bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent network effects along the axis of gene expression during prostate cancer progression
Authors: Charmpi Konstantina , Guo Tiannan , Zhong Qing , Wagner Ulrich , Sun Rui , Toussaint Nora C. , Fritz Christine E. , Yuan Chunhui , Chen Hao , Rupp Niels J. , Christiansen Ailsa , Rutishauser Dorothea , Rüschoff Jan H. , Fankhauser Christian , Saba Karim , Poyet Cedric , Hermanns Thomas , Oehl Kathrin , Moore Ariane L. , Beisel Christian , Calzone Laurence , Martignetti Loredana , Zhang Qiushi , Zhu Yi , Martínez María Rodríguez , Manica Matteo , Haffner Michael C. , Aebersold Ruedi , Wild Peter J. , Beyer Andreas 
Published: February 2020

AbstractBackgroundTumor-specific genomic aberrations are routinely determined by high throughput genomic measurements. It remains unclear though, how complex genome alterations affect molecular networks through changing protein levels, and consequently biochemical states of tumor tissues.ResultsHere, we investigated the propagation of genomic effects along the axis of gene expression during prostate cancer progression. For that, we quantified genomic, transcriptomic and proteomic alterations based on 105 prostate samples, consisting of benign prostatic hyperplasia regions and malignant tumors, from 39 prostate cancer patients. Our analysis revealed convergent effects of distinct copy number alterations impacting on common downstream proteins, which are important for establishing the tumor phenotype. We devised a network-based approach that integrates perturbations across different molecular layers, which identified a sub-network consisting of nine genes whose joint activity positively correlated with increasingly aggressive tumor phenotypes and was predictive of recurrence-free survival. Further, our data revealed a wide spectrum of intra-patient network effects, ranging from similar to very distinct alterations on different molecular layers.ConclusionsThis study uncovered molecular networks with remarkably convergent alterations across tumor sites and patients, but it also exposed a diversity of network effects: we could not identify a single sub-network that was perturbed in all high-grade tumor regions.
A Single Nucleotide Polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated North American Cannabis
Authors: Henry Philippe , Khatodia Surender , Kapoor Karan , Gonzales Britni , Middleton Alexis , Hong Kevin , Hilyard Aaron , Johnson Steve , Allen Davis , Chester Zachary , Jin Dan , Jule José Carlos Rodriguez , Wilson Iain , Gangola Manu , Broome Jason , Caplan Deron , Adhikary Dinesh , Deyholos Michael K. , Morgan Michael , Hall Oliver W. , Guppy Brent , Orser Cindy 
Published: February 2020

AbstractBackgroundThe taxonomic classification of the Cannabis genus has been delineated through three main types:sativa(long and less branched plant with long and narrow leaves),indica(short but highly branched plant with broader leaves) andruderalis(wild type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origin of each group and putative chemotypic and pharmacology.MethodsHere we describe a thorough investigation of cannabis accessions using a set of 22 highly informative and polymorphic SNP markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations and demonstrate the utility of this assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education.ResultsThe main outcomes are the identification of 5 clusters in the sample set available, including industrial hemp, resin hemp which likely underwent a bottleneck to stabilize CBDA accumulation (Type II & III). THC resin (type I) make up the other three clusters with terpinolene (colloquial “sativa” or “NLD”), myrcene/pinene and myrcene/limonene (colloquial “indica”, “BLD”), which also putatively harbour an active CBCAS.ConclusionThe functional basis of key traits is also discussed as recently enabled by the NCBI Cannabis sativa Annotation Release 100, allowing for hypothesis testing with regards to secondary metabolite production as well as other key traits of importance for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.
Digital transformation in supply chain, challenges and opportunities in SMEs: a case study of Al-Rumman Pharma
Authors: Faridi Mohammad Rishad , Malik Azam 
Published: February 2020

Learning outcomes
Digital skills change management skills problem solving skills.

Case overview/synopsis
Al-Rumman Pharma is headquartered in Dubai, is an integrated international pharmaceutical company providing a wide range of pharmaceutical solutions to manufacture high quality and affordable generic medicines. It holds credibility amongst healthcare professionals and patients, across the Middle East and North African (MENA) markets. Their quality assurance is fostered by high levels of reliability and order fulfillment, which differentiates them from their competitors. Recently, they have been facing technology fatigue meant as an organization suffering from overwhelming options and choices in technology, this contributes to turbulent and confused states of mind when considering technology adaptation. This case evolves specifically from a procurement perspective, the pressure of high expectation and severe compliance clauses from key suppliers, particularly large corporations with monopolies in supplies who have the tendency to dominate and dictate terms to the small and medium enterprises (SMEs). For example, forcing SME’s to adopt specific technological frameworks to be trade partners. Another conflict is that while the SME’s do value the contribution of the procurement function, the shift from tactical to strategic mindset is not robust enough. Is this a dilemma? Ms Mary buyer at Al-Rumman Pharma, which is SME in operation, is facing challenges from key suppliers because of her tactical buying approach and adoption of multiple technological frameworks from various key suppliers, which are neither integrated nor compatible with each other. Her transition from traditional buying to a more strategic sourcing approach is what the need of the hour is. Prior information technology role was more as support at Al-Rumman Pharma and Chief Executive Officer Dr Mubeen Ahmad Khan did technology adopted decisions in isolation but today the company needs an integrative approach with forward thinking and also kept the legacy intact. Resistance to change was very inevitable once it was integrated.

Complexity academic level
This case has been particularly focused on undergraduates in the final semester of management courses, as well as masters level students specializing in supply chain and operation management courses. It is also for practitioner procurement and supply chain managers going for various supply chain management related certification courses. Students who have studied procurement management are most suitable to accomplish this case study. Executives pursuing a business program are also recommended to study this case.

Supplementary materials
Teaching Notes are available for educators only.

Subject code
CSS 9: Operations and logistics.
A study of the balancing of lean thinking and stakeholder salience in decision-making
Authors: Bader Bruce H. , Badar M. Affan , Rodchua Suhansa , McLeod Alister 
Published: February 2020

PurposeThis research brings together two streams of thought applied to decision-making: lean thinking and stakeholder theory. Both have been identified as ways to improve organizational value. Previous studies disagree regarding whether they can work together. This study investigates if managers balance stakeholders and lean thinking in decision-making.Design/methodology/approachThis research investigates if both lean thinking and stakeholder salience share common literature by using data mining. It surveys organizations that perceive themselves as lean and have multiple diverse stakeholders to determine whether waste and salience are considered when making decisions. An ANOVA is done to see if organization type, management level, organization size, geographic location, or lean maturity has an effect on the priority of stakeholder salience or lean thinking's waste variants when making decisions.FindingsFindings of this research are: 1) stakeholders salience criteria are considered more often than lean thinking's waste variants in decision-making by managers as a whole and in particular by middle-level managers and senior managers. However, lean thinking's waste variants are considered as often as stakeholder salience criteria by first-line managers. 2) The ranking of stakeholder salience in making decisions is not affected by organization type, respondent position, organization size, perceived lean experience, or geographic location. The organization type, organization size, lean experience, and location do not affect the ranking of lean thinking variants either. But the ranking of lean thinking's waste variants is significantly different for first-line, middle-level, and senior managers. Middle-level managers rank lean thinking higher than that of either first-line or senior-level. Because of this, middle managers have a more balanced approach in using lean thinking and stakeholder salience than other managers. 3) Stakeholder salience criteria have a significantly higher ranking than lean thinking variants in making decisions for all organization types: manufacturing and nonmanufacturing.Originality/ValueThis research demonstrates a significant disconnect exists between lean thinking and demands of stakeholders that impacts the value of an organization, and only middle-level managers bring balance and awareness of both streams of thought. An empirical instrument has been developed to balance the stakeholder salience criteria with the lean thinking variants.
Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)
Authors: Luehrmann Martin , Cortesi Fabio , Cheney Karen L. , de Busserolles Fanny , Marshall N. Justin 
Published: February 2020

Abstract

Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels.
This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large‐scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level.
To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common.
We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.
We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.
Species predominantly found in exposed microhabitats had higher expression of the short‐wavelength‐sensitive violet opsin (SWS2B) and lower expression of the dim‐light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue‐green central part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden in the reef substrate had a higher expression of the long‐wavelength‐sensitive red opsin.
We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.
Retinal topography did not show co‐adaptation with microhabitat use, but data suggested co‐adaptation with feeding mode.
We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems—and possibly those of other (reef) fishes—have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats.

A free Plain Language Summary can be found within the Supporting Information of this article.
Intraspecific variation in surface water uptake in a perennial desert shrub
Authors: Zaiats Andrii , Lazarus Brynne E. , Germino Matthew J. , Serpe Marcelo D. , Richardson Bryce A. , Buerki Sven , Caughlin T. Trevor 
Published: February 2020

Abstract

Despite broad recognition that water is a major limiting factor in arid ecosystems, we lack an empirical understanding of how this resource is shared and distributed among neighbouring plants. Intraspecific variability can further contribute to this variation via divergent life‐history traits, including root architecture. We investigated these questions in the shrub Artemisia tridentata and hypothesized that the ability to access and utilize surface water varies among subspecies and cytotypes.

We used an isotope tracer to quantify below‐ground zone of influence in A. tridentata, and tested whether spatial neighbourhood characteristics can alter plant water uptake. We introduced deuterium‐enriched water to the soil in plant interspaces in a common garden experiment and measured deuterium composition of plant stems. We then applied spatially explicit models to test for differential water uptake by A. tridentata, including intermingled populations of three subspecies and two ploidy levels.

The results suggest that lateral root functioning in A. tridentata is associated with intraspecific identity and ploidy level. Subspecies adapted to habitats with deep soils generally had a smaller horizontal reach, and polyploid cytotypes were associated with greater water uptake compared to their diploid variants. We also found that plant crown volume was a weak predictor of water uptake, and that neighbourhood crowding had no discernable effect on water uptake.

Intraspecific variation in lateral root functioning can lead to differential patterns of resource acquisition, an essential process in arid ecosystems in the contexts of changing climate and seasonal patterns of precipitation. Altogether, we found that lateral root development and activity are more strongly related to genetic variability within A. tridentata than to plant size. Our study highlights how intraspecific variation in life strategies is linked to mechanisms of resource acquisition.

A free Plain Language Summary can be found within the Supporting Information of this article.
Progress and prospects in the management of bacterial infections and developments in Phytotherapeutic modalities
Authors: Akram Muhammad , Riaz Muhammad , Munir Naveed , Rasul Akhtar , Daniyal Muhammad , Ali Shah Syed Muhammad , Shariati Mohammad Ali , Shaheen Ghazala , Akhtar Naheed , Parveen Farzana , Akhter Naheed , Owais Ghauri Aymen , Chishti Abdul Wadood , Usman Sarwar Muhammad , Said Khan Fahad 
Published: February 2020

AbstractThe advent of antibiotics revolutionized medical care resulting in significantly reduced mortality and morbidity caused by infectious diseases. However, excessive use of antibiotics has led to the development of antibiotic resistance and indeed, the incidence of multidrug‐resistant pathogens is considered as a major disadvantage in medication strategy, which has led the scholar's attention towards innovative antibiotic sources in recent years. Medicinal plants contain a variety of secondary metabolites with a wide range of therapeutic potential against the resistant microbes. Therefore, the aim of this review is to explore the antibacterial potential of traditional herbal medicine against bacterial infections. More than 200 published research articles reporting the therapeutic potential of medicinal plants against drug‐resistant microbial infections were searched using different databases such as Google Scholar, Science Direct, PubMed and the Directory of Open Access Journals (DOAJ), etc., with various keywords like medicinal plants having antibacterial activities, antimicrobial potentials, phytotherapy of bacterial infection, etc. Articles were selected related to the efficacious herbs easily available to local populations addressing common pathogens. Various plants such as Artocarpus communis, Rheum emodi, Gentiana lutea L., Cassia fistula L., Rosemarinus officinalis, Argemone maxicana L, Hydrastis canadensis, Citrus aurantifolia, Cymbopogon citrates, Carica papaya, Euphorbia hirta, etc, were found to have significant antibacterial activities. Although herbal preparations have promising potential in the treatment of multidrug‐resistant bacterial infection, still more research is required to isolate phytoconstituents, their mechanism of action as well as to find their impacts on the human body.
Incidence of lichen sclerosus and subsequent causes of death: a nationwide Finnish register study
Authors: Halonen P , Jakobsson M , Heikinheimo O , Gissler M , Pukkala E 
Published: February 2020

ObjectiveTo assess the incidence of lichen sclerosus (LS) in women and the all‐cause and cause‐specific mortality of women with LS.DesignPopulation‐based descriptive study.SettingFinland.PopulationAll Finnish women, including 7790 women diagnosed with LS during the period 1969–2012.MethodsInformation gathered from the Finnish Hospital Discharge Register on women with LS was combined with dates and causes of death from Statistics Finland and the Finnish Cancer Registry. Population statistics are from Statistics Finland.Main outcome measuresCrude and age‐adjusted incidence rates of LS and standardised mortality ratios (SMRs).ResultsThe incidence rate of LS adjusted for age (European Standard Population) increased from 14 per 100 000 woman‐years in 2003 to 22 per 100 000 woman‐years in 2010–2012. The age‐specific incidence rate was highest in postmenopausal women (24–53 per 100 000) but was also elevated in girls aged 5–9 years (seven per 100 000). The all‐cause mortality of women with LS was lower than in the general female population (SMR 0.84, 95% CI 0.78–0.90), mostly as a result of decreased mortality from circulatory diseases (SMR 0.80, 95% CI 0.72–0.89) and dementia and Alzheimer’s disease (SMR 0.75, 95% CI 0.62–0.88). The cancer mortality equalled that of the population, but the vulvar cancer mortality was increased (SMR 28.1, 95% CI 19.3–39.4).ConclusionsLichen sclerosus is a common disease of elderly women. The overall mortality is decreased whereas the mortality as a result of vulvar cancer is increased.Tweetable abstractThe likelihood of getting LS by age 80 years is 1.6%. The mortality of women with LS is reduced compared with that of the population.
Deoxynivalenol: Masked forms, fate during food processing, and potential biological remedies
Authors: Guo Hongyan , Ji Jian , Wang Jia‐sheng , Sun Xiulan 
Published: February 2020

AbstractDeoxynivalenol (DON) has drawn global attention because of its prevalence and significant effects on human or animal health. Biological remedies for DON have been developed from preharvest to postharvest. Applying microbes, including bacteria, fungi (yeast and molds), and enzymes, results in inhibited synthesis, structural destruction, or adsorption of DON. DON can be degraded into masked forms by phase I metabolism or phase II metabolism. During food processing, DON content changes dynamically and is even transformed. Physical, chemical, thermal, or biological processes physically reduce DON content. Temperature, heating time, enzymes, food additives, microorganisms, food composition, contamination level, and other ingredients are key factors. Although DON content can be reduced during food processing, increases in other toxins, such as DON‐3‐β‐d‐glucoside and 3‐acetyl‐DON, can be potentially risky. The application of biodegradation methods in food processing bears research significance. Both microorganisms and enzymes can be potentially used. Novel techniques, such as RNA interference, omics technologies, or enzymes coupled with the genetic engineering method, can be introduced. This review systematically updates the understanding of masked forms of DON, biological degradation strategy, fate of DON during processing, and future trends for biodegradation. Challenges to the successful application of biological methods may include the stability and suitability of the detoxification agents, security of degradation products, and successful application for industrial production.
Incidence and outcomes of aortic dissection for emergency departments in New South Wales, Australia 2017–2018: A data linkage study
Authors: Dinh Michael M , Bein Kendall J , Delaney John , Berendsen Russell Saartje , Royle Tim 
Published: February 2020

AbstractObjectiveThe aims of the present study were to describe the age‐specific incidence and 30‐day mortality of aortic dissection patients presenting to the EDs in New South Wales (NSW).MethodsThis was a data linkage study involving emergency, inpatient and death registry administrative data from NSW.ResultsThe present study found 273 instances of aortic dissection in NSW from July 2017 to July 2018. Calculated incidence was 3.47 per 100 000. Incidence increased exponentially with age. The 30‐day mortality rate among this cohort was 35.53% (n = 97). Mortality was significantly associated with age and pre‐existing comorbidity burden, but was not associated with gender, level of hospital or time of presentation.ConclusionsThe present study found the incidence of aortic dissection within the NSW population to be 3.4 per 100 000. The incidence of aortic dissection in our population increased from 8.6 per 100 000 for people aged between 60 and 80 years to 32 per 100 000 for those aged over 80 years.
Structural characterization of the micropatterned egg plastron in the mosquito, Aedes albopictus
Authors: Kim Hoon , Sun Yan , Bae Chae‐Gyeom , Moon Myung‐Jin 
Published: February 2020

AbstractEggs of the Asian tiger mosquito Aedes albopictus are fully covered with an air‐covering plastron network that enables them to stay below the surface of the water. Scanning electron microscopy revealed that the chorionic surface was covered with clusters of globular tubercles of different sizes. Histologically, the eggshell provides a typical water‐repellent microarchitecture consisting of an outer exochorion, a membranous endochorion and an intermediate pillar layer. The eggshell has a distinct chorionic tubercle that increases the surface area for gas exchange to enhance respiration capacity. In particular, the chorionic wall gives rise to a hexagonal pattern with smooth and elevated boundaries. In A. albopictus, a set of micropatterns for each hexagon was specified, and each central tubercle was surrounded by 20 small peripheral tubercles. Our fine structural analysis revealed that the partitioning of the surface into numerous hexagonal chorionic sculptures is associated with the Voronoi partition (tessellation), based on the distance to a point in a specific area of the plane. Therefore, the micropatterned surface of the mosquito eggshell appears to not only resist wetting by hydrostatic pressure but also provide resistance to lysate deposition by the biofouling process.