bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution
Authors: Panibe Jerome P. , Wang Long , Lee Yi-Chen , Wang Chang-Sheng , Li Wen-Hsiung 
Published: March 2022

Abstract
Background
Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits.

Results
Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response.

Conclusions
We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1’s blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
A scalable association rule learning and recommendation algorithm for large-scale microarray datasets
Authors: Li Haosong , Sheu Phillip C.-Y. 
Published: March 2022

AbstractAssociation rule learning algorithms have been applied to microarray datasets to find association rules among genes. With the development of microarray technology, larger datasets have been generated recently that challenge the current association rule learning algorithms. Specifically, the large number of items per transaction significantly increases the running time and memory consumption of such tasks. In this paper, we propose the Scalable Association Rule Learning (SARL) heuristic that efficiently learns gene-disease association rules and gene–gene association rules from large-scale microarray datasets. The rules are ranked based on their importance. Our experiments show the SARL algorithm outperforms the Apriori algorithm by one to three orders of magnitude.
Degradation insight of organophosphate pesticide chlorpyrifos through novel intermediate 2,6-dihydroxypyridine by Arthrobacter sp. HM01
Authors: Mali Himanshu , Shah Chandni , Patel Darshan H. , Trivedi Ujjval , Subramanian R. B. 
Published: March 2022

AbstractOrganophosphates (OPs) are hazardous pesticides, but an indispensable part of modern agriculture; collaterally contaminating agricultural soil and surrounding water. They have raised serious food safety and environmental toxicity that adversely affect the terrestrial and aquatic ecosystems and therefore, it become essential to develop a rapid bioremediation technique for restoring the pristine environment. A newly OPs degrading Arthrobacter sp. HM01 was isolated from pesticide-contaminated soil and identified by a ribotyping (16S rRNA) method. Genus Arthrobacter has not been previously reported in chlorpyrifos (CP) degradation, which shows 99% CP (100 mg L−1) degradation within 10 h in mMSM medium and also shows tolerance to a high concentration (1000 mg L−1) of CP. HM01 utilized a broad range of OPs pesticides and other aromatic pollutants including intermediates of CP degradation as sole carbon sources. The maximum CP degradation was obtained at pH 7 and 32 °C. During the degradation, a newly identified intermediate 2,6-dihydroxypyridine was detected through TLC/HPLC/LCMS analysis and a putative pathway was proposed for its degradation. The study also revealed that the organophosphate hydrolase (opdH) gene was responsible for CP degradation, and the opdH-enzyme was located intracellularly. The opdH enzyme was characterized from cell free extract for its optimum pH and temperature requirement, which was 7.0 and 50 °C, respectively. Thus, the results revealed the true potential of HM01 for OPs-bioremediation. Moreover, the strain HM01 showed the fastest rate of CP degradation, among the reported Arthrobacter sp.
Graphical Abstract
tiRNA-Val promotes angiogenesis via Sirt1–Hif-1α axis in mice with diabetic retinopathy
Authors: Xu Yan , Zou Haidong , Ding Qi , Zou Yuelan , Tang Chun , Lu Yuyu , Xu Xun 
Published: March 2022

Abstract
Background
Diabetic retinopathy (DR) is a specific microvascular complication arising from diabetes, and its pathogenesis is not completely understood. tRNA-derived stress-induced RNAs (tiRNAs), a new type of small noncoding RNA generated by specific cleavage of tRNAs, has become a promising target for several diseases. However, the regulatory function of tiRNAs in DR and its detailed mechanism remain unknown.

Results
Here, we analyzed the tiRNA profiles of normal and DR retinal tissues. The expression level of tiRNA-Val was significantly upregulated in DR retinal tissues. Consistently, tiRNA-Val was upregulated in human retinal microvascular endothelial cells (HRMECs) under high glucose conditions. The overexpression of tiRNA-Val enhanced cell proliferation and inhibited cell apoptosis in HRMECs, but the knockdown of tiRNA-Val decreased cell proliferation and promoted cell apoptosis. Mechanistically, tiRNA-Val, derived from mature tRNA-Val with Ang cleavage, decreased Sirt1 expression level by interacting with sirt1 3'UTR, leading to the accumulation of Hif-1α, a key target for DR. In addition, subretinal injection of adeno-associated virus to knock down tiRNA-Val in DR mice ameliorated the symptoms of DR.

Conclusion
tiRNA-Val enhance cell proliferation and inhibited cell apoptosis via Sirt1/Hif-1α pathway in HRMECs of DR retinal tissues.
A pilot single-blind parallel randomised controlled trial comparing kinesiology tape to compression in the management of subacute hand oedema after trauma
Authors: Miller Leanne , Jerosch-Herold Christina , Shepstone Lee 
Published: March 2022

Abstract
Background
Hand oedema is a common consequence of hand trauma or surgery. There are numerous methods to reduce hand oedema but lack high-quality evidence to support best practice. The primary objective of this pilot trial was to assess study feasibility when comparing treatments for subacute hand oedema after trauma.

Methods
A parallel two-arm pilot randomised controlled trial was conducted in the hand therapy department at a regional hospital in Norfolk between October 2017 and July 2018. Patients were eligible if 18 years or over, referred to hand therapy with subacute hand oedema. Randomisation was on a 1:1 basis to treatment as usual (TAU) (compression, elevation and massage) or trial treatment (TT) (kinesiology tape, elevation and massage). One blinded assessor completed all assessments (prior to randomisation, 4 and 12 weeks later). Data on study feasibility, adherence and acceptability of treatments were collected. The primary outcome measure was hand volume (volumetry). Patient-rated severity (0–5 Likert scale), hand health profile of the Patient Evaluation Measure (PEM) and quality of life (EQ-5D-5L) were also recorded.

Results
Forty-five patients were screened for eligibility and 26 consented and were randomised with 13 patients in each treatment arm. Twelve participants were lost to follow-up leaving 7 participants in each group included in the analysis. Assessor blinding was maintained in 64% of participants (9/14). Total mean acceptability scores, out of 100, were higher for TAU (87.9) than TT (76.1). Health resource use results showed TT was marginally cheaper (~£2 per patient) than TAU.
Individual adherence ranged between 39 and 100%, with higher levels of overall adherence seen in the TAU group. Four participants (28%) reported adverse effects (TT group n = 3, TAU group n = 1).

Conclusion
This pilot trial has identified that modifications are required in order to make a full-scale trial feasible. They include a formal assessment of treatment fidelity, research staff assisting with screening and recruitment of participants and multiple blinded assessors at each study site. Whilst not designed as an efficacy trial, it should be acknowledged that the small sample size and high loss to follow-up meant very small numbers were included in the final analysis resulting in wide confidence intervals and therefore low precision in parameter estimates.

Trial registration
International Standard Randomised Controlled Trial Number: 94083271. Date of registration 16th August 2017.

Trial funding
National Institute for Health Research Trainees Co-ordinating Centre (TCC); Grant Codes: CDRF-2014-05-064
Can programmatic inputs improve adolescent mothers’ access to maternal care in rural Bangladesh? Nine years of evidence from a cohort study
Authors: Rahman Aminur , Begum Tahmina , Austin Anne , Hasan Md. , Alam Nurul , Anwar Iqbal , Taneepanichskul Surasak 
Published: March 2022

Abstract
Background
Adolescent mothers (Girls aged 15–19) constitute 8% of annual global births, but account for 10% of annual maternal deaths. WHO recommended 4–8 Antenatal Care (ANC) visits, in addition to quality care and facility-based deliveries, are well-documented interventions to reduce maternal and child morbidity and mortality. Determinants of maternal and child health care in Bangladesh have received considerable attention, but less attention has been focused on adolescent mothers. This study explores the factors associated with 4 or more (4 +) ANC visits and facility-based delivery among adolescent mothers in one rural area of Bangladesh.

Methods
This study uses Health and Demographic Surveillance System (HDSS) data. We conducted a comparative study on trends in 4 + ANC visits and facility-based deliveries among adolescent mothers (10–19 years) residing in an intervention area (icddr,b service area, ISA) against a comparison area (government service areas, GSA) of HDSS between 2007 and 2015. Totally, 4,996 adolescent mothers were included in the final analysis. Binary logistic regression was used to document the statistical difference on outcome indicators in the two study areas.

Results
Trends in 4 + ANC visits and facility-based deliveries were higher in the ISA relative to the GSA. The adjusted odds of an adolescent mother accessing 4 + ANC visits in the GSA, relative to ISA, were 0.57 (95% CI 0.49–0.66, p value < 0.05); the adjusted odds of an adolescent mother accessing facility-based delivery in the ISA, relative to GSA, were 6.63 (95% CI: 5.85–7.52, p value < 0.05). Increasing numbers of ANC visits were associated with increases in facility-based births in both the ISA and GSA.

Conclusion
This study documented that both 4 + ANC visits and facility delivery rates among adolescent mothers are much higher in the ISA than GSA. Increasing 4 + ANC visits and facility deliveries over the years, particularly in the ISA, coincide with programmatic efforts to improve the quality and availability of maternal and newborn health services. Learning from existing interventions in ISA and applying them to other areas will strengthen Bangladesh’s efforts to improve maternal and newborn health outcomes and achieve the Sustainable Development Goal 3 (SDG 3).
Bioaccumulation of heavy metals in silver catfish (Chrysichthys nigrodigitatus) and tilapia fish (Oreochromis niloticus) from the brackish and freshwater in South-West, Nigeria
Authors: Abidemi-Iromini Atilola O. , Bello-Olusoji Oluayo. A. , Adebayo Isaac A. 
Published: March 2022

Abstract
Background
Chrysichthys nigrodigitatus (CN) and Oreochromis niloticus (ON) health status were investigated in Asejire Reservoir (AR) and Lagos Lagoon (LL), South-west Nigeria. Fish samples collected were separated into sexes. Growth pattern {length (cm); weight (g), Isometric index, condition factor (K)} were measured. Heavy metals (lead (Pb), iron (Fe), zinc (Zn), copper (Cu), and chromium (Cr) in ppm concentrations were determined in Lagos Lagoon and Asejire reservoir.

Results
Fish samples ranged at one male to one or two females. No significant difference in length and weight of O. niloticus between locations. Significant difference in weight occurred in C. nigrodigitatus between locations; highest condition factor was recorded in Asejire Reservoir O. niloticus, (ARON); lowest condition factor was observed in Asejire Reservoir C. nigrodigitatus (ARCN) as this indicated a negative allometric value, normal in Bagridae species. Male species possessed higher condition (K)—factor than female species within locations, between locations, between species, and within species, female C. nigrodigitatus having higher condition factor than male ARCN. Highest isometric value occurred in ARON and lowest in Lagos Lagoon C. nigrodigitatus (LLCN). Male ARON had highest isometric value, and O. niloticus species had higher isometric value (b ≤ 3) and positive allometric (b > 3); and C. nigrodigitatus has negative allometric (b < 3). Heavy metals Zn had highest value, while Cr ranked lowest value for ARON. Lagos Lagoon O. niloticus (LLON) Zn had highest value while Pb had lowest value. LLCN heavy metals determined revealed Zn had highest value, while Cr had lowest value; and ARCN heavy metals determined revealed Zn had highest value, and Cr had lowest. In all, Zinc (Zn) was top-ranked.

Conclusion
Results indicate niche response and performance as species specific; while environmental influence and stressors, food availability and reproduction factors contribute to well-being of fish. The heavy metals influence on the fish species is of public concern to man to avoid food poisoning.
Evaluation of bacterial formulations as potential biocontrol agents against the southern root-knot nematode, Meloidogyne incognita
Authors: Rani Priyanka , Singh Mohinder , Prashad Hema , Sharma Monika 
Published: March 2022

Abstract
Background
Bacterial bioagents, Pseudomonas fluorescens, P. putida, Bacillus amyloliquifaciens, and B. megaterium, have management potential against root-knot nematode (RKN), Meloidogyne incognita, in bottle gourd.

Results
Field and laboratory experiments were conducted to evaluate the effect of bacterial bioagents Bacillus megaterium 1% WP (2 × 106 CFU/g), B. amyloliquifaciens 1% WP (2 × 108 CFU/g), Pseudomonas putida 1% WP (2 × 108 CFU/g), P. fluorescens 1% WP (2 × 109 CFU/g) on egg hatching and juvenile mortality of root-knot nematode, M. incognita. All the bacterial species inhibited the egg hatching in M. incognita and caused juvenile mortality. The lowest mean egg hatching in 120 h. after treatment was observed in P. putida (20.9% mean egg hatching), followed by P. fluorescens (21.1%), B. amyloliquifaciens (23.7%), and B. megaterium (24.7%) at 4% concentration of the formulated product against (47%) egg hatching in control. The juvenile mortality was found highest (57.1% mean mortality) in P. fluorescens in 120 h. of exposure, followed by P. putida (56.13%), B. megaterium (54.46%), and B. amyloliquifaciens (53.13%) at 4% concentration against 0.46 mean juvenile mortality in control, where distilled water was used. Under field conditions, the bottle gourd seeds that were treated either with B. amyloliquefaciens, B. megaterium, P. fluorescens, or P. putida at 10 g/kg seed along with the application of neem cake (1t/ha) significantly resulted in reduced root gall index and the number of nematode juveniles in soil and roots than the non-treated control.

Conclusion
This study revealed that the tested bacterial bioagents, namely B. amyloquefaciens, B. megaterium, P. fluorescens, and P. putida, showed the potential for controlling of root knot nematode (RKN) in the laboratory as well as in field conditions in bottle gourd.
Making Land and Water Meet: The Cycling of Nutrients between Fields and Ponds in Pre-Modern Europe
Authors: HOFFMANN RICHARD C. , WINIWARTER VERENA 
Published: March 2022

Abstract
Medieval and early modern records show certain practices were common in traditional European aquaculture. These, combined with advice in coeval treatises on agricultural management, demonstrate how European agroecosystems linked terrestrial and aquatic operations to pursue a net energy gain in their outputs. Critical reading of three distinct bodies of sources: early modern European agricultural manuals, literature on fish culture compiled in western Latin Christendom, and managerial records of fourteenth-through seventeenth-century fish culture enterprises establishes two new understandings. First, land manages took self-conscious measures to integrate their arable and pond cultures with the aim of conserving and recycling essential nutrients. Second, agricultural handbooks from this period both reflected traditional practices of illiterate peasant farmers (and hence their "traditional ecological knowledge") and informed certain managerial decisions.
Inertial biometry from commercial 3D body meshes
Authors: Minetti Alberto E. , Ruggiero Luca 
Published: March 2022

ABSTRACT
Body segments inertial parameters (or, more generally encompassing humans and animal species, inertial biometry), often necessary in kinetics calculations, have been obtained in the past from cadavers, medical 3D imaging, 3D scanning, or geometric approximations. This restricted the inertial archives to a few species. The methodology presented here uses commercial 3D meshes of human and animal bodies, which can be further re-shaped and ‘posed’, according to an underlying skeletal structure, before processing. The sequence of steps from virtually chopping the mesh to the estimation of inertial parameters of body segments is described. The accuracy of the method is tested by comparing the estimated results to real data published for humans (male and female), horses, and domestic cats. The proposed procedure opens the possibility of remarkably expanding biomechanics research when body size and shape change, or when external tools, such as prosthesis and sport material, take part in biological movement.
Rectified random cell motility as a mechanism for embryo elongation
Authors: Regev Ido , Guevorkian Karine , Gupta Anupam , Pourquié Olivier , Mahadevan L. 
Published: March 2022

ABSTRACT
The body of vertebrate embryos forms by posterior elongation from a terminal growth zone called the tail bud. The tail bud is a source of highly motile cells that eventually constitute the presomitic mesoderm (PSM), a tissue that plays an important role in elongation movements. PSM cells establish an anterior-posterior cell motility gradient that parallels a gradient associated with the degradation of a specific cellular signal (FGF) known to be implicated in cell motility. Here, we combine the electroporation of fluorescent reporters in the PSM with time-lapse imaging in the chicken embryo to quantify cell diffusive movements along the motility gradient. We show that a simple microscopic model for random cell motility induced by FGF activity along with geometric confinement leads to rectified tissue elongation consistent with our observations. A continuum analog of the microscopic model leads to a macroscopic mechano-chemical model for tissue extension that couples FGF activity-induced cell motility and tissue rheology, and is consistent with the experimentally observed speed and extent of elongation. Together, our experimental observations and theoretical models explain how the continuous addition of cells at the tail bud combined with lateral confinement can be converted into oriented movement and drive body elongation.
Phosphorylated paxillin and phosphorylated FAK constitute subregions within focal adhesions
Authors: Bachmann Michael , Skripka Artiom , Weißenbruch Kai , Wehrle-Haller Bernhard , Bastmeyer Martin 
Published: March 2022

ABSTRACT
Integrin-mediated adhesions are convergence points for multiple signaling pathways. Their inner structure and diverse functions can be studied with super-resolution microscopy. Here, we examined the spatial organization within focal adhesions by analyzing several adhesion proteins with structured illumination microscopy (SIM). Paxillin (Pax) serves as a scaffold protein and signaling hub in focal adhesions, and focal adhesion kinase (FAK, also known as PTK2) regulates the dynamics of adhesions. We found that their phosphorylated forms, pPax and pFAK, form spot-like, spatially defined clusters within adhesions in several cell lines and confirmed these findings with additional super-resolution techniques. These clusters showed a more regular separation from each other compared with more randomly distributed signals for FAK or paxillin. Mutational analysis indicated that the active (open) FAK conformation is a prerequisite for the pattern formation of pFAK. Live-cell super-resolution imaging revealed that organization in clusters is preserved over time for FAK constructs; however, distance between clusters is dynamic for FAK, while paxillin is more stable. Combined, these data introduce spatial clusters of pPax and pFAK as substructures in adhesions and highlight the relevance of paxillin–FAK binding for establishing a regular substructure in focal adhesions.
Reciprocal regulation of p21 and Chk1 controls the cyclin D1-RB pathway to mediate senescence onset after G2 arrest
Authors: Lossaint Gérald , Horvat Anđela , Gire Véronique , Bačević Katarina , Mrouj Karim , Charrier-Savournin Fabienne , Georget Virginie , Fisher Daniel , Dulić Vjekoslav 
Published: March 2022

ABSTRACT
Senescence is an irreversible withdrawal from cell proliferation that can be initiated after DNA damage-induced cell cycle arrest in G2 phase to prevent genomic instability. Senescence onset in G2 requires p53 (also known as TP53) and retinoblastoma protein (RB, also known as RB1) family tumour suppressors, but how they are regulated to convert a temporary cell cycle arrest into a permanent one remains unknown. Here, we show that a previously unrecognised balance between the cyclin-dependent kinase (CDK) inhibitor p21 and the checkpoint kinase Chk1 controls cyclin D–CDK activity during G2 arrest. In non-transformed cells, p21 activates RB in G2 by inhibiting cyclin D1 complexed with CDK2 or CDK4. The resulting G2 exit, which precedes the appearance of senescence markers, is associated with a mitotic bypass, Chk1 downregulation and reduction in the number of DNA damage foci. In p53/RB-proficient cancer cells, a compromised G2 exit correlates with sustained Chk1 activity, delayed p21 induction, untimely cyclin E1 re-expression and genome reduplication. Conversely, Chk1 depletion promotes senescence by inducing p21 binding to cyclin D1– and cyclin E1–CDK complexes and downregulating CDK6, whereas knockdown of the checkpoint kinase Chk2 enables RB phosphorylation and delays G2 exit. In conclusion, p21 and Chk2 oppose Chk1 to maintain RB activity, thus promoting the onset of senescence induced by DNA damage in G2.