem, but they still have limitations. Therefore, we suggest a new method that enhances the effectiveness of high-throughput data analysis with random walks.

Results

We developed a new random walk-based algorithm named prioritization with a warped network (PWN), which employs a warped network to achieve enhanced performance. Network warping is based on both internal and external features: graph curvature and prior knowledge.

Conclusions

We showed that these compositive features synergistically increased the resulting performance when applied to random walk algorithms, which led to PWN consistently achieving the best performance among several other known methods. Furthermore, we performed subsequent experiments to analyze the characteristics of PWN.
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Authors: Vieira Ivo Henrique Provensi , Botelho Eduardo Buganemi , de Souza Gomes Thales Junior , Kist Roger , Caceres Rafael Andrade , Zanchi Fernando Berton
Published: March 2023

Background

The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists.

Results

Here, we have developed the VisualDynamics—a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation.

Conclusions

VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https://visualdynamics.fiocruz.br/login, is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub https://github.com/LABIOQUIM/visualdynamics.
Full-length transcriptome profiling for fruit development in Diospyros oleifera using nanopore sequencing
Authors: Xu Yang , Liu Cui-yu , Cheng Wen-qiang , Wu Kai-yun , Gong Bang-chu
Published: March 2023

Objectives

Diospyros oleifera, one of the most economically important Diospyros species, is an ideal model for studying the fruit development of persimmon. While, the lack of whole-transcriptome has hindered the complex transcriptional regulation mechanisms of sugar and tannin during fruit development.

Data description

We applied Oxford Nanopore Technologies to six developmental stage of fruit from D. oleifera for use in transcriptome sequencing. As a result of full-length transcriptome sequencing, 55.87 Gb of clean data were generated. After mapping onto the reference genome of D. oleifera, 51,588 full-length collapsing transcripts, including 2,727 new gene loci and 43,223 transcripts, were obtained. Comprehensively annotated, 38,086 of new transcripts were functional annotation, and 972 lncRNAs, 7,159 AS events were predicted. Here, we released the transcriptome database of D. oleifera at different stage of fruit development,which will provide a fundamention of to investigatethe transcript structure, variants and evolution of persimmon.