jimnoneill/paper-to-field-training huggingface dataset:
Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids

Field: Agricultural and Biological Sciences (Life Sciences)

Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III polyketide synthase (PKS) gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five PeqPKS, eight DcaPKS and six AshPKS genes in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica, respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in P. equestris and two proteins each in D. catenatum and A. shenzhenica clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive cis-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of PKS genes and biotechnological production of polyketides.Communicated by Ramaswamy H. Sarma.
Numerical and theoretical studies of turbulence and transport with E ×B shear flows

Field: Physics and Astronomy (Physical Sciences)

Abstract. A report is given of: (a) a substantial transport reduction by the turbulence driven E×B flows observed in three dimensional non-linear gyrokinetic simulations of microturbulence in magnet-ically confined toroidal plasmas; (b) an analytical derivation of the effective shearing rate for the time dependent E×B flow; (c) an interpretation of experimental data using linear gyrokinetic microinsta-bility rotation models of E ×B shear; (d) other developments in gyrokinetic theory and simulation. 1.
VP07.01: How adenomyosis changes throughout pregnancy: a retrospective study

Field: Medicine (Health Sciences)

To study how adenomyosis modifies in pregnancy and to correlate these changes to maternal and fetal outcomes. Retrospective cohort study including 254 women between 2016 and 2020. Inclusion criteria were: ≧1 transvaginal ultrasound (TV-US) (performed before conception/1st trimester) to assess the presence of adenomyosis, ≧1 scan available per trimester (if ongoing pregnancy) and complete information of maternal and neonatal outcomes. Exclusion criteria were: twins, uterine malformations or fetal anomalies. Adenomyosis was diagnosed with ≧1 criteria from the MUSA classification or the adenomyosis consensus classification system at TV-US. 144 (86.27%) 26 (89.65%) 54 (81.81%) 2 (100%) 226 (85.28%) 1 (100%) 23 (13.77%) 3 (10.34%) 12 (18.18%) 39 (14.71%) 1 (0.003%) 167 (63.01%) 29 (10.94%) 66 (24.90%) 2 (0.007%) The globular aspect of the uterus was the commonest sign reported in 79% women with adenomyosis in the 1st trimester: it progressively disappeared, being present in 38% and 2% women in the 2nd and 3rd trimester respectively and again visible in the post-partum in 65% women. Asymmetrical thickening (30%) and cysts (23%) were also reported in the 1st trimester and disappeared during pregnancy. Adenomyosis was associated with miscarriage (OR 5.9 95%CI 2.4-14.9, p < 0.001) also when considering only normal conception (OR 5.1 95%CI 1.8-14.2, p = 0.002) or correcting for maternal age (aOR 5.9, CI95% 2.3-15.2, p < 0.001). GA at delivery was significantly lower in women with adenomyosis compared to controls (P = 0.004). Caesarean sections (CS) rate was higher than in controls (OR 2.5, CI95% 1.3-4.8, p = 0.007) and this was confirmed (OR 2.4 CI95% 1.1-5, p = 0.02) also after excluding women with previous CS. Signs of adenomyosis can be identified in pregnancy and progressively disappear during gestation but are clinically relevant: adenomyosis was associated with an increased risk of miscarriage. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Factors Affecting the Adoption of Organic Farming in Peshawar-Pakistan

Field: Agricultural and Biological Sciences (Life Sciences)

This study was conducted to investigate the factors affecting the adoption of organic farming in Peshawar-Pakistan. A total of 100 respondents were randomly selected from the four different cultivated areas of Peshawar, namely Palosi, Regi, Ternab and Pushtakhara. Binary logistic re-gression was used in this study to categorize the organic farming into adoption and non-adoption. The purpose of this model was to check the event probability for a categorical response variable with two outcomes. The results of the binary logistic show that factors affecting adoption of organic farming have a significant effect on the farmer productivity. Moreover, cost, productivity, profitability, compatibility and efficiency have a positive and significant effect. Thus, it is obvious that adopting organic farming not only to increase the farmer income but also to protect environmental pollution by avoiding the toxic chemical and fertilizer. Finally, we suggest that government agencies, extension and research institution should play a vital role to strengthen the awareness and advantages of organic farming.
Childhood Autism Spectrum Disorders With and Without Epilepsy

Field: Medicine (Health Sciences)

This prospective cross-sectional study compared 25 children with pervasive developmental disorder and epilepsy and 25 children having pervasive developmental disorder without epilepsy on pervasive developmental disorder scores, Childhood Autism Rating Scale scores, language disability, presence of regression, and epileptiform abnormalities. Epilepsy phenotype was also studied. Children with pervasive developmental disorder and epilepsy had higher pervasive developmental disorder scores ( P = .001), higher Childhood Autism Rating Scale scores ( P = .016), and lower social quotient ( P = .09). More than 50% of children with pervasive developmental disorder and epilepsy and 12% of children having pervasive developmental disorder without epilepsy had epileptiform abnormalities in electroencephalography (EEG). Regression of milestones was significantly associated with epilepsy and epileptiform abnormalities. Children with pervasive developmental disorder and epilepsy might have a worse developmental trajectory requiring intensive management. A behavioral phenotype of autism may coexist often in children with epilepsy, EEG abnormalities, and regression. Seizures might be difficult to control in these children despite adequate compliance. Studies with larger sample size and longitudinal follow-up will provide better understanding.
Colloidal and Nanosized Catalysts in Organic Synthesis:XXVI. Amines Alkylation with Alcohols Catalyzed by γ-Al2O3-Supported Nickel and Copper Nanoparticles

Field: Chemical Engineering (Physical Sciences)

Amines alkylation with alcohols catalyzed by γ-Al2O3-supported nickel and copper nanoparticles under continuous process conditions at atmospheric hydrogen pressure and 180–220°С has led to the formation of alkylated products with selectivity up to 100%.
The Effectiveness of Ecklonia Cava Kjellman Extract in Improving Menopausal Syndrome in Osteoporosis and Depression

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Ecklonia cava (EC) is a natural material commonly used to decrease swelling, allergy, cancer, and sleep issues. Using EC has been reported to regulate hormones during ovarian failure in an aromatase inhibition rodent model. The aim of this study was to investigate EC’s benefits on ovariectomized female mice. Hormone replacement therapy is beneficial in menopause, but the risk of side effects increases. In the present study, alkaline phosphatase (ALP) activity and tryptophan hydroxylases (TPHs) expression were studied after the EC extracts were incorporated as elemental, phloroglucinol, eckol, dieckol, 6,6′-biekcol, and 8,8′-bieckol. In this in vivo study, the following seven groups of 10-week-old Balb/c female mice were evaluated over 8 weeks: normal mice (Sham), ovariectomized mice (OVX), ovariectomized and restraint stressed mice (OVX + R), ovariectomized and 17β-estradiol-treated mice (OVX + R + E2), ovariectomized and fluoxetine-treated mice (OVX + R + E2), and ovariectomized and EC-extract-treated mice (OVX + R + EC150 or OVX + R + EC300). The serum lipid profile, bone loss, and depressive symptoms were investigated in an ovariectomized and restraint-stressed mice model. In the in vitro models, ALP activity was dose-dependently upregulated by EC, including phloroglucinol, eckol, dieckol, 6,6′-biekcol, and 8,8′-bieckol, in RBL-2H3 cells. The transcripts of TPH1 and TPH2 were induced by EC and/or its elements (phloroglucinol, eckol, dieckol, 6,6′-biekcol, and 8,8′-bieckol) in RBL-2H3 cells. The re-uptake activity of serotonin (5-HT) was also decreased by EC and its ingredients such as phloroglucinol, eckol, dieckol, 6,6′-biekcol, and 8,8′-bieckol. In the models, the serum cholesterol and triglyceride levels were downregulated in OVX + R mice by EC treatment. The bone mineral density (BMD) was determined in EC-treated groups, and the bone metabolism markers, CTX and osteocalcin, were also reduced to normal levels. The depression experiments revealed that the immobility time was shortened in the forced-swimming test in OVX + R mice. Moreover, the serum serotonin level was promoted by EC treatment in OVX + R mice. These results showed that EC extract inhibits bone loss and depressive symptoms in a menopausal mouse model by modulating bone metabolism markers (CTX and osteocalcin) and serotonin level in OVX + R mice.
Singapore Pie in Global Chinese Education: Inheritance and Innovation in Chinese Literature Education in Singapore

Field: Arts and Humanities (Social Sciences)

Singapore’s Chinese literature education has continuously evolved and advanced over the years, forming a unique style in global Chinese education, which can be described as: “Singapore pie”. Through its bilingual policy, the Singapore government has been committed to creating a pool of bicultural talents, by supplementing the teaching of Chinese language with classes on Chinese literature and culture. This thesis seeks to understand the pros and cons of Chinese literature education in Singapore by analysing its development over the years. The teaching of Chinese literature began with the first wave of Chinese migration to Nanyang in the 19th century, and from there, it went through three phases of development: relocation, adjustment, and burgeoning
A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy

Field: Chemistry (Physical Sciences)

Nature-inspired molecular machines can exert mechanical forces by controlling and varying the distance between two molecular subunits in response to different inputs. Here, we present an automated molecular linear actuator composed of T7 RNA polymerase (T7RNAP) and a DNA [2]rotaxane. A T7 promoter region and terminator sequences are introduced into the rotaxane axle to achieve automated and iterative binding and detachment of T7RNAP in a self-controlled fashion. Transcription by T7RNAP is exploited to control the release of the macrocycle from a single-stranded (ss) region in the T7 promoter to switch back and forth from a static state (hybridized macrocycle) to a dynamic state (movable macrocycle). During transcription, the T7RNAP keeps restricting the movement range on the axle available for the interlocked macrocycle and prevents its return to the promotor region. Since this range is continuously depleted as T7RNAP moves along, a directional and active movement of the macrocycle occurs. When it reaches the transcription terminator, the polymerase detaches, and the system can reset as the macrocycle moves back to hybridize again to the ss-promoter docking site. The hybridization is required for the initiation of a new transcription cycle. The rotaxane actuator runs autonomously and repeats these self-controlled cycles of transcription and movement as long as NTP-fuel is available.
[Ultrastructural demonstration of the human papilloma virus (HPV) in oral proliferative lesions].

Field: Medicine (Health Sciences)

The Human Papilloma Virus (HPV) has been found in a series of benign proliferative lesions of the skin and mucosa. The virus has also been found in verrucous laryngeal carcinoma and carcinomas of the oral cavity and other organs. DNA hybridization techniques have made it possible to classify 51 types of HPVs, some appearing to be associated with specific lesions. In order to study the intracellular distribution of HPVs, an ultrastructural morphological analysis was performed with an electron microscope on 10 specimens taken from 5 patients. The specimens were obtained through large excisional biopsy, histologically classified as "fibropapilloma". For each patient specimens were taken from the clinically evident lesion and from the surrounding clinically normal mucosa. The specimens were fixed in glyceraldehyde, washed in a cacodylate buffer, post-fixed in potassium ferrocyanide reduced-osmium tetroxide, stained with uranyl acetate and included in EPON 812. The tissue was subjected to amylase digestion prior to electron microscope examination. A great number of viral particles were found in both the nucleus and the cytoplasm, without forming crystal array structures as typically described for the verruca vulgaris virus (HPV-2). No significant differences could be found between the cells derived from the clinical lesion and those derived from the surrounding mucosa. The passage of viral particles from infected to as yet uninfected cells through the intercellular space could be seen. The high intracytoplasmatic presence of the virus, and its clear abundance in those cells surrounding the clinical lesion, is felt to be of special interest.
The Use of Allograft Skin for the Treatment of Darier Disease

Field: Medicine (Health Sciences)

ABSTRACT Darier disease is an autosomal dominant skin disorder characterized by keratotic papules. After their appearance, these lesions tend to grow over time, producing large and exudative plaques that compromise the general condition of the affected patient’s skin. The authors report the clinical case of a patient affected by Darier disease with superinfected de-epithelialized areas over 30% of his body. In addition to antibiotic and antifungal therapy, providers used allograft skin to cover the injured areas and stimulate their progressive re-epithelialization with complete healing after 2 months. To the authors’ knowledge, this is the first clinical case of treating Darier disease with allograft skin on an extensively damaged area. The effectiveness of this treatment may lead clinicians to consider allograft skin tissue a new, alternative dressing to treat Darier disease when this pathologic condition manifests with extensive eroded skin.
Baobab (<i>Adansonia digitata</i> L.) seed protein utilization in young albino rats I: Biochemical ingredients and performance characteristics

Field: Agricultural and Biological Sciences (Life Sciences)

Raw, cooked and HCl-extracted baobab, Adansonia digitata seed meals were used for biological and nutritional evaluation studies. The seed is low in protein (16.60g/100g DM) but could be a good source of oil (17.50g/100g) and minerals, particularly sod um, potassium and phosphorus, which contained 228.0, 1429.0 and 924.5 mg/100gDM respectively. Low levels of antinutritional factors such as tannin, phytate, cyanide, oxalate, nitrate/nitrite and absence o tryps n inhibitors were observed. Seed protein is high in sul ur-amino acid, with a chemical score (CS) of 126.80, but marginally limiting in lysine and threonine, with CS of 64.31 and 85.59 respectively based on the preschool age (2-5yrs) reference protein requirement. The seed oil contain appreciable level of unsaturated fatty acids with oleic and linoleic acids making up 66.32% of total fatty acids. The raw diet was similar to the casein diet in weight gain, feed intake, net protein retention (NPR) and true digestibility (TD) but significant y inferior in protein eff c ency ratio (PER). Cooking did not have any significant effect on feed intake but significantly lowered the weight gain relative to the raw and casein diets. HClextracted meal exerted signi icantly lower weig h t g a i n c o m p a r e d t o the raw, cooked and casein diets It is concluded that the raw seed showed promise as a source of food supplement and is likely to be satisfactory in supporting growth and maintenance in livestock feeding. i
Using Power, Privilege, and Intersectionality to Understand, Disrupt, and Dismantle Oppressive Structures within Academia: A Design Case

Field: Social Sciences (Social Sciences)

Abstract Many of us are working to create a more inclusive and socially just culture within engineering education and engineering. Despite significant effort, marginalization and discrimination continue, buoyed by systems of oppression. How can we disrupt and dismantle oppressive systems in engineering education? In our work, we explore how power and privilege are enacted within leadership teams that aim to create revolutionary changes within engineering departments. Based on this work, we developed the POWER protocol (Privilege and Oppression: Working for Equitable Recourse), a workshop that guides engineering educators to identify and understand the intersectional nature of power and privilege before planning strategies to disrupt, disarm, and dismantle it. In this paper, we present a design case to show how this workshop has evolved. We provide the POWER protocol in the appendix so that others can adapt this workshop for their own contexts. In the interactive session at CoNECD, we will take attendees through part of the POWER protocol (we will scope the workshop to fit in the time allotted; the full workshop is 1.5 hours) to examine how power, privilege, and intersectionality can help attendees frame their experiences and begin to understand how their everyday experiences may be influenced by systemic oppression. To guide this process, we orient around the question: How can we become aware of power and privilege on collaborative academic teams in order to better affect social change and improve interdisciplinary and cross-identity/boundary interactions, communication, and inclusivity? We hope that through interactive sessions such as this that we can all become more persistent and sophisticated in our efforts to dismantle some of these forms of power and privilege within the university, especially those aspects that continue to oppress and oftentimes push marginalized people and perspectives out of academia. Our interactive approach will position attendees to bring this protocol back to their institutions and adapt it to their own contexts. In the tradition of the design case such as those published by the International Journal of Designs for Learning, we detail how our contexts and the literature informed the iterative development of the POWER protocol in this paper. We provide a vivid account of the POWER protocol and a facilitation guide that others can use and adapt in their own contexts. Using a narrative format, we share a forthright account of our development process. Design cases are valuable in highlighting distinctive aspects of how a design came to be; by sharing our design decisions along with the design, others may gain insight into both what has made our design successful, and where it may be brittle when used in new contexts. Finally, we describe how we will engage attendees in the CoNECD session.
HMG box‐containing protein 1 (HBP1) as a downstream signaling effector of EGFR in oral cancer

Field: Medicine (Health Sciences)

Aberrant activation of the epidermal growth factor (EGF) receptor (EGFR) signaling in the squamous cell carcinomas of the head and neck (SCCHN) is often associated with inauspicious prognosis and low survival. Transcription factor HMG box‐containing protein 1 (HBP1) functions as a potential tumor repressor in various cancers; however, its role in oral cancer is still unclear. Analysis of human oral cancer specimens revealed that the mean HBP1 mRNA level in tumors was significantly lower than that of the normal tissues, and that the concurrent status of low HBP1 and high EGFR was associated with the invasiveness of oral cancer. To explore the potential link between EGFR signaling and HBP1, we treated EGFR‐overexpressing oral cancer cell lines, HSC‐3 and FaDu, with EGFR inhibitors, AG1478 and Erlotinib, or EGFR siRNA, and found that EGFR down‐regulation increased HBP1 expression. Administration of phosphatidylinositol 3‐kinase (PI3K) inhibitor, Ly294002, decreased Akt phosphorylation and increased HBP1 expression. Overall, the expression of Akt and HBP1 acted in a reciprocal manner. Moreover, HBP1 knockdown in HSC‐3 cells enhanced in vitro colony formation and in vivo xenograft tumor growth. HBP1 knockdown attenuated Erlotinib‐mediated cyclin D1 reduction and subsequent G1 arrest. Together, our data reveal a novel role of HBP1 as a downstream effector of the EGFR/Akt signaling pathway in oral cancer.
Binding of the synaptic vesicle radiotracer [11C]UCB-J is unchanged during functional brain activation using a visual stimulation task

Field: Neuroscience (Life Sciences)

The positron emission tomography radioligand [ 11 C]UCB-J binds to synaptic vesicle glycoprotein 2 A (SV2A), a regulator of vesicle release. Increased neuronal firing could potentially affect tracer concentrations if binding site availability is altered during vesicle exocytosis. This study assessed whether physiological brain activation induces changes in [ 11 C]UCB-J tissue influx ( K 1 ), volume of distribution ( V T ), or binding potential ( BP ND ). Healthy volunteers ( n = 7) underwent 60-min [ 11 C]UCB-J PET scans at baseline and during intermittent presentation of 8-Hz checkerboard visual stimulation. Sensitivity to intermittent changes in kinetic parameters was assessed in simulations, and visual stimulation was repeated using functional magnetic resonance imaging to characterize neural responses. V T and K 1 were determined using the one-tissue compartment model and BP ND using the simplified reference tissue model. In primary visual cortex, K 1 increased 34.3 ± 15.5% ( p = 0.001) during stimulation, with no change in other regions ( ps > 0.12). K 1 change was correlated with fMRI BOLD response (r = 0.77, p = 0.043). There was no change in V T (−3.9 ± 8.8%, p = 0.33) or BP ND (−0.2 ± 9.6%, p = 0.94) in visual cortex nor other regions ( ps > 0.19). Therefore, despite robust increases in regional tracer influx due to blood flow increases, binding measures were unchanged during stimulation. [ 11 C]UCB-J V T and BP ND are likely to be stable in vivo measures of synaptic density.