OpenMed/multicare-articles huggingface dataset:
qPortal: A platform for data-driven biomedical research
Authors: Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen
Journal: PLoS One (2018)
MeSH terms: Biomedical Research / statistics & numerical data, Computing Methodologies, Software, Research Support, Non-U.S. Gov't, Computational Biology / methods, Computational Biology / statistics & numerical data, Database Management Systems / statistics & numerical data, Databases, Factual / statistics & numerical data, Databases, Genetic / statistics & numerical data, High-Throughput Nucleotide Sequencing / statistics & numerical data, Humans, Internet, User-Computer Interface, Workflow

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.
Vaginal Bleeding as Initial Presentation of an Aggressive Renal Cell Carcinoma: A Case Report and Review of the Literature
Authors: Antonio R Jimenez, Maria Del Mar Rivera Rolon, Eduardo Eyzaguirre, Cecilia Clement
Journal: Case Rep Pathol (2018)
MeSH terms: Case Reports

Introduction:
Renal cell carcinoma is the third most common urogenital cancer. In some patients, it can metastasize to distant organs. Metastasis to the vagina is extremely rare.
Case presentation:
A 54-year-old female with unremarkable history presented to the clinic with a chief complaint of vaginal bleeding. Further examination identified a pedunculated mass on the vaginal wall. Histologic examination revealed a metastatic clear cell renal cell carcinoma. Radiological studies then revealed a left renal mass and bilateral adrenal masses. The patient underwent a nephrectomy, adrenalectomy, and resection of the vaginal mass. The mass in the vagina has since recurred.
Conclusion:
We report the first known case of vaginal metastasis as initial presentation of a renal cell carcinoma with rhabdoid features. Postmenopausal women with renal cell carcinoma who present with vaginal bleeding should undergo a thorough inspection of the vaginal wall for the potential of metastatic neoplasms.
Treatment of pulmonary sequestrations by means of endovascular embolization: future or fashion?
Authors: Jeroen Diks, P Ronald Schütte, David Cheung, J Marco Schnater
Journal: Case Rep Med (2011)
MeSH terms: Case Reports

Bronchopulmonary sequestration is a rare malformation of the lower respiratory tract. Several methods of treatment have been described since the first publication. We present two cases of female adult patients with bronchopulmonary sequestration. In the first patient an unsuccessful attempt to treat the bronchopulmonary sequestration by means of arterial embolization is described. She was subsequently treated by means of surgical resection, which was the primary treatment for the second patient. Although endovascular techniques are becoming promising, in our opinion surgical resection remains the unique treatment for bronchopulmonary sequestration.
Neurofibromatosis Type 1 Associated with Hashimoto's Thyroiditis: Coincidence or Possible Link
Authors: Junaid Nabi
Journal: Case Rep Neurol Med (2013)

Introduction. Hashimoto's thyroiditis is a common form of chronic autoimmune thyroid disease (AITD) and often coexists with other autoimmune diseases, but Hashimoto's thyroiditis associated with an autosomal dominant neurofibromatosis type 1 is exceedingly rare. Case Presentation. A 30-year-old Bengali woman presented to the OPD with complaints of aching pain and tingling sensation in her hands and feet. Physical examination revealed dysmorphic facies, nodular swelling in the neck, cafe-au-lait spots, and neurofibromas covering the entire surface of her body. Her thyroid hormones were within normal limits. Thyroid ultrasound revealed a cystic area in the left lobe of the gland, and ultrasound-guided fine needle aspiration cytology revealed lymphocytic infiltration of the gland, suggesting Hashimoto's thyroiditis. High levels of autoimmune antibodies such as antithyroglobulin and antimicrosomal antibodies confirmed the diagnosis. Conclusion. When encountered with a patient of Neurofibromatosis type 1, a physician should be careful about the possibility of a concomitant autoimmune disease. Clinical presentation of neurofibromatosis and Noonan syndrome often overlaps and recent studies have implicated a mutation in NF1 gene in the etiology of NFNS. More extensive reports and further investigations of such patients having combination of neurofibromatosis type 1 and autoimmune thyroiditis will certainly provide better understanding of this link in the near future.
The role of grievance in fatal family violence and implications for the construct of lone actor grievance-fuelled violence
Authors: Alannah J Cooper, Michele T Pathé, Troy E McEwan
Journal: Front Psychol (2022)
Keywords: family violence, fatal family violence, femicide, filicide, grievance, grievance-fuelled violence, intimate partner homicide, lone actor
MeSH terms: Systematic Review

Introduction:
The concept of lone actor grievance fuelled violence assumes that homicides that occur in very different contexts can be thought about in a consistent manner because they share common motivations and resultant emotional states like resentment, outrage or revenge. Fatal family violence has been largely excluded from discussions of lone actor grievance-fuelled homicide, based on the assumption that it is conceptually different. This scoping review examines similarities and discrepancies between the characteristics and motivations of perpetrators of fatal family violence and those who have engaged in lone actor grievance-fuelled homicide outside the family context, and the relevance of the concept of grievance-fuelled violence to fatal family violence.
Methods:
This study reviewed published case studies and case series, resulting in a dataset of 102 homicide cases from 36 studies, of which there were 38 fatal family violence cases and 64 categorised as lone actor grievance-fuelled homicide.
Results:
Twenty of the 38 fatal family violence cases were identified as being grievance-fuelled, based on the presence of motivations consistent with definitions in the grievance literature. Whilst there were some offence similarities between the fatal family violence cases (e.g., location of offence), those driven by grievance were more similar to lone actor grievance-fuelled homicide in other ways (e.g., offender's gender and offence methods). In both these categories violence was predominantly motivated by grievance and a desire for revenge, whereas non-grievance fatal family violence cases were predominantly motivated by altruism.
Discussion:
The motivations that defined behaviour as lone actor grievance-fuelled homicide were equally apparent in a sub-group of fatal family violence, implying that some family violence cases can be integrated into the construct of lone actor grievance-fuelled homicide in future research and theorising.
Pembrolizumab-Induced Isolated Cranial Neuropathy: A Rare Case Report and Review of Literature
Authors: Francesco Bruno, Rosa Antonietta Palmiero, Bruno Ferrero, Federica Franchino, Alessia Pellerino, Enrica Milanesi, Riccardo Soffietti, Roberta Rudà
Journal: Front Neurol (2021)
Keywords: anti-pd1 agents, autoimmune neuropathy, case report, immune-related neurological complications, neurological immune-related adverse effects, pembrolizumab
MeSH terms: Case Reports

Introduction: Anti-PD1 agents are widely used in the treatment of solid tumors. This has prompted the recognition of a class of immune-related adverse events (irAEs), due to the activation of autoimmune T-cells. Pembrolizumab is an anti-PD1 agent, which has been related to an increased risk of various neurological irAE (n-irAEs). Here, we present a rare case of pembrolizumab-induced neuropathy of cranial nerves. Case Report: A 72-year-old patient was diagnosed with a lung adenocarcinoma in February 2018 (EGFR-, ALK-, and PDL1 90%). According to the molecular profile, pembrolizumab was started. After three administrations, the patient developed facial paresis, ptosis, ophthalmoplegia, and dysphonia. As brain metastases and paraneoplastic markers were excluded, a drug-related disorder was suspected and pembrolizumab was discontinued. A nerve conduction study and electromyography excluded signs of neuropathy and myopathy at four limbs, and repetitive nerve stimulation was negative. However, altered blink reflex and nerve facial conduction were consistent with an acute neuropathy of the cranial district. Thus, the patient was treated with two cycles of intravenous immunoglobulins (IVIg), which rapidly allowed improvement of both symptoms and neurophysiological parameters. However, the patient died in October 2018 for a progression of lung tumor. Discussion: Only 16 cases of pembrolizumab-related neuropathies have been described so far. Our case is of particular interest for the isolated involvement of cranial nerves and the prompt response to IVIg. Conclusion: N-irAEs are insidious conditions that require solid knowledge of onco-immunotherapy complications: it is mandatory not to delay any treatment that would potentially modify the course of a neurological complication.
Secondary donor-derived humanized CD19-modified CAR-T cells induce remission in relapsed/refractory mixed phenotype acute leukemia after allogeneic hematopoietic stem cell transplantation: a case report
Authors: Meng-Yun Li, Zhi-Hong Lin, Ming-Ming Hu, Li-Qing Kang, Xiao-Xia Wu, Qi-Wei Chen, Xin Kong, Jian Zhang, Hui-Ying Qiu, De-Pei Wu
Journal: Biomark Res (2020)
Keywords: cd19, chimeric antigen receptor t cells, donor-derived, humanized, mixed phenotype acute leukemia
MeSH terms: Case Reports

Background:
Mixed phenotype acute leukemia (MPAL) is a rare leukemia and is regarded as a high-risk entity with a poor prognosis. Induction therapy of an acute lymphoblastic leukemia type or hybrid regimen and hematopoietic stem cell transplantation has been recommended for MPAL. However, the optimal therapies for relapsed or refractory MPAL remain unclear, especially for relapse after stem cell transplantation. Donor-derived chimeric antigen receptor T (CAR-T) cell therapy may be a promising therapeutic option for patients with MPAL who express target antigens and have relapsed after stem cell transplantation. However, recurrence remains a challenge, and reinfusion of CAR-T cells is not always effective. An infusion of secondary donor-derived humanized CD19-modified CAR-T cells may be effective in inducing remission.
Case presentation:
We report a case of MPAL with CD19 expression. The patient was treated with acute lymphoblastic leukemia-like induction and consolidation therapies but remained positive for SET-NUP214 fusion gene transcript. He subsequently underwent a haploidentical stem cell transplantation but relapsed within 6 months. He then underwent donor-derived CD19-targeted CAR-T cell therapy and achieved a sustained, complete molecular remission. Unfortunately, he developed a CD19-positive relapse after 2 years. Donor-derived humanized CD19-directed CAR-T cells induced a second complete molecular remission without severe cytokine release syndrome or acute graft-versus-host disease.
Conclusion:
This case demonstrated the efficacy and safety of humanized donor-derived CD19-modified CAR-T cell infusion for treating the recurrence of MPAL previously exposed to murine-derived CD19-directed CAR-T cells.
A misdiagnosis of traumatic hypersupination of the distal radioulnar joint: a case report
Authors: Vipin Asopa, Robert J Douglas, Andrew D Saies, James S Church
Journal: Case Rep Orthop (2013)

Traumatic hypersupination injury of the distal radioulnar joint is a rare injury, and occurs when sufficient supination force is applied to the joint so as to tear the volar radioulnar ligament, resulting in separation of the triangular fibrocartilage complex, and subluxation of the tendon of extensor carpi ulnaris. This allows the distal ulna to rotate such that the ulnar styloid comes to lie adjacent to the ulna notch of the radius. Treatment of this injury requires manipulation of the joint, under anaesthesia or sedation. We describe a case where posttraumatic radiological investigation of a patient with an anatomical variation of the wrist when in supination resembled a traumatic hypersupination injury of the distal radioulnar joint. A review of the literature has revealed this to be the first reported case of this type.
Positive myositis-specific autoantibodies during COVID-19: a case report
Authors: Asma Ben Abdelkrim, Mariam Ghozzi, Ghada Saad, Sarra Melayah, Taieb Ach, Ibtissem Ghedira, Koussay Ach
Journal: Pan Afr Med J (2022)
Keywords: covid-19, autoimmunity, case report, diabetes mellitus, myositis
MeSH terms: Autoimmune Diseases, COVID-19 / complications, Myositis / diagnosis, Myositis / drug therapy, Case Reports, Adult, Autoantibodies, Female, Humans, SARS-CoV-2, Autoantibodies

Viral infection is known to be a trigger of autoimmune diseases. Numerous cases of coronavirus disease 2019 (COVID-19) with autoimmune manifestations have been reported and several authors have highlighted the relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and autoimmune diseases. Autoimmune myopathies being one of these manifestations. A 27-year-old diabetic woman was admitted for management of acido-ketosis decompensation of her diabetes secondary to SARS-CoV-2 infection. During hospitalization, she developed muscle weakness and increased creatine kinase levels, which led us to assay the autoimmunity pattern which became positive for myositis-specific autoantibodies against single recognition particle (anti-SRP). The patient was treated with intense hydration with clinical and biological improvement and anti-SRP disappeared two months later. Positive myositis auto-antibodies are one of the autoimmune complications that could be seen during and after the SARS-CoV-2 infection.
Priapism, ecstasy, and marijuana: is there a connection?
Authors: Quan T Tran, Robyn A Wallace, Esther H A Sim
Journal: Adv Urol (2008)
MeSH terms: Case Reports

Priapism is a urological emergency with multiple aetiologies including drug induced. Currently, there have been no reports of priapism induced by the combination of ecstasy and marijuana. We speculated on the potential mechanisms for acute drug-induced priapism resulting from ingestion of these two common illicit drugs.
Intrasellar chondroid chordoma: a case report
Authors: Renata M Hirosawa, Antonio B A Santos, Mariana M França, Viciany Erique Fabris, Ana Valéria B Castro, Marco A Zanini, Vania S Nunes
Journal: ISRN Endocrinol (2011)
MeSH terms: Case Reports

Chordomas are tumors derived from cells that are remnants of the notochord, particularly from its proximal and distal extremes, they are mainly midline and represent approximately 1% of all malignant bone tumors and 0.1 to 0.2% of intracranial neoplasms. Chordomas involving the sellar region are rare. Herein, we describe a 57-year-old male patient presenting with a history of retro-orbital headache, progressive loss of vision, and clinical features of hypopituitarism, for over 2 months. During evaluation, the CT scan revealed a large contrast-enhancing intrasellar tumor with a 3.6-cm largest diameter. The patient underwent transsphenoidal partial resection of the tumor, and histological examination was consistent with the diagnosis of chondroid chordoma. Although chordomas are rare, they may be considered to constitute a differential diagnostic of pituitary adenomas, especially if a calcified intrasellar tumor with bone erosion is diagnosed.
A Rare Case of Endometriosis of the Small Bowel
Authors: Moisés R Zepeda, Su K Win
Journal: Case Rep Pathol (2021)
MeSH terms: Case Reports

Endometriosis of the small bowel is a rare clinical event. The clinical condition presents with vague abdominal symptoms and is usually not diagnosed acutely, unless clinicians have a high index of suspicion. Most patients are diagnosed after multiple clinical encounters. We present a case of endometriosis causing small bowel obstruction diagnosed postsurgically.
Cerebral Amyloid Angiopathy Related Inflammation With Prominent Meningeal Involvement. A Report of 2 Cases
Authors: Agnès Aghetti, Damien Sène, Marc Polivka, Natalia Shor, Sarah Lechtman, Hugues Chabriat, Eric Jouvent, Stéphanie Guey
Journal: Front Neurol (2019)
Keywords: cerebral amyloid angiopathy (caa), cerebral amyloid angiopathy-related inflammation (caa-ri), meningeal inflammation, subarachnoid hemorrhage, xanthochromia
MeSH terms: Case Reports

Cerebral amyloid angiopathy related inflammation (CAA-RI) is a rare form of CAA characterized by subacute encephalitic symptoms (cognitive decline, seizures, focal deficits) associated with extensive and confluent white matter lesions co-localizing with lobar microbleeds on brain MRI. We report two cases of unusual CAA-RI mimicking meningoencephalitis but without typical brain lesions on FLAIR and T2* sequences. These 2 cases may extend the clinical spectrum of CAA-RI by suggesting the possible occurrence of quite purely meningeal forms of CAA-RI.
Climate change mitigation strategies in the forest sector: biophysical impacts and economic implications in British Columbia, Canada
Authors: Zhen Xu, Carolyn E Smyth, Tony C Lemprière, Greg J Rampley, Werner A Kurz
Journal: Mitig Adapt Strateg Glob Chang (2018)
Keywords: cbm-cfs3, climate change mitigation strategy, forest sector, mitigation cost, socio-economic impact

Managing forests to increase carbon sequestration or reduce carbon emissions and using wood products and bioenergy to store carbon and substitute for other emission-intensive products and fossil fuel energy have been considered effective ways to tackle climate change in many countries and regions. The objective of this study is to examine the climate change mitigation potential of the forest sector by developing and assessing potential mitigation strategies and portfolios with various goals in British Columbia (BC), Canada. From a systems perspective, mitigation potentials of five individual strategies and their combinations were examined with regionally differentiated implementations of changes. We also calculated cost curves for the strategies and explored socio-economic impacts using an input-output model. Our results showed a wide range of mitigation potentials and that both the magnitude and the timing of mitigation varied across strategies. The greatest mitigation potential was achieved by improving the harvest utilization, shifting the commodity mix to longer-lived wood products, and using harvest residues for bioenergy. The highest cumulative mitigation of 421 MtCO2e for BC was estimated when employing the strategy portfolio that maximized domestic mitigation during 2017-2050, and this would contribute 35% of BC's greenhouse gas emission reduction target by 2050 at less than $100/tCO2e and provide additional socio-economic benefits. This case study demonstrated the application of an integrated systems approach that tracks carbon stock changes and emissions in forest ecosystems, harvested wood products (HWPs), and the avoidance of emissions through the use of HWPs and is therefore applicable to other countries and regions.
Cholesterol granuloma of the frontal sinus: a case report
Authors: Manola Marco, Casorelli Ida, Pietrafesa Francesco Luigi, Mottola Giampiero, Lacerenza Domenico, Battiloro Giuseppe, Patitucci Giuseppe, Vita Giulia Anna Carmen
Journal: Case Rep Otolaryngol (2012)

Cholesterol granulomas are common in the mastoid antrum and air cells of the temporal bone. In the paranasal sinuses, especially in the frontal sinus, they have occasionally been mentioned in the literature. The pathogenesis is unknown, but the majority of the authors support the concept of airway obstruction in the cells well pneumatised of temporal bone and paranasal sinuses. The authors report a case of cholesterol granuloma of the frontal sinus treated with radical surgical techniques, and they also recommend an endoscopic approach to frontal sinus to restore or enlarge the nose-frontal canal and promote drainage and ventilation of the frontal sinus.
How Colposcopy Misses Invasive Cervical Cancer: A Case Report from the IMPROVE-COLPO Study
Authors: Jeff Livingston, Emmanouil Papagiannakis
Journal: Case Rep Obstet Gynecol (2016)

Colposcopy with biopsy is pivotal to cervical cancer prevention programs as it is called to identify the precancerous lesions on patients that screen positive. We present a cervical cancer case from IMPROVE-COLPO, a postmarketing, multicenter, two-arm observational study on US community colposcopy that collects outcomes with the adjunctive Dynamic Spectral Imaging (DSI) in its prospective arm. A 45-year-old woman was seen for suffering of heavy periods. She had cytology of Atypical Squamous Cells of Undetermined Significance (ASC-US) and was Human Papillomavirus (HPV) positive. Her colposcopy did not recognize the underlying condition and opted for no biopsy. The DSI assessment led to a biopsy of a lesion challenging traditional colposcopic templates: small, away from the cervical os, with slow acetowhitening development. Pathology review revealed the presence of invasive squamous carcinoma. In the era of sensitive screening, it is concerning that invasive cancers can challenge colposcopy and that the way to improve colposcopy is to collect multiple biopsies from each patient. The case presented indicates that the adjunctive objective assessment by DSI increases reassurance that observations outside of traditional standard visual templates are not underestimated or ignored.