OpenMed/multicare-articles huggingface dataset:
A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments
Authors: Asta Laiho, Laura L Elo
Journal: PLoS One (2014)
MeSH terms: Exons, Gene Expression Profiling / methods, Sequence Analysis, RNA / methods, Research Support, Non-U.S. Gov't, Female, Humans, Male, RNA / genetics, Software, RNA

RNA-sequencing (RNA-seq) has rapidly become the method of choice in many genome-wide transcriptomic studies. To meet the high expectations posed by this technology, powerful computational techniques are needed to translate the measurements into biological and biomedical understanding. A number of statistical procedures have already been developed to identify differentially expressed genes between distinct sample groups. With these methods statistical testing is typically performed after the data has been summarized at the gene level. As an alternative strategy, developed with the aim to improve the results, we demonstrate a method in which statistical testing at the exon level is performed prior to the summary of the results at the gene level. Using publicly available RNA-seq datasets as case studies, we illustrate how this exon-based strategy can improve the performance of the widely used differential expression software packages as compared to the conventional gene-based strategy. In particular, we show how it enables robust detection of moderate but systematic changes that are missed when relying on single gene-level summary counts only.
Case report: Analysis of novel compound heterozygous TPP1 variants in a Chinese patient with neuronal ceroid lipofuscinosis type 2
Authors: Sui-Bing Miao, Hui Guo, De-Xian Kong, Yuan-Yuan Zhao, Shu-Hong Pan, Yan Jiang, Xing Gao, Xiao-Hua Wu
Journal: Front Genet (2022)
Keywords: molecular analysis, neuronal ceroid lipofuscinosis type 2 (cln2), splicing assay, tripeptidyl peptidase i (tpp1), variant
MeSH terms: Case Reports

Neuronal ceroid lipofuscinosis type 2 (CLN2) is an autosomal recessive neurodegenerative disease caused by variants in the TPP1 gene that lead to the deficiency of the lysosomal enzyme tripeptidyl peptidase I (TPP1) activity. Herein, we report a rare case of CLN2 caused by two novel variants of TPP1. The patient presented with seizures at onset, followed by progressive cognitive impairment, motor decline, and vision loss. Novel compound heterozygous variants, c.544_545del and c.230-3C>G, in TPP1 were identified by whole-exome sequencing. The variant assessment showed that the c.544_545del is a frameshift variant mediating mRNA decay and that c.230-3C>G is a splice variant generating aberrantly spliced TPP1 mRNA, as confirmed by a Splicing Reporter Minigene assay. In conclusion, clinical history, variant assessment, and molecular analyses demonstrate that the novel compound heterozygous variants are responsible for CLN2 disease in this patient. This study expands the mutation spectrum of TPP1.
Unusual Etiology of Acute Wrist Pain: Acute Calcific Tendonitis of the Flexor Carpi Ulnaris Mimicking an Infection
Authors: Man R Shim
Journal: Case Rep Orthop (2018)
MeSH terms: Case Reports

Acute calcific tendonitis is a common cause of musculoskeletal pain. However, it seldom affects the hand and wrist. For that reason, it is frequently mistaken for more common etiologies. This study reports a case of acute calcific tendinitis of the flexor carpi ulnaris, which was initially misdiagnosed as cellulitis, in a 65-year-old woman, who was unnecessarily prescribed with antibiotics. However, further evaluation confirmed the correct diagnosis of acute calcific tendinitis and her symptoms were subsequently resolved within 2 weeks with rest, wrist immobilization, and an intake of anti-inflammatories. This case underscores the need for the physicians to be aware of this less common but important cause of acute wrist pain in order to prevent misdiagnosis and avoid unnecessary medical treatments.
Case report: An infant boy with X-linked sideroblastic anaemia successfully treated by umbilical cord blood haematopoietic stem cell transplantation
Authors: Zhongyang Ma, Dongjun Li, Xue Yang, Juan Liang, Yiping Zhu
Journal: Front Genet (2022)
Keywords: alas2, x-linked sideroblastic anaemia, xlsa, case report, congenital sideroblastic anaemia, cord blood transplantation, haematopoietic stem cell transplantation, vein occlusion liver disease
MeSH terms: Case Reports

X-linked sideroblastic anaemia (XLSA) is an inherited disorder caused by mutations in genes encoding proteins involved in the biosynthesis of haem. The pathogenic gene, as well as the pathogenesis and diagnosis of XLSA, have been fully elucidated in previous studies. However, only a few new advances have been made in managing XLSA in recent years, and blood transfusion remains the primary treatment. We report a case of umbilical cord blood haematopoietic stem cell transplantation in a male infant diagnosed with XLSA who was born with asphyxia due to severe anaemia. Early hepatic vein occlusion occurred after transplantation. However, this complication was rapidly controlled after active treatment, and the child's quality of life improved significantly. Haematopoietic stem cell transplantation is a promising alternative treatment for XLSA.
Primary intraosseous squamous cell carcinoma arising from an odontogenic keratocyst: a case report and literature review
Authors: Sandhya Tamgadge, Avinash Tamgadge, Neha Modak, Sudhir Bhalerao
Journal: Ecancermedicalscience (2013)
Keywords: carnoy’s solution, mandible, odontogenic keratocyst, p53, primary intraosseous squamous cell carcinoma
MeSH terms: Case Reports

Primary intraosseous squamous cell carcinoma (PIOSCC) derived from an odontogenic keratocyst (OKC) is a rare malignant neoplasm of the jaws, which is locally aggressive with quite poor prognosis. The incidence of carcinomas arising in odontogenic cysts was reported to be approximately 1-2/1000. The number of well-documented cases of PIOSCC ex OKC is extremely small; hence, no sufficient incidence data are available in the literature. Overall, the survival rate of an individual, which is a period of two years, is very poor, and this can be attributed to the delayed diagnosis. But knowledge of the histopathological and immunohistological features of PIOSCC allows accurate and early diagnosis of the lesion so that an early and appropriate treatment can be instituted for better prognosis. The following report describes an extremely rare case of PIOSCC of the mandible derived from an OKC in a 20-year-old female patient.
Multilobular tumor of the zygomatic bone in a dog
Authors: L Leonardi, A Carrano, L Stoppini, M Floris
Journal: Open Vet J (2014)
Keywords: dog, multilobular tumor of bone, zygomatic bone
MeSH terms: Case Reports

Multilobular tumor of bone (MTB) (also known as Multilobular Osteochondrosarcoma) is an uncommon bone tumor frequently located on the skull of dogs, rarely on the ribs or pelvis. These neoplasms are slow growing, locally invasive, and have the potential to compress and invade the brain. A 10-year-old mixed breed dog was presented with a history of approximately 4 months of progressive growth of a left zygomatic mass. Radiographic investigation revealed a finely granular or stippled non homogeneous radiopaque mass involving the zygomatic arch. After surgery, grossly the neoplasm consisted of multiple, variably sized, grayish-white to yellow nodules separated by collagenous septa of different thickness. Histologically, the tumor was characterized by the presence of multiple lobules containing osteoid and cartilage, separated by a net of fibrous septae. This neoplastic pattern was consistent with a typical multilobular tumor of bone and based on clinical, radiographical, gross and light microscopic findings the definitive diagnosis was made. While reviewing veterinary literature only few cases of MTB were found in dogs.
Rare complication of coupled VASER liposuction and Renuvion technologies: a case report
Authors: Moraya Alqahtani, Nehal Mahabbat, Khalid Fayi
Journal: Case Reports Plast Surg Hand Surg (2023)
Keywords: j-plasma, liposuction, renuvion
MeSH terms: Case Reports

This study presents the case of a women, who underwent VASER-assisted liposuction of the abdomen coupled with Renuvion skin tightening by J-Plasma for skin retraction. She developed pain and moderate surgical emphysema. Radiological findings showed moderate subcutaneous emphysema. There were no signs of viscus perforation, or pneumothorax.
Metastatic pancreatic adenocarcinoma presenting as large bowel obstruction: A case report
Authors: Felipe Pacheco, Emmanuel Luciano, Danielle Hebert, Omar Marar
Journal: Int J Surg Case Rep (2023)
Keywords: case report, large bowel obstruction, metastatic pancreatic cancer
MeSH terms: Case Reports

Introduction and importance:
The incidence of pancreatic cancer has gradually increased over the past decades. Metastatic pancreatic cancer to the colon is rare with only seven cases reported. Symptomatic metastasis to the colon as the initial presentation of pancreatic adenocarcinoma has only been reported in two occasions prior to this report.
Case presentation:
In this report, the diagnosis and operative management of a 78-year-old male who presented with three days of obstipation and computed tomography evidence of an annular obstructing mass in the sigmoid colon in addition to a pancreatic body and lesser sac mass involving the gastric antral region. The patient underwent a laparoscopic sigmoidectomy with end colostomy. Pathology revealed metastatic adenocarcinoma of pancreatic origin. The postoperative period was unremarkable, and the patient was referred to medical oncology to pursue further treatment.
Clinical discussion:
Symptomatic metastasis to the colon as the initial presentation of pancreatic adenocarcinoma is exceedingly rare. To our knowledge, this is the 3rd case to be reported and the second that was located in the sigmoid colon.
Conclusion:
The presentation of metastatic pancreatic cancer to the colon causing a colonic obstruction is rare but should be considered in cases of atypical synchronic masses in cross-sectional imaging. When metastatic disease is suspected in the sigmoid colon, it is advisable to perform a colostomy instead of an anastomosis to avoid the potential risk of anastomotic leak that could delay the immediate need for systemic therapy.
Bilateral Breast Phyllodes Tumor in Androgen Insensitivity Syndrome
Authors: Aishwarya Sunil Dutt, Girish Bakhshi, Chandrakant Sabale, Ravi Landge, Sushrut Baligar, Rajalakshmi V, Madhu Jha, Sampada Joshi, Chettubattina Ravi Teja
Journal: Surg J (N Y) (2023)
Keywords: complete androgen insensitivity syndrome, phyllodes, testis
MeSH terms: Case Reports

Phyllodes is a rare tumor found exclusively in females. It can be classified into benign, intermediate, or malignant variety based on the aggressive nature of the disease. With adequate preoperative clinical assessment combined with histopathology and radiological investigations the adequate treatment strategy can be formulated to avoid future recurrences. Complete androgen insensitivity syndrome (CAIS) is associated with a genotypic male, which can be confirmed by karyotyping, with phenotypic female characteristics. The present case is the first case of bilateral breast phyllodes tumor in a patient with CAIS. Preoperative assessment was suggestive of bilateral phyllodes tumor with bilateral gonads in the inguinal region which was confirmed to be testis postoperatively on histopathological analysis. A brief case report with review of literature is presented.
Statin-Induced Rhabdomyolysis Due to Pharmacokinetic Changes From Biliary Obstruction in a Patient With Metastatic Prostate Cancer
Authors: Sai Prasad Desikan, Phillip Sobash, Andrew Fisher, Raman Desikan
Journal: J Investig Med High Impact Case Rep (2020)
Keywords: drug-drug interaction(s), obstructive jaundice, prostate cancer, rhabdomyolysis
MeSH terms: Androstenes / adverse effects, Hydroxymethylglutaryl-CoA Reductase Inhibitors / adverse effects, Rhabdomyolysis / chemically induced, Simvastatin / adverse effects, Case Reports, Aged, Cholestasis / etiology, Diagnosis, Differential, Humans, Male, Prostatic Neoplasms, Castration-Resistant / drug therapy, Rhabdomyolysis / diagnosis, Androstenes, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Simvastatin, abiraterone

Statins work synergistically with androgen receptor blockers and androgen biosynthesis inhibitors, improving survival in patients with metastatic castration resistant prostate cancers (mCRPCs). Survival improvement is more pronounced for patients receiving androgen biosynthesis inhibitors compared with patients receiving androgen receptor blockers. A rare adverse interaction between simvastatin and abiraterone (Zytiga), an androgen biosynthesis inhibitor, was observed in a patient with mCRPC due to pharmacokinetic changes resulting from obstructive jaundice.
Early Orthopaedic Treatment of Hemifacial Microsomia
Authors: Diana Cassi, Marisabel Magnifico, Mauro Gandolfinini, Ilda Kasa, Giovanni Mauro, Alberto Di Blasio
Journal: Case Rep Dent (2017)
MeSH terms: Case Reports

The aim of this paper is to report treatment effects of functional therapy in a growing patient affected by hemifacial microsomia (HM). According to Kaban's classification, the patient was classified as grade IIa as she presented all mandibular and temporomandibular joint components and a normal shaped, hypoplastic mandible. The therapeutic approach included the use of an asymmetrical functional activator (AFA) to stimulate the growth of the affected side and consequently to improve symmetry of the mandible and maxillary deficiency. Further effects were the lengthening of the mandibular ramus, restoration of occlusion, and expansion of soft tissues.
Malignant transformation of abdominal wall endometriosis with lymph node metastasis: Case report and review of literature
Authors: Francesc Fargas Fàbregas, Maite Cusidó Guimferrer, Francesc Tresserra Casas, Sonia Baulies Caballero, Rafael Fábregas Xauradó
Journal: Gynecol Oncol Case Rep (2014)
Keywords: lymph node metastasis, malignant endometriosis

•A simple endometriosis can result in malignancy pathology, as a neoplasia.•Wall-abdominal tumors and soft tissue as a possible differential diagnosis of abdominal wall endometriosis•Preperitoneal node-metastasis as malignancy of endometriosis in previous cesarean scar.
Primary spindle cell sarcoma of the heart treated with carbon-ion radiotherapy: Case report
Authors: Ikuko Shibasaki, Shigeru Toyoda, Yusuke Takei, Masayuki Chida, Hirotsugu Fukuda
Journal: Int J Surg Case Rep (2020)
Keywords: carbon-ion radiotherapy, primary cardiac tumor, spindle cell sarcoma
MeSH terms: Case Reports

Introduction:
Primary cardiac sarcoma is a rare malignant cardiac neoplasm with a poor prognosis. No evidence-based guidelines exist regarding surgical treatment management, although some case reports have been published. We report the outcome of a patient with spindle cell sarcoma of the heart treated postoperatively with carbon-ion radiotherapy and chemotherapy.
Presentation of case:
A 16-year-old female patient was noted to have abnormal electrocardiogram results for 2 consecutive years at a high school medical check. She was referred to our hospital and a cardiac tumor in the left atrium was suspected. The preoperative diagnosis was myxoma, but abnormalities were also observed macroscopically during surgery, and a diagnosis of spindle cell sarcoma was made by rapid intraoperative pathological analysis. We resected the tumor as much as possible with surgery, but the tumor in the left lower pulmonary vein could not be respected. We performed carbon-ion radiotherapy postoperatively. She experienced recurrence 1 year later and tumor growth 2 years later. We considered additional surgical treatment, but eventually selected chemotherapy. She died 4 years and 7 months after initial surgery.
Conclusion:
Spindle cell sarcoma is a rare disease with a poor prognosis. Although no optimal treatment method has been established, in the present case, incomplete surgical resection and postoperative carbon-ion radiotherapy were performed, yielding a relatively long survival period.
Duplication of C7orf58, WNT16 and FAM3C in an obese female with a t(7;22)(q32.1;q11.2) chromosomal translocation and clinical features resembling Coffin-Siris Syndrome
Authors: Jun Zhu, Jun Qiu, Gregg Magrane, Malak Abedalthagafi, Andrea Zanko, Mahin Golabi, Farid F Chehab
Journal: PLoS One (2012)
MeSH terms: Abnormalities, Multiple / diagnosis, Chromosome Duplication / genetics, Cytokines / genetics, Hand Deformities, Congenital / diagnosis, Intellectual Disability / diagnosis, Micrognathism / diagnosis, Neoplasm Proteins / genetics, Obesity / diagnosis, Obesity / genetics, Translocation, Genetic / genetics, Wnt Proteins / genetics, Case Reports, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Child, Chromosome Breakpoints, Chromosomes, Human, Pair 22 / genetics, Chromosomes, Human, Pair 7 / genetics, DNA Mutational Analysis, Diagnosis, Differential, Exome / genetics, Face / abnormalities, Female, Humans, Neck / abnormalities, Cytokines, FAM3C protein, human, Neoplasm Proteins, WNT16 protein, human, Wnt Proteins, Coffin-Siris syndrome

We characterized the t(7;22)(q32;q11.2) chromosomal translocation in an obese female with coarse features, short stature, developmental delay and a hypoplastic fifth digit. While these clinical features suggest Coffin-Siris Syndrome (CSS), we excluded a CSS diagnosis by exome sequencing based on the absence of deleterious mutations in six chromatin-remodeling genes recently shown to cause CSS. Thus, molecular characterization of her translocation could delineate genes that underlie other syndromes resembling CSS. Comparative genomic hybridization microarrays revealed on chromosome 7 the duplication of a 434,682 bp region that included the tail end of an uncharacterized gene termed C7orf58 (also called CPED1) and spanned the entire WNT16 and FAM3C genes. Because the translocation breakpoint on chromosome 22 did not disrupt any apparent gene, her disorder was deemed to result from the rearrangement on chromosome 7. Mapping of yeast and bacterial artificial chromosome clones by fluorescent in situ hybridization on chromosome spreads from this patient showed that the duplicated region and all three genes within it were located on both derivative chromosomes 7 and 22. Furthermore, DNA sequencing of exons and splice junctional regions from C7orf58, WNT16 and FAM3C revealed the presence of potential splice site and promoter mutations, thereby augmenting the detrimental effect of the duplicated genes. Hence, dysregulation and/or disruptions of C7orf58, WNT16 and FAM3C underlie the phenotype of this patient, serve as candidate genes for other individuals with similar clinical features and could provide insights into the physiological role of the novel gene C7orf58.
Male DCIS diagnosed after use of over-the-counter hormonal supplement
Authors: S O Agbroko, K E Rojas, D M Manasseh, P Borgen
Journal: Int J Surg Case Rep (2019)
Keywords: atypical ductal hyperplasia, ductal carcinoma in-situ, gynecomastia, male breast cancer, mastectomy

Introduction:
Male breast cancer is a rare disease. Although epidemiologic and genetic factors are associated with male breast cancer, hormonal factors may also play a role.
Case presentation:
We report the case of a 39-year-old BRCA negative male patient taking a sexual performance enhancement supplement who presented with worsening asymmetric gynecomastia and unilateral spontaneous bloody nipple discharge and was found to have ductal carcinoma in-situ.
Discussion:
The altered cellular environment related to the hormone contents of the supplement coincided with the rapid worsening of his gynecomastia and may have played a role in the development of the ductal carcinoma in-situ, or growth of an existing focus.
Conclusion:
The use of hormonal male enhancement supplements can lead to higher levels of androgens in users. It is possible for this altered hormonal environment to cause the growth of tumor or promote the progression of an existing focus.
Children and COVID- 19 infection: A case series of Iran
Authors: Mohsen Mohammadi, Masood Kiani, Sanaz Mehrabani, Maryam Nikpour
Journal: Caspian J Intern Med (2022)
Keywords: covid- 19 infection, case series, children
MeSH terms: Case Reports

Background:
World Health Organization (WHO) declared COVID -19 infection a global pandemic. Children have milder disease than adults but different aspects of disease in children are not fully understood.
Case presentation:
We describe 5 pediatric patients with COVID-19 that referred to Amirkola Children's Hospital, Babol, Iran. The youngest patient was 4 years old and the oldest was 12 years old. Three patients were males. None of the patients had a history of contacts with symptomatic patients with COVID -19. The most common symptoms included fever, cough, anorexia, weakness and diarrhea. One patient had gastrointestinal symptoms without respiratory symptoms. All patients had elevated ESR and CRP. Three of them had lymphopenia. RT-PCR was positive in all patients. Management included supportive care, antibiotics, antiviral treatment and hydroxychloroquine. All patients were discharged with good condition.
Conclusion:
Children may have a variety of symptoms including respiratory or gastrointestinal symptoms. Mortality is rare in children and prognosis is better than the adults.
Phenotypic and genetic characterization of a patient with a de novo interstitial 14q24.1q24.3 deletion
Authors: Elisa Tassano, Andrea Accogli, Serena Panigada, Patrizia Ronchetto, Cristina Cuoco, Giorgio Gimelli
Journal: Mol Cytogenet (2014)
Keywords: array-cgh, de novo, genotype-phenotype correlation, interstitial 14q241q243 deletion
MeSH terms: Case Reports

Background:
Interstitial deletions of chromosome bands 14q24.1q24.3 are very rare with only three reported cases.
Results:
We describe a 7-year-old boy with a 5.345 Mb de novo interstitial deletion at 14q24.1q24.3 band detected by array-CGH who had a complex phenotype characterized by seizures, congenital heart defects, dysmorphisms, psychomotor delay, and bronchopulmonary, skeletal, and brain anomalies.
Conclusion:
The deleted region contains numerous genes, but we focused our attention on three of them (C14orf169, NUMB, and PSEN1), which could account, at least partially, for the phenotype of the boy. We therefore discuss the involvement of these genes and the observed phenotype compared to that of previously described patients.
Case Report: Novel NIPBL Variants Cause Cornelia de Lange Syndrome in Chinese Patients
Authors: Ying Peng, Changbiao Liang, Hui Xi, Shuting Yang, Jiancheng Hu, Jialun Pang, Jing Liu, Yingchun Luo, Chengyuan Tang, Wanqin Xie, Hua Wang
Journal: Front Genet (2021)
Keywords: cornelia de lange syndrome, nipbl, snp array, prenatal diagnosis, whole-exome sequencing
MeSH terms: Case Reports

Cornelia de Lange syndrome (CdLS) is a genetic disorder characterized by multisystemic malformations. Mutation in the NIPBL gene accounts for nearly 60% of the cases. This study reports the clinical and genetic findings of three cases of CdLS from unrelated Chinese families. Clinically, all the three cases were classified as classic CdLS based on the cardinal (distinctive facial features and limb malformations) and suggestive (developmental delay, growth retardation, microcephaly, hirsutism, etc.) manifestations. SNP array detected a novel de novo heterozygous microdeletion of 0.2 Mb [arr[GRCh37]5p13.2(36848530_37052821) × 1] that spans the first 43 exons of NIPBL in the fetus with nuchal translucency thickening in case 1. Whole-exome sequencing in family trios plus Sanger sequencing validation identified a de novo heterozygous NIPBL c.5566G>A (p.R1856G) mutation in the fetus with intrauterine growth retardation in case 2 and a novel de novo heterozygous NIPBL c.448dupA (p.S150Kfs*23) mutation in the proband (an 8-month-old girl) in case 3. The cases presented in this study may serve as references for increasing our understanding of the mutation spectrum of NIPBL in association with CdLS.