bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pipeline for targeted metagenomics of environmental bacteria
Authors: Grieb Anissa , Bowers Robert M. , Oggerin Monike , Goudeau Danielle , Lee Janey , Malmstrom Rex R. , Woyke Tanja , Fuchs Bernhard M. 
Published: February 2020

Abstract
Background
Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses.

Methods
Cells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity.

Results
Pure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade.

Conclusions
With the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades.
A thermo-elastoplastic self-consistent homogenization method for inter-granular plasticity with application to thermal ratcheting of TATB
Authors: Bennett Kane C. , Zecevic Miroslav , Luscher Darby J. , Lebensohn Ricardo A. 
Published: February 2020

AbstractA novel thermo-elastoplastic self-consistent homogenization model for granular materials that exhibit inter-granular plasticity is presented. The model, TEPSCA, is made possible by identifying a new inter-granular plastic Eshelby-like tensor. A micromechanical model of interfacial yielding between grains of a Mohr–Coulomb type is provided, which is relatable to the description of imperfect interfaces within the paradigm of self-consistent homogenization. The local grain constitutive laws are consistent with the description of an interphase layer comprised of local pore volume between grains, such that inelastic inter-particle displacements are directly relatable to changes in bulk porosity, i.e., dilation. The model was developed for the purpose of modeling thermally induced plasticity—the phenomenon known as thermal ratcheting or “ratchet growth”—of composites made from the high explosive triaminotrinitrobenzene (TATB). Model simulations are compared to ratchet growth measurements during cyclic thermal loading of a TATB pellet under stress-free conditions.
Enriched homogenized model for viscoelastic plane wave propagation in periodic layered composites
Authors: Tan Swee Hong , Poh Leong Hien 
Published: February 2020

AbstractAn enriched homogenized model is developed based on a proposed homogenization strategy, to describe the wave propagation behaviour through periodic layered composites. The intrinsic parameters characterising the micro-inertia effect and non-local interactions are defined transparently in terms of the constituent materials’ properties and volume fractions. The framework starts with the introduction of an additional kinematic field to characterise the displacement of the stiff layer, before setting up macro kinematic fields to account for the average deformation of the constituent materials within a segmented unit cell. Relationships between these macro average strain fields are determined based on suitable micro-mechanical arguments. The Hill–Mandel condition is next applied to translate the energy statements from micro to macro. A system of coupled governing equations of motion is finally extracted naturally at the macro level via Hamilton’s Principle. Through a series of benchmark examples, it is shown that the proposed model exhibits excellent predictive capabilities over a broad range of loading frequencies.
Top online luxury apparel and accessories retailers: what are they doing right?
Authors: Mu Wenzhao , Lennon Sharron J. , Liu Wenqiao 
Published: February 2020

AbstractMany luxury firms have successfully adopted online sales and online sales growth has outperformed offline sales growth. As online luxury sales continue to grow, service expectations in digital and instore channels are also expected to grow. To add to the research literature, the top performing 46 luxury apparel and accessories websites identified in the Luxury e-Commerce Report from Internet Retailer were content analyzed to determine the state of the art in top performing luxury retail websites in providing needed information (international customer service attributes). Those top performing websites were then compared to 44 randomly selected similar websites on the same attributes to determine how the two groups of websites compared in terms of international customer service attributes. Although top performing luxury retail websites are providing important customer service information that facilitates online purchasing, there is room for improvement. In comparing the two groups of online luxury merchants, each group had strengths and weaknesses. Overall, merchants performed at a suboptimal level on provision of many customer service attributes, need improvement on others, and performed well on a few attributes. These luxury fashion online retailers are at an early stage in providing important customer service attributes on their websites.
The association of urinary uric acid excretion with ambulatory blood pressure values in patients with chronic kidney disease
Authors: Xu Ying , Zhou Xun , Zheng Yuqi , Guan Haochen , Fu Chensheng , Xiao Jing , Ye Zhibin 
Published: February 2020

Abstract
Background
To analyze the association between hypertension and urinary uric acid excretion in patients with chronic kidney disease (CKD).

Methods
We screened 87 patients who had been admitted at the Dept of Nephrology, Huadong hospital between April 2017 to April 2019 who had completed 24-h ambulatory blood pressure monitoring and retained 24-h urine biochemical test specimens, thirty adult patients (age ≤ 65 years) with CKD 1–2 stages were recruited in the study. Pearson’s correlation analysis and multiple linear regression analysis were used to study the correlation of urinary uric acid excretion with ambulatory blood pressure values and the association of morning mean diastolic pressure (mMDP), night mean diastolic pressure (nMDP) and CV of dMSP (coefficient of variation of day mean systolic pressure) with fractional excretion of uric acid (FEua) and uric acid clearance rate (Cur). Independent T test was used to compare the differences of blood pressure values in FEua1 (FEua< 6.0%) and FEua2 (FEua≥6.0%) or Cur1 (Cur < 6.2 ml/min/1.73 m2) and Cur2 (Cur ≥ 6.2 ml/min/1.73m2) groups according to the median of FEua or Cur, respectively.

Results
After adjusting for confounding factors, multiple linear regression analysis showed that FEua was positively associated with the mMDP and nMDP, Cur was positively associated with CV of dMSP. Levels of mMDP and nMDP in FEua1 group was lower than that in FEua2 group (both P < 0.05), level of CV of dMSP in Cur2 group were higher than that in Cur1 group (P < 0.01).

Conclusions
We demonstrated that there is a positive correlation of FEua with morning and night mean diastolic pressure separately and Cur is positively related to CV of dMSP in CKD population. Monitoring the trend of urinary uric acid, may have a role in the early detection for hypertension or relative risks in the population of CKD.
Painful myokymia after surgery in a patient with Isaacs’ syndrome: a case report
Authors: Okutani Hiroai , Okano Yukari , Hirose Munetaka 
Published: February 2020

Abstract
Background
Isaacs’ syndrome is a peripheral nerve hyperexcitability syndrome and rare acquired channel disease. The symptoms (myokymia, neuromyotonia, and muscle spasm) emerge even during sleep. This report describes the anesthetic management, especially neuromuscular blocking drugs and postoperative pain, in a case of Isaacs’ syndrome.

Case presentation
A 63-year-old woman with Isaacs’ syndrome underwent elective laparoscopic distal gastrectomy under general anesthesia without epidural anesthesia. She received double filtration plasmapheresis four times to alleviate symptoms before surgery. To avoid a prolonged neuromuscular blockade, we performed total intravenous anesthesia and titrated muscle relaxant with neuromuscular monitoring. Anesthetic management was performed without any problems. However, pain management after surgery proved difficult as she experienced severe pain due to myokymia.

Conclusions
Despite attempts to minimize symptoms, severe postoperative pain associated with myokymia occurred. Continuous regional anesthesia should be considered to treat pain from abnormal discharge in the central nervous system in Isaacs’ syndrome.
Molecular Basis of CYP19A1 Deficiency in a 46,XX Patient With R550W Mutation in POR: Expanding the PORD Phenotype
Authors: Parween Shaheena , Fernández-Cancio Mónica , Benito-Sanz Sara , Camats Núria , Rojas Velazquez Maria Natalia , López-Siguero Juan-Pedro , Udhane Sameer S , Kagawa Norio , Flück Christa E , Audí Laura , Pandey Amit V 
Published: February 2020

Abstract

Context
Mutations in cytochrome P450 oxidoreductase (POR) cause a form of congenital adrenal hyperplasia (CAH). We report a novel R550W mutation in POR identified in a 46,XX patient with signs of aromatase deficiency.

Objective
Analysis of aromatase deficiency from the R550W mutation in POR.

Design, setting, and patient
Both the child and the mother had signs of virilization. Ultrasound revealed the presence of uterus and ovaries. No defects in CYP19A1 were found, but further analysis with a targeted Disorders of Sexual Development NGS panel (DSDSeq.V1, 111 genes) on a NextSeq (Illumina) platform in Madrid and Barcelona, Spain, revealed compound heterozygous mutations c.73_74delCT/p.L25FfsTer93 and c.1648C &gt; T/p.R550W in POR. Wild-type and R550W POR were produced as recombinant proteins and tested with multiple cytochrome P450 enzymes at University Children’s Hospital, Bern, Switzerland.

Main outcome measure and Results
POR-R550W showed 41% of the WT activity in cytochrome c and 7.7% activity for reduction of MTT. Assays of CYP19A1 showed a severe loss of activity, and CYP17A1 as well as CYP21A2 activities were also lost by more than 95%. Loss of CYP2C9, CYP2C19, and CYP3A4 activities was observed for the R550W-POR. Predicted adverse effect on aromatase activity as well as a reduction in binding of NADPH was confirmed.

Conclusions
Pathological effects due to POR-R550W were identified, expanding the knowledge of molecular pathways associated with aromatase deficiency. Screening of the POR gene may provide a diagnosis in CAH without defects in genes for steroid metabolizing enzymes.
Loss-of-Function Variants in TBC1D32 Underlie Syndromic Hypopituitarism
Authors: Hietamäki Johanna , Gregory Louise C , Ayoub Sandy , Iivonen Anna-Pauliina , Vaaralahti Kirsi , Liu Xiaonan , Brandstack Nina , Buckton Andrew J , Laine Tiina , Känsäkoski Johanna , Hero Matti , Miettinen Päivi J , Varjosalo Markku , Wakeling Emma , Dattani Mehul T , Raivio Taneli 
Published: February 2020

Abstract

Context
Congenital pituitary hormone deficiencies with syndromic phenotypes and/or familial occurrence suggest genetic hypopituitarism; however, in many such patients the underlying molecular basis of the disease remains unknown.

Objective
To describe patients with syndromic hypopituitarism due to biallelic loss-of-function variants in TBC1D32, a gene implicated in Sonic Hedgehog (Shh) signaling.

Setting
Referral center.

Patients
A Finnish family of 2 siblings with panhypopituitarism, absent anterior pituitary, and mild craniofacial dysmorphism, and a Pakistani family with a proband with growth hormone deficiency, anterior pituitary hypoplasia, and developmental delay.

Interventions
The patients were investigated by whole genome sequencing. Expression profiling of TBC1D32 in human fetal brain was performed through in situ hybridization. Stable and dynamic protein-protein interaction partners of TBC1D32 were investigated in HEK cells followed by mass spectrometry analyses.

Main Outcome Measures
Genetic and phenotypic features of patients with biallelic loss-of-function mutations in TBC1D32.

Results
The Finnish patients harboured compound heterozygous loss-of-function variants (c.1165_1166dup p.(Gln390Phefs*32) and c.2151del p.(Lys717Asnfs*29)) in TBC1D32; the Pakistani proband carried a known pathogenic homozygous TBC1D32 splice-site variant c.1372 + 1G &gt; A p.(Arg411_Gly458del), as did a fetus with a cleft lip and partial intestinal malrotation from a terminated pregnancy within the same pedigree. TBC1D32 was expressed in the developing hypothalamus, Rathke’s pouch, and areas of the hindbrain. TBC1D32 interacted with proteins implicated in cilium assembly, Shh signaling, and brain development.

Conclusions
Biallelic TBC1D32 variants underlie syndromic hypopituitarism, and the underlying mechanism may be via disrupted Shh signaling.
Outcome of management of brain abscess in children
Authors: Khan Ikram Ullah , Latif Abdul , Ashraf Muhammad , Chishti Muhammad Kashif , Sadiq Sadia 
Published: February 2020

Objective: To find out the outcome of management of brain abscess in children.
Methods: This is prospective observational study conducted in the Department of Paediatric Neurosurgery at Children’s Hospital and Institute of Child Health, Multan from July 2014 to June 2017. Children up to the age of 14 years suffering from brain abscess were admitted. After taking clinical history, general and systemic physical examination and necessary investigations, abscess was evacuated and abscess wall excised after performing craniotomy. Data was collected on a predesigned performa. Results were analyzed and compared with national and international literature through statistical package for social sciences (SPSS-20).
Results: Twenty five patients up to 14 years of age were included. Seventeen (68%) were male and eight (32%) female. Fever and vomiting were present in all 25 (100%) patients. Paranasal sinusitis was predisposing causative factor in 9(36%) followed by otitis media in 7 (28%). Abscess was present in frontal lobe in 9 (36%), temporoparietal region in 8 (32%), posterior fossa in 5 (20%) and multiple abscesses in 3 (12%). Craniotomy was performed, pus evacuated and abscess wall excised in all 25 (100%) patients. Three (12%) patients expired.
Conclusion: Incidence of brain abscess can be decreased by treatment of its predisposing causes as sinusitis and otitis media. Small abscess less than 2cm can be treated with antibiotics. Complete evacuation of pus and excision of abscess wall after performing craniotomy along with appropriate antibiotics is gold standard management of brain abscess in children.
doi: https://doi.org/10.12669/pjms.36.3.1087
How to cite this:Khan IU, Latif A, Ashraf M, Chishti MK, Sadiq S. Outcome of management of brain abscess in children. Pak J Med Sci. 2020;36(3):306-309. doi: https://doi.org/10.12669/pjms.36.3.1087
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.
Role of Methyl Prednisolone in Longitudinal Extensive Transverse Myelitis (LETM) in Children
Authors: Ashfaq Muhammad Azeem , Javed Iram , Arshad Muhammad , Yaseen Muhammad Rizwan 
Published: February 2020

Objective: The role of methyl prednisolone in longitudinal extensive transverse myelitis in children is not completely discovered in developing country like Pakistan. So this is the first study which aimed to evaluate the efficacy of methyl prednisolone in longitudinal extensive transverse myelitis in children.
Methods: This is quasi experimental hospital based descriptive prospective study. The data was collected from 34 children admitted in Paediatric Neurology department through Outpatient/emergency department in Children’s Hospital and the Institute of Child Health, Lahore for period of one year from January 2018 to December 2018. The children full filling the inclusion criteria were observed before and after giving injection methyl prednisolone 30mg/kg/dose (maximum dose one Gram irrespective of the body weight) once daily for five days in the form of intravenous infusion.
Results: Complete recovery was seen in 41.2% while 58.8% showed partial recovery. The correlation of response to treatment (recovery) with gender, area of spinal cord involvement, muscle power and autonomic dysfunction is found at significance level of five percent according to Chi square test.
Conclusion: Early consideration and administration of methyl prednisolone in longitudinally extensive transverse myelitis in children can be beneficial and can help to reduce the morbidity.
doi: https://doi.org/10.12669/pjms.36.3.1232
How to cite this:Ashfaq MA, Javed I, Arshad M, Yaseen MR. Role of Methyl Prednisolone in Longitudinal Extensive Transverse Myelitis (LETM) in Children. Pak J Med Sci. 2020;36(3):451-455. doi: https://doi.org/10.12669/pjms.36.3.1232
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.
Prevalence of Vitamin-D deficiency is related to severity of liver damage in Hepatitis-C patients
Authors: Falak Sadia , Aftab Lubna , Saeed Muhammad , Islam Aftab 
Published: February 2020

Objective: Serum Vitamin-D plays pivotal role in inflammatory and infectious diseases; among them liver infections are more distinct. This study was aimed to determine Vitamin-D status in HCV-infected patients and healthy controls in Faisalabad, Pakistan.
Methods: We performed randomized cross-sectional study of 74 individuals from 20th August, 2017 to 20th February 2018 at The University of Faisalabad and Dar us Shifa Clinic, Faisalabad. Fifty-one patients were hepatitis C RNA-PCR positive (22 compensated cirrhotic and 29 decompensated cirrhotic patients). In addition, 23 subjects without liver disease were recruited as healthy control. HCV RNA–PCR was performed by ARTUS ® HCV QS-RGQ V1. Vitamin-D levels were measured by chemiluminescence. SPSS version 20 was used for statistical analysis.
Results: The mean level of Vitamin-D was significantly lower in HCV patients in compensated and decompensated cirrhotic patients (26.85 ng/mL & 20.65 ng/mL respectively) as compared to healthy controls (30.41 ng/mL). This study showed sub optimal level of Vitamin-D in 76.5% of HCV patients. Vitamin-D insufficiency (21-29 ng/mL) as prevalent among healthy individuals (47.8%) as well as in HCV patients (39.2%) (P < 0.001). In addition, Vitamin-D levels showed inverse relationship with more severe conditions of liver disease as 55.2% of decompensated cirrhosis patients were sufferer of Vitamin-D deficiency as compared to 13.6% deficiency of Vitamin-D in compensated cirrhotic group (P <0.0001).
Conclusion: Suboptimal levels of Vitamin-D (deficiency or insufficiency) are prevalent in patients having hepatitis C infection as compared to healthy controls. Deficiency of Vitamin-D was directly associated with severity of disease.
doi: https://doi.org/10.12669/pjms.36.3.1490
How to cite this:Falak S, Aftab L, Saeed M, Islam A. Prevalence of Vitamin-D deficiency is related to severity of liver damage in Hepatitis-C patients. Pak J Med Sci. 2020;36(3):445-450. doi: https://doi.org/10.12669/pjms.36.3.1490
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.
Association of lamina cribrosa morphometry with retinal nerve fiber layer loss and visual field defects in primary open angle glaucoma
Authors: Naz Ayesha Saba , Qamar Aisha , Haque Sama Ul , Zaman Yawar , Faheem Faisal 
Published: February 2020

Objectives: To calculate the anterior lamina cribrosa depth (ALCD) and lamina cribrosa thickness (LCT) in primary open angle glaucoma (POAG) patients and controls and to correlate lamina cribrosa (LC) parameters to retinal nerve fiber layer thickness (RNFLT) and visual field (VF) defects.
Methods: The study was conducted from November 2018 to March 2019. A total of 60 correspondents (30 cases and 30 controls) were assessed for general ophthalmological investigations including intraocular pressure (IOP), axial length AXL, ophthalmoscopy, visual field (VF) testing and spectral domain ocular computed tomography (SDOCT).
Results: The mean age of subjects was 62 years (Cases 67.30±1.2, controls 57.32±1.1) with more male participants. Intraocular pressure [IOP (19.85 ±1.4)], AXL (22.85 ± 1.6), VF defects (8.30 ± 4.5), RNFLT (72.58 ± 13.2) and LCT (162.51 ± 64.62) were statistically significant in POAG patients as compared to the controls.
Conclusion: A thinner LC in POAG correlated significantly with the RNFLT and VF defects. LC anatomical parameters can be estimated with precision using SDOCT with enhanced depth imaging (EDI).
doi: https://doi.org/10.12669/pjms.36.3.1553
How to cite this:Naz AS, Qamar A, Sama-Ul-Haque, Zaman Y, Faheem F. Association of lamina cribrosa morphometry with retinal nerve fiber layer loss and visual field defects in primary open angle glaucoma. Pak J Med Sci. 2020;36(3):521-525. doi: https://doi.org/10.12669/pjms.36.3.1553
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.