bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon
Authors: Serrani-Yarce Juan Carlos , Escamilla-Trevino Luis , Barros Jaime , Gallego-Giraldo Lina , Pu Yunqiao , Ragauskas Art , Dixon Richard A. 
Published: February 2021

Abstract
Background
Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called “esters” pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the “reverse” direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass Brachypodium distachyon has two HCT genes, but lacks a classical CSE gene. This study was therefore conducted to evaluate the utility of HCT as a target for lignin modification in a species with an “incomplete” shikimate shunt.

Results
The kinetic properties of recombinant B. distachyon HCTs were compared with those from Arabidopsis thaliana, Medicago truncatula, and Panicum virgatum (switchgrass) for both the forward and reverse reactions. Along with two M. truncatula HCTs, B. distachyon HCT2 had the least kinetically unfavorable reverse HCT reaction, and this enzyme is induced when HCT1 is down-regulated. Down regulation of B. distachyon HCT1, or co-down-regulation of HCT1 and HCT2, by RNA interference led to reduced lignin levels, with only modest changes in lignin composition and molecular weight.

Conclusions
Down-regulation of HCT1, or co-down-regulation of both HCT genes, in B. distachyon results in less extensive changes in lignin content/composition and cell wall structure than observed following HCT down-regulation in dicots, with little negative impact on biomass yield. Nevertheless, HCT down-regulation leads to significant improvements in biomass saccharification efficiency, making this gene a preferred target for biotechnological improvement of grasses for bioprocessing.
Elucidating the cellular mechanism for E2-induced dermal fibrosis
Authors: Baker Frost DeAnna , Savchenko Alisa , Ogunleye Adeyemi , Armstrong Milton , Feghali-Bostwick Carol 
Published: February 2021

Abstract
Background
Both TGFβ and estradiol (E2), a form of estrogen, are pro-fibrotic in the skin. In the connective tissue disease, systemic sclerosis (SSc), both TGFβ and E2 are likely pathogenic. Yet the regulation of TGFβ in E2-induced dermal fibrosis remains ill-defined. Elucidating those regulatory mechanisms will improve the understanding of fibrotic disease pathogenesis and set the stage for developing potential therapeutics. Using E2-stimulated primary human dermal fibroblasts in vitro and human skin tissue ex vivo, we identified the important regulatory proteins for TGFβ and investigated the extracellular matrix (ECM) components that are directly stimulated by E2-induced TGFβ signaling.

Methods
We used primary human dermal fibroblasts in vitro and human skin tissue ex vivo stimulated with E2 or vehicle (ethanol) to measure TGFβ1 and TGFβ2 levels using quantitative PCR (qPCR). To identify the necessary cell signaling proteins in E2-induced TGFβ1 and TGFβ2 transcription, human dermal fibroblasts were pre-treated with an inhibitor of the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) pathway, U0126. Finally, human skin tissue ex vivo was pre-treated with SB-431542, a TGFβ receptor inhibitor, and ICI 182,780, an estrogen receptor α (ERα) inhibitor, to establish the effects of TGFβ and ERα signaling on E2-induced collagen 22A1 (Col22A1) transcription.

Results
We found that expression of TGFβ1, TGFβ2, and Col22A1, a TGFβ-responsive gene, is induced in response to E2 stimulation. Mechanistically, Col22A1 induction was blocked by SB-431542 and ICI 182,780 despite E2 stimulation. Additionally, inhibiting E2-induced ERK/MAPK activation and early growth response 1 (EGR1) transcription prevents the E2-induced increase in TGFβ1 and TGFβ2 transcription and translation.

Conclusions
We conclude that E2-induced dermal fibrosis occurs in part through induction of TGFβ1, 2, and Col22A1, which is regulated through EGR1 and the MAPK pathway. Thus, blocking estrogen signaling and/or production may be a novel therapeutic option in pro-fibrotic diseases.
Comprehensive assessment of alterations in hand deformities over 11 years in patients with rheumatoid arthritis using cluster analysis and analysis of covariance
Authors: Toyama Shogo , Tokunaga Daisaku , Tsuchida Shinji , Kushida Rie , Oda Ryo , Kawahito Yutaka , Takahashi Kenji 
Published: February 2021

AbstractBackgroundAlthough drug therapy for rheumatoid arthritis (RA) has recently improved, treating patients with established disease, whose hands have three major deformities (thumb deformity, finger deformities, and ulnar drift), remains a challenge. The underlying complex pathophysiology makes understanding these deformities difficult, and comprehensive assessment methods require accumulated skill with long learning curves. We aimed to establish a simpler composite method to understand the pathophysiology of and alterations in the hand deformities of patients with RA.MethodsWe established a rheumatoid hand cohort in 2004 and clinically evaluated 134 hands (67 patients). We repeated the evaluations in 2009 (100 hands of 52 patients) and 2015 (63 hands of 37 patients) after case exclusion. Thumb deformities, finger deformities (swan-neck and boutonnière deformity), and ulnar drift were semi-quantitated and entered as parameters into a two-step cross-sectional cluster analysis for the data in 2004. The parameters in each cluster were plotted at each evaluation point. Two-way analysis of covariance was used to examine whether differences existed between evaluation points and clusters of deformity parameters.ResultsFive clusters most appropriately described hand deformity: (i) cluster 1, minimal deformity; (ii) cluster 2, type 1 thumb deformity; (iii) cluster 3, thumb deformity and severe boutonnière deformity; (iv) cluster 4, type 2 or 3 thumb deformity and severe ulnar drift; and (v) cluster 5, thumb deformity and severe swan-neck deformity. Clusters 1 and 2 had higher function than cluster 5, and cluster 3 had moderate function. Clusters 1–4 had similar disease duration but showed different paths of deformity progression from disease onset. Clusters 1 and 2 represented conservative deformity parameters and clusters 3, 4, and 5 represented progressive deformity parameters. Over time, thumb deformity evolved into other types of deformities and swan-neck deformity worsened significantly.ConclusionsOur comprehensive analysis identified five deformity patterns and a progressive course in the rheumatoid hand. Knowledge of the characteristics of progressive deformity parameters may allow rheumatologists to more easily implement practical interventions and determine functional prognosis.
Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA
Authors: Siregar Iskandar Zulkarnaen , Dwiyanti Fifi Gus , Pratama Rahadian , Matra Deden Derajat , Majiidu Muhammad 
Published: February 2021

Abstract
Objectives
Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.).

Data description
Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.
An accelerated viscosity forward-backward splitting algorithm with the linesearch process for convex minimization problems
Authors: Suantai Suthep , Jailoka Pachara , Hanjing Adisak 
Published: February 2021

AbstractIn this paper, we consider and investigate a convex minimization problem of the sum of two convex functions in a Hilbert space. The forward-backward splitting algorithm is one of the popular optimization methods for approximating a minimizer of the function; however, the stepsize of this algorithm depends on the Lipschitz constant of the gradient of the function, which is not an easy work to find in general practice. By using a new modification of the linesearches of Cruz and Nghia [Optim. Methods Softw. 31:1209–1238, 2016] and Kankam et al. [Math. Methods Appl. Sci. 42:1352–1362, 2019] and an inertial technique, we introduce an accelerated viscosity-type algorithm without any Lipschitz continuity assumption on the gradient. A strong convergence result of the proposed algorithm is established under some control conditions. As applications, we apply our algorithm to solving image and signal recovery problems. Numerical experiments show that our method has a higher efficiency than the well-known methods in the literature.
A rare case report: an inextricable shoulder pain as the exclusive presentation of lung adenocarcinoma with metastasis over contralateral clavicle
Authors: Wu Karl , Huang Yu-Hao 
Published: February 2021

Abstract
Background
Lung cancer is the fourth most common form of the tumor spreading to the bone. Among all patients of lung carcinoma, the most common sites of bone metastasis are vertebrae, ribs, and pelvis. By comparison, the clavicle is an extremely rare site of metastases not only in the population of lung cancers but among all types of tumors. Enlightened by this existing fact, we would like to share our experience of management of an uncommon clavicular metastasis and illuminate the obscure mechanism of its scarcity.

Case presentation
A 56-year-old female without any preknown systemic disease had suffered from a sole intermittent right shoulder pain without any other discomfort for 3 months. Physical examination performed at our orthopedic department showed tenderness over the right distal third of the clavicle with limited range-of-motion of the right shoulder. EGFR-mutated lung adenocarcinoma with metastasis over the right clavicle resulting in a pathological fracture was diagnosed according to the result of the incisional biopsy. Concurrent chemoradiation therapy accompanied with target therapy was performed. Eighteen months postoperatively, the clavicle pain was found to be subsided with stationary bony lesion under appropriate medication and palliative radiotherapy during the subsequent follow-up.

Conclusions
The clavicle is an exceedingly unusual site with 2% of metastatic involvement of all type of tumors and only 1% among the population of carcinoma of lung due to its scanty red marrow and sparse vascular supply. Despite the unpleasant prognosis of clavicular metastasis from primary lung adenocarcinoma, promising quality of life is achievable under multidisciplinary management.
Impact of segmentation and discretization on radiomic features in 68Ga-DOTA-TOC PET/CT images of neuroendocrine tumor
Authors: Liberini Virginia , De Santi Bruno , Rampado Osvaldo , Gallio Elena , Dionisi Beatrice , Ceci Francesco , Polverari Giulia , Thuillier Philippe , Molinari Filippo , Deandreis Désirée 
Published: February 2021

Abstract
Objective
To identify the impact of segmentation methods and intensity discretization on radiomic features (RFs) extraction from 68Ga-DOTA-TOC PET images in patients with neuroendocrine tumors.

Methods
Forty-nine patients were retrospectively analyzed. Tumor contouring was performed manually by four different operators and with a semi-automatic edge-based segmentation (SAEB) algorithm. Three SUVmax fixed thresholds (20, 30, 40%) were applied. Fifty-one RFs were extracted applying two different intensity rescale factors for gray-level discretization: one absolute (AR60 = SUV from 0 to 60) and one relative (RR = min-max of the VOI SUV). Dice similarity coefficient (DSC) was calculated to quantify segmentation agreement between different segmentation methods. The impact of segmentation and discretization on RFs was assessed by intra-class correlation coefficients (ICC) and the coefficient of variance (COVL). The RFs’ correlation with volume and SUVmax was analyzed by calculating Pearson’s correlation coefficients.

Results
DSC mean value was 0.75 ± 0.11 (0.45–0.92) between SAEB and operators and 0.78 ± 0.09 (0.36–0.97), among the four manual segmentations. The study showed high robustness (ICC > 0.9): (a) in 64.7% of RFs for segmentation methods using AR60, improved by applying SUVmax threshold of 40% (86.5%); (b) in 50.9% of RFs for different SUVmax thresholds using AR60; and (c) in 37% of RFs for discretization settings using different segmentation methods. Several RFs were not correlated with volume and SUVmax.

Conclusions
RFs robustness to manual segmentation resulted higher in NET 68Ga-DOTA-TOC images compared to 18F-FDG PET/CT images. Forty percent SUVmax thresholds yield superior RFs stability among operators, however leading to a possible loss of biological information. SAEB segmentation appears to be an optimal alternative to manual segmentation, but further validations are needed. Finally, discretization settings highly impacted on RFs robustness and should always be stated.
The effect of clay content on the relation between uniaxial compressive strength and needle penetration index for clay-bearing rocks
Authors: Kahraman Sair , Aloglu A. Sercan , Saygin Egemen , Aydin Bilal 
Published: February 2021

AbstractThe needle penetration index (NPI) test is a non-destructive test that is applicable both in the field and laboratory, and does not require any special sample preparation. This test has been used for the estimation of physico-mechanical properties of soft rocks. In this study, the influence of the clay content on the relation between uniaxial compressive strength (UCS) and the NPI has been investigated for some clay-bearing rocks. The needle penetration tests were carried out at nine different gallery faces during the Cayirhan Coal Mine excavations, and the NPI values were calculated. Claystone, clayey limestone and clay blocks were collected from the locations on which the NPI tests were performed for the determination of rock strength and clay contents. The clay contents and clay fractions of the samples were determined using XRD analysis. A strong correlation has been found between the UCS and the NPI, but some of the data points were scattered. Strong correlations were also found between the NPI and both the total clay content and the smectite content. The UCS values were also strongly correlated to the total clay content and the smectite content. A multiple regression analysis was performed to determine the influence of clay content on the UCS-NPI relation and a very strong model was derived. The correlation coefficient of the multiple regression model is fairly higher than that of the UCS-NPI relation derived by using simple regression analysis. Concluding remark is that the clay content significantly affects the UCS-NPI relation in clay-bearing rocks.
Evolution of the ACSM Guidelines
Authors: Franklin Barry A. 
Published: February 2021

Apply it!
This article summarizes recent advances in exercise testing and prescription for varied populations, environments, and medical conditions, including brain-related diseases, as detailed in the just released 11th edition of ACSM’s Guidelines for Exercise Testing and Prescription.
▪ This article provides a historical perspective, new insights, and practical implications of the recently released 11th edition of ACSM’s Guidelines for Exercise Testing and Prescription.
▪ This article summarizes key recent findings relative to exercise testing, exercise training, and exercise prescription in the prevention and treatment of cardiovascular disease.
Post operative sore throat: Comparison between Macintosh versus Video Laryngoscope in patients intubated by trainee anaesthetists - A Randomised Control Trial
Authors: Kapadia Amin Ahmed , Shafiq Faraz , Raza Amir 
Published: February 2021

Objectives: Postoperative sore throat (POST) is a common complication related to endotracheal intubation. The aim of this study was to compare the incidence of POST in patients intubated by trainee anaesthetist using Video LaryngoscopeTM (VDL) or Conventional Macintosh Laryngoscope (CL).
Methods: Total 110 patient scheduled for elective laparoscopic cholecystectomy were included from main operating room of Aga Khan University Hospital between June 2017-2018. The standardized perioperative protocol was used for general anaesthesia. Selected patients were randomly allocated into conventional laryngoscopy (CL) group or video laryngoscopy (VDL) group. The evaluation of sore throat was done at 1st, 12th and 24th hour postoperatively using a ten-point visual analogue scale.
Results: The demographic characteristics, including intubation time, related complications or any other maneuver required were similar between the groups. The incidence of POST at 1st hour was 47% patients in CL group and 38% in VDL group (p=0.335). At 12th hour, 34.5% patients in CL and 38% in VDL reported POST (p=0.692). Similarly at 24th hour, 25% patients in CL and 16% in VDL group reported POST (p=0.669).
Conclusions: There was no significant difference in incidence of POST for patients intubated by trainee anaesthetists using either CL or VDL. Objective evidence of training and laryngoscope technique can impact of POST.
Registered at ClinicalTrials.gov Identifier: NCT04334616.
doi: https://doi.org/10.12669/pjms.37.3.3365
How to cite this:Kapadia AA, Shafiq F, Raza A. Post operative sore throat: Comparison between Macintosh versus Video Laryngoscope in patients intubated by trainee anaesthetists - A Randomised Control Trial. Pak J Med Sci. 2021;37(3):764-769. doi: https://doi.org/10.12669/pjms.37.3.3365
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Resilience and its relationship with spiritual wellbeing among patients with heart failure
Authors: Razaghpoor Ali , Rafiei Hossein , Taqavi Fateme , Hashemi Seyedeh Mahnaz 
Published: February 2021

Background/Aims The importance of resilience among patients with chronic diseases has been demonstrated, but rarely among patients with heart failure. This study examines resilience and its relationship with spiritual wellbeing among this patient group. Methods This descriptive study was carried out with 130 patients with heart failure in Iran. The tools used were a 29-item resilience scale and the Paloutzian and Ellison Spiritual Wellbeing scale. Results The average resilience score was 107±19.5. Among the demographic variables, age, education, duration of disease and the presence of other concomitant diseases were significantly correlated with the patients' total resilience scores (P<0.05). The average spiritual wellbeing score was 83.12, with results showing a significant and direct relationship between resilience and spiritual wellbeing (P=0.001, r=0.386). Conclusions: Levels of resilience have a strong relationship with spiritual wellbeing among patients with heart failure. Therefore, building resilience should be incorporated into holistic care of these patients.
Challenges and opportunities identified for lymphoedema services in Wales during the COVID-19 pandemic
Authors: Gabe-Walters Marie , Noble-Jones Rhian 
Published: February 2021

Background: During the COVID-19 pandemic, lymphoedema staff adapted services, providing care remotely, and worked in other NHS sectors. The impact on services and staff must be understood in order to safeguard patient care and foster workforce resilience. Aims: To evaluate the experiences of clinical and non-clinical lymphoedema staff in Wales during the COVID-19 pandemic. Methods: An anonymous online survey, based on scoping work, was sent out via the Welsh lymphoedema services mailing list. Findings: 71% (68/96) of eligible lymphoedema staff completed the survey. More than half supported lymphoedema services (40/68) with the remaining staff deployed elsewhere. Overall, staff and services felt prepared for new ways of working. Concerns about others and the future burden on services when life returned to normal were reported. Opportunities identified included education initiatives and virtual services. Conclusion: Lymphoedema services were well prepared to deliver virtually, enable effective care and share knowledge. Co-ordinated efforts to uphold patient advocacy will support virtual services to meet their needs.
Heavy Alcohol Use Is Associated With Gastric Cancer: Analysis of the National Health and Nutrition Examination Survey From 1999 to 2010
Authors: Laszkowska Monika , Rodriguez Steven , Kim Judith , Hur Chin 
Published: February 2021

INTRODUCTION:
Evidence regarding the association between alcohol use and gastric cancer (GC) has been inconsistent.

METHODS:
Adults who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2010 were included. Multivariable regression was used to assess the association between GC and heavy alcohol use (≥5 alcoholic drinks daily).

RESULTS:
Of 470,168 individuals surveyed, 342 had a history of GC. Heavy alcohol use was associated with GC (odds ratio 3.13, 95% confidence interval 1.15–8.64) on multivariable analysis.

DISCUSSION:
This is the largest study to our knowledge to demonstrate an association between heavy alcohol use and GC in the United States.
Bone Marrow Suppression Associated With Celiac Disease in a 4-Year-Old Boy
Authors: Watson Ashleigh , Kolinski Julie , Suchi Mariko , Elkadri Abdul 
Published: February 2021

ABSTRACT
Celiac disease is an immune-mediated process against gluten, resulting in inflammation and villous atrophy of the duodenum. Symptoms of malabsorption characterize the classic presentation; however, abdominal pain, constipation, and nutritional deficiencies can also be seen. We present a case of a 4-year-old boy who was found to have celiac disease after presenting with diarrhea, abdominal pain, weight loss, and new-onset pancytopenia. Symptoms resolved, and laboratory values normalized after the initiation of a gluten-free diet, indicating the bone marrow suppression was due to celiac disease, which needs to be considered when hematologic abnormalities are present, even in the absence of gastrointestinal symptoms.
The Pillow Sign: Is It Always Benign?
Authors: Alvencar Sujay , Holzwanger Erik , Dhingra Rohit , Karagozian Raffi , Olans Lori , Natov Nikola S. 
Published: February 2021

ABSTRACT
Mucosa-associated lymphoid tissue (MALT) lymphoma is classically found in the stomach; however, in less common, cases can be found in extragastric locations. Colonic MALTomas are exceedingly rare and comprise a small group of extragastric cases. There is no standardized approach for optimal management of this disease. We report a case of a colonic MALT lymphoma found on colonoscopy that demonstrated the pillow sign and appearance of a benign lipoma. Despite antimicrobial and endoscopic therapy, the malignancy reoccurred in a patient with chronic hepatitis B, thereby precluding one of the mainstays of treatment, rituximab, until viral eradication.