bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures
Authors: Suphavilai Chayaporn , Chia Shumei , Sharma Ankur , Tu Lorna , Da Silva Rafael Peres , Mongia Aanchal , DasGupta Ramanuj , Nagarajan Niranjan 
Published: December 2021

AbstractWhile understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of cancer omics datasets, we highlight the importance of intra-tumor transcriptomic heterogeneity (ITTH) for predicting clinical outcomes. Leveraging single-cell RNA-seq (scRNA-seq) with a recommender system (CaDRReS-Sc), we show that heterogeneous gene-expression signatures can predict drug response with high accuracy (80%). Using patient-proximal cell lines, we established the validity of CaDRReS-Sc’s monotherapy (Pearson r>0.6) and combinatorial predictions targeting clone-specific vulnerabilities (>10% improvement). Applying CaDRReS-Sc to rapidly expanding scRNA-seq compendiums can serve as in silico screen to accelerate drug-repurposing studies. Availability: https://github.com/CSB5/CaDRReS-Sc.
Thymoma may explain the confusion: a case report
Authors: Maaroufi Abdelkhaleq , Assoufi Naoufal , Essaoudi Mohamed Amine , Fatihi Jamal 
Published: December 2021

Abstract
Background
The association of inflammatory myopathy and myasthenia gravis is a rarely described entity whose clinical presentation has always been intriguing because of the great clinical similarity between these two pathologies. The presence of a thymic pathology often explains this combination, whose mechanisms are very complex.

Case presentation
A 56-year-old woman of North African origin, was hospitalized to explore the Raynaud phenomenon associated with proximal muscle weakness, pain, and arthralgia. There was no rash, and neuromuscular examination had revealed proximal tetraparesis and mild neck weakness. Tendon reflexes were normal. There was no abnormal nail fold capillaroscopy. A significant titer of muscle enzymes had been shown on blood tests, and autoimmune screening for myositis-specific and myositis-associated autoantibodies was negative. Electromyography had shown a myopathic pattern, and muscle biopsy confirmed an inflammatory myopathy. Although steroids were introduced, the clinical course was unsatisfactory; ophthalmic and bulbar symptomatology appeared. The association of myasthenia gravis was confirmed by an elevated level of serum acetylcholine receptor. A chest computed tomography scan had identified a thymoma. Treated with prednisone, pyridostigmine, and thymectomy, the patient’s clinical and biological evolution was favorable.

Conclusion
This case illustrates an exceptional association of two entities and the difficulty encountered during their diagnosis and treatment. The management of these two diseases is different, so it is essential to recognize this concomitant presentation.
Prevalence and predictors of self-medication among university students in Ethiopia: a systematic review and meta-analysis
Authors: Fetensa Getahun , Tolossa Tadesse , Etafa Werku , Fekadu Ginenus 
Published: December 2021

Abstract
Background
Self-medication of medicines is a global issue particularly among those with good access and familiarity with medications such as university students. It has a significant impact on drug resistance and medication-related complications. There are limited and inconsistent studies on self-medication practices in Ethiopia. The aim of this systematic review and meta-analysis was to estimate the pooled prevalence of self-medication and its predictors among university students in Ethiopia.

Methods
A systematic review and meta-analysis was conducted to assess the prevalence and predictors of self-medication among university students in Ethiopia. Published articles from various electronic databases such as Medline, Hinari, Pub Med, Cochrane library, and the Web of Science were accessed. In addition, a manual search was performed including Google Scholar. Searching of articles were searched from January 1st to February 1, 2021. All observational studies conducted among university students in English language were included in the review. Two reviewers independently assessed articles before inclusion in the final review using the Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument (JBI-MAStARI) instrument for critical appraisal. The I2 test was used to assess heterogeneity. Since the included studies exhibited high heterogeneity, a random-effects model was used to estimate the pooled prevalence of self-medication.

Results
We found of 812 published and unpublished studies in our search. Finally, 31 full-text studies were reviewed, and 13 studies fulfilled the inclusion criteria and were included in the final meta-analysis. A total of 5377 study respondents from 13 studies were included in the study. The results of our study revealed that the pooled prevalence of self-medication among university students was 49.41% (95% CI 38.67%, 60.13%). The included studies had a sample size ranging from 250 to 792 with the lowest prevalence (19.87%) of self-medication from the University of Gondar, whereas the highest prevalence (77.01%) was recorded in a study conducted at Arsi University. From the pooled estimation, there was a significant association between self-medication and income (OR = 0.67: 95% CI 0.55–0.80). However, the association between self-medication and year of study and sex of participants was insignificant.

Conclusion
The pooled prevalence of self-medication among Ethiopian university students was relatively high compared to the current global health problem with an increase in anti-microbial resistance. Health professionals and concerned bodies should pay attention to raising awareness regarding the consequences of using medications without prescription.
Immobilization of transaminase from Bacillus licheniformis on copper phosphate nanoflowers and its potential application in the kinetic resolution of RS-α-methyl benzyl amine
Authors: Lambhiya Shraddha , Patel Gopal , Banerjee Uttam Chand 
Published: December 2021

AbstractThis study reports the isolation and partial purification of transaminase from the wild species of Bacillus licheniformis. Semi-purified transaminase was immobilized on copper nanoflowers (NFs) synthesized through sonochemical method and explored it as a nanobiocatalyst. The conditions for the synthesis of transaminase NFs [TA@Cu3(PO4)2NF] were optimized. Synthesized NFs revealed the protein loading and activity yield—60 ± 5% and 70 ± 5%, respectively. The surface morphology of the synthesized hybrid NFs was examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), which revealed the average size to be around 1 ± 0.5 μm. Fourier-transform infrared (FTIR) was used to confirm the presence of the enzyme inside the immobilized matrix. In addition, circular dichroism and florescence spectroscopy were also used to confirm the integrity of the secondary and tertiary structures of the protein in the immobilized material. The transaminase hybrid NFs exhibited enhanced kinetic properties and stability over the free enzyme and revealed high reusability. Furthermore, the potential application of the immobilized transaminase hybrid NFs was demonstrated in the resolution of racemic α-methyl benzylamine.
Graphical Abstract
Revisiting a low-dimensional model with short range interactions and mean field critical behavior
Authors: Grassberger Peter 
Published: December 2021

Abstract
In all local low-dimensional models, scaling at critical points deviates from mean ﬁeld behavior – with one possible exception. This exceptional model with “ordinary” behavior is an inherently non-equilibrium model studied some time ago by H.-M. Bröker and myself. In simulations, its 2-dimensional version suggested that two critical exponents were mean-ﬁeld, while a third one showed very small deviations. Moreover, the numerics agreed almost perfectly with an explicit mean ﬁeld model. In the present paper we present simulations with much higher statistics, both for 2d and 3d. In both cases we ﬁnd that the deviations of all critical exponents from their mean ﬁeld values are non-leading corrections, and that the scaling is precisely of mean ﬁeld type. As in the original paper, we propose that the mechanism for this is “confusion”, a strong randomization of the phases of feed-backs that can occur in non-equilibrium systems.
The Learning of the Mind as an Ideological Movement: Probing the Historical Origins of the School of Wang Yangming
Authors: Kun Jiao 
Published: December 2021

Abstract
As an influential scholar, the Ming 明 Neo-Confucian master Wang Yangming 王陽明 (1472–1529) was also active in the political world. While showing philosophical ingenuity, Wang launched an ideological movement which reached beyond Neo-Confucian discourse and into the social and political spheres. By promoting his xinxue 心學 teachings, Wang aimed to change Ming political life through fostering a moral retrenchment among future officials. To achieve his goals, Wang Yangming implemented several strategies, such as turning to humble local literati for a following, teaching them as a sitting official, and supporting nonofficial academies with his political power. These strategies succeeded to some extent, in part because the Ming court had relaxed the ideological intolerance of the early Ming. The real-world background of Wang Yangming's success can be further explored by comparing Wang with his two predecessors, Xue Xuan 薛瑄 (1389–1464) and Wu Yubi 吳與弼 (1391–1469).
Recurrent Low-Grade Gliomas: Does Reoperation Affect Neurocognitive Functioning?
Authors: Ng Sam , Lemaitre Anne-Laure , Moritz-Gasser Sylvie , Herbet Guillaume , Duffau Hugues 
Published: December 2021

BACKGROUND:
Reoperations in patients with recurrent low-grade gliomas (RLGG) were proposed to control tumor residual and delay the risk of malignant transformation over time.

OBJECTIVE:
To investigate neurocognitive outcomes in patients with RLGG who underwent a second surgery with awake monitoring.

METHODS:
In this retrospective study, patients who underwent a second awake surgery for RLGG were included. Patients had presurgical and 3-mo postsurgical neuropsychological assessments. Data were converted into Z-scores and combined by the cognitive domain. Number of patients with cognitive deficits (Z-score <−1.65), variations of Z-scores, and extent of resection (EOR) were analyzed.

RESULTS:
Sixty-two patients were included (mean age: 41.2 ± 10.0 yr). None had permanent neurological deficits postoperatively. Eight patients (12.9%) had a cognitive deficit preoperatively. Four additional patients (6.5%) had a cognitive deficit 3 mo after reoperation. Among other patients, 13 (21.0%) had a mild decline without cognitive deficits while 29 (46.8%) had no change of their performances and 8 (12.9%) improved. Overall, 94.2% of the patients returned to work. There were no correlations between EOR and Z-scores. Total/subtotal resections were achieved in 91.9% of the patients (mean residual: 3.1 cm3). Fifty-eight patients (93.5%) were still alive after an overall follow-up of 8.3 yr.

CONCLUSION:
Reoperation with awake monitoring in patients with RLGG was compatible with an early recovery of neuropsychological abilities. Four patients (6.5%) presented a new cognitive deficit at 3 mo postoperatively. Total/subtotal resections were achieved in most patients. Based on these favorable outcomes, reoperation should be considered in a more systematic way.
Genetic variation in haemoglobin is associated with evolved changes in breathing in high-altitude deer mice
Authors: Ivy Catherine M. , Wearing Oliver H. , Natarajan Chandrasekhar , Schweizer Rena M. , Gutiérrez-Pinto Natalia , Velotta Jonathan P. , Campbell-Staton Shane C. , Petersen Elin E. , Fago Angela , Cheviron Zachary A. , Storz Jay F. , Scott Graham R. 
Published: December 2021

ABSTRACT
Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated whether genetic variants in haemoglobin (Hb) that contribute to high-altitude adaptation in deer mice (Peromyscus maniculatus) are associated with evolved changes in the control of breathing. We created F2 inter-population hybrids of highland and lowland deer mice to test for phenotypic associations of α- and β-globin variants on a mixed genetic background. Hb genotype had expected effects on Hb–O2 affinity that were associated with differences in arterial O2 saturation in hypoxia. However, high-altitude genotypes were also associated with breathing phenotypes that should contribute to enhancing O2 uptake in hypoxia. Mice with highland α-globin exhibited a more effective breathing pattern, with highland homozygotes breathing deeper but less frequently across a range of inspired O2, and this difference was comparable to the evolved changes in breathing pattern in deer mouse populations native to high altitude. The ventilatory response to hypoxia was augmented in mice that were homozygous for highland β-globin. The association of globin variants with variation in breathing phenotypes could not be recapitulated by acute manipulation of Hb–O2 affinity, because treatment with efaproxiral (a synthetic drug that acutely reduces Hb–O2 affinity) had no effect on breathing in normoxia or hypoxia. Therefore, adaptive variation in Hb may have unexpected effects on physiology in addition to the canonical function of this protein in circulatory O2 transport.
Contributions to medical literature by Indus Hospital Health Network through Research
Authors: Jawaid Shaukat Ali 
Published: December 2021

doi: https://doi.org/10.12669/pjms.38.ICON-2022.5757
How to cite this:Jawaid SA. Contributions to medical literature by Indus Hospital Health Network through Research. Pak J Med Sci. 2022;38(2):331-332. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5757
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.
Rapidly progressive glomerulonephritis in children
Authors: Moorani Khemchand N , Aziz Madiha , Amanullah Farhana 
Published: December 2021

Rapidly progressive glomerulonephritis (RPGN), characterized by a rapid development of nephritis with loss of kidney function in days or weeks, is typically associated histologically, with crescents in most glomeruli; and is a challenging problem, particularly in low resource settings. RPGN is a diagnostic and therapeutic emergency requiring prompt evaluation and treatment to prevent poor outcomes. Histopathologically, RPGN consists of four major categories, anti-glomerular basement membrane (GBM) disease, immune complex mediated, pauci-immune disorders and idiopathic /overlap disorders. Clinical manifestations include gross hematuria, proteinuria, oliguria, hypertension and edema. Diagnostic evaluation, including renal function tests, electrolytes, urinalysis/microscopy and serology including (anti GBM antibody, antineutrophil cytoplasmic antibody (ANCA)) starts simultaneously with management. An urgent renal biopsy is required to allow specific pathologic diagnosis as well as to assess disease activity and chronicity to guide specific treatment. The current guidelines for management of pediatric RPGN are adopted from adult experience and consist of induction and maintenance therapy. Aggressive combination immunosuppression has markedly improved outcomes, however, nephrotic syndrome, severe acute kidney injury requiring dialysis, presence of fibrous crescents and chronicity are predictors of poor renal survival. RPGN associated post infectious glomerulonephritis (PIGN) usually has good prognosis in children without immunosuppression whereas immune-complex-mediated GN and lupus nephritis (LN) are associated with poor prognosis with development of end stage kidney disease (ESKD) in more than 50% and 30% respectively. Given the need for prompt diagnosis and urgent treatment to avoid devastating outcomes, we conducted a review of the latest evidence in RPGN management to help formulate clinical practice guidance for children in our setting.Information sources and search strategy: The search strategy was performed in the digital databases of PubMed, Cochrane Library, google scholar, from their inception dates to December 2020. Three investigators independently performed a systematic search using the following search terms “Rapidly progressive glomerulonephritis” “children” “crescentic glomerulonephritis” “management” at the same time, backtracking search for references of related literature.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5774
How to cite this:Moorani KN, Aziz M, Amanullah F. Rapidly progressive glomerulonephritis in children. Pak J Med Sci. 2022;38(2):417-425. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5774
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.
The Effects of live- in rehabilitation on ARV adherence, abstinence from drugs and lifestyle modification in people who inject drugs (PWID) Living with HIV – A clinic review
Authors: Hussain Aneela , Rahim Anum , Sheikh Anila , Jiwani Ahsun 
Published: December 2021

Background & Objective: HIV/AIDS is mostly seen in people who inject recreational drugs (PWID). Adherence has to be optimum for its treatment to be effective. Compliance to HIV medication has been problematic in PWID making HIV control difficult. Many studies in the past have validated educational activities like rehabilitation programs beneficial in maintaining regularity in medication intake. This brought us to the question of looking at such programs and its effects on our population. This study was conducted to assess the impact of other perspectives of abstinence and adherence including family support and employment status on a person’s willingness for treatment continuation and avoidance of drugs.
Methods: A retrospective chart review of 241 PWID was conducted to assess adherence to antiretroviral agents (ARVs) and abstinence from recreational drugs post visit to the rehabilitation center. Associations with family support, marital status, employment, income and back to work status were also assessed.
Results: Adherence to ARVs had significant statistical association with marital status (p=0.025), starting work again (p=0.001), family support (p=0.009), employment status (p=0.009) and monthly income (p=0.025). While family support (p=0.033), employment status (p<0.0001), Going back to work (p<0.0001), mode of travel to Rehabilitation center (p<0.0001) and monthly income (p=0.004) were associated with abstinence from drugs. Duration of rehabilitation or age had no effect on adherence or abstinence in our patient population of PWID.
Conclusion: Family and spousal support and employment promote optimal ARV compliance and should be encouraged when starting ARVs. Enrollment in a long-term complementing educational program would further enhance ARV intake and abstinence.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5780
How to cite this:Hussain A, Rahim A, Sheikh A, Jiwani A. The Effects of live- in rehabilitation on ARV adherence, abstinence from drugs and lifestyle modification in people who inject drugs (PWID) Living with HIV – A clinic review. Pak J Med Sci. 2022;38(2):411-416. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5780
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.
Disseminated cryptococcal infection in a lymphoma suspected patient
Authors: Khursheed Nazia , Umer Amna , Adnan Fareeha 
Published: December 2021

Cryptococcus neoformans is an opportunistic pathogen, mainly responsible for meningitis in immunodeficient individuals. We report a rare case of dessiminated cryptococcosis in a six years old boy, patient was being evaluated for lymphoma. In the present case the causative agent was Cryptococcus neoformans. It was diagnosed through Bactec, aerobic blood culture bottle. The cause of hospitalization of the patient was fever with abdominal pain. Blood and CSF culture revealed the presence of Cryptococcus neoformans which was further confirmed by urease test and corn meal tween agar (CMT). In the present case fungus was unusually isolated earlier from blood culture rather than cerebrospinal fluid.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5784
How to cite this:Khursheed N, Umer A, Adnan F. Disseminated cryptococcal infection in a lymphoma suspected patient. Pak J Med Sci. 2022;38(2):430-432. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5784
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.
Patient perception regarding privacy and confidentiality: A study from the emergency department of a tertiary care hospital in Karachi, Pakistan
Authors: Saleem Syed Ghazanfar , Ali Saima , Ghouri Nida , Maroof Quratulain , Jamal Muhammad Imran , Aziz Tariq , Shapiro David , Rybarczyk Megan 
Published: December 2021

Background and Objective: Maintaining privacy and ensuring confidentiality with patients is paramount to developing an effective patient-provider relationship. This is often challenging in over-crowded Emergency Departments (EDs). This survey was designed to explore patients’ perceptions on maintenance of privacy and confidentiality and their subsequent interactions with providers in a busy tertiary care hospital in Karachi.
Methods: Trained nursing staff conducted structured interviews with 571 patients who presented to The Indus Hospital (TIH) ED from January to December 2020. All patients were 14 years of age or older, could speak and understand Urdu, and provide informed consent. Patients were asked about their perceptions of privacy and confidentiality in the ED and whether this affected their interactions with providers.
Results: Respondents were primarily men (64%) under the age of 45 (62%) presenting for the first time (49%). The majority of patients felt that privacy and confidentiality were maintained, however 10% of patients reported that they had rejected examination due to privacy concerns and 15% of patients reported that they had changed or omitted information provided to a provider due to confidentiality concerns. There was correlation between privacy and confidentiality concerns and patient-provider interactions (p<0.0001).
Conclusions: Despite the often over-crowded and busy environment of the ED, patients generally felt that privacy and confidentiality were maintained. Given the correlation between perception and behavior and the importance of an effective patient-provider relationship, particularly in the acute setting when morbidity and mortality is high, initiatives that focus on maintaining privacy and confidentiality should be pursued.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5785
How to cite this:Saleem SG, Ali S, Ghouri N, Maroof Q, Jamal MI, Aziz T, et al. Patient perception regarding privacy and confidentiality: A study from the emergency department of a tertiary care hospital in Karachi, Pakistan. Pak J Med Sci. 2022;38(2):351-355. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5785
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.