tbuckley/cabot-search huggingface dataset:
Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain
Authors: Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Momoki Hirai, Keiji Terao, Yutaka Suzuki, Sumio Sugano, Katsuyuki Hashimoto
Journal: Genome biology (2001)

The complete assignment of the protein-coding regions of the human genome is a major challenge for genome biology today. We have already isolated many hitherto unknown full-length cDNAs as orthologs of unidentified human genes from cDNA libraries of the cynomolgus monkey (Macaca fascicularis) brain (parietal lobe and cerebellum). In this study, we used cDNA libraries of three other parts of the brain (frontal lobe, temporal lobe and medulla oblongata) to isolate novel full-length cDNAs.The entire sequences of novel cDNAs of the cynomolgus monkey were determined, and the orthologous human cDNA sequences were predicted from the human genome sequence. We predicted 29 novel human genes with putative coding regions sharing an open reading frame with the cynomolgus monkey, and we confirmed the expression of 21 pairs of genes by the reverse transcription-coupled polymerase chain reaction method. The hypothetical proteins were also functionally annotated by computer analysis.The 29 new genes had not been discovered in recent explorations for novel genes in humans, and the ab initio method failed to predict all exons. Thus, monkey cDNA is a valuable resource for the preparation of a complete human gene catalog, which will facilitate post-genomic studies.
Outcome results of antituberculous treatment in latent or manifest tuberculosis patients featuring granulomatous uveitis
Authors: Tulin Cagatay, Zeki Kilicaslan, Aysen Erer, Ayse Yilduz Tas, Penbe Cagatay, Ilknur Tugal Tutkun
Journal: European Respiratory Journal (2011)

Ocular tuberculosis is a rare disease.The most common form of ocular tuberculosis is granulomatous uveitis. It is often a result of haematogenous spread or hypersensitivity reaction to the mycobacterium tuberculosis antigen from distant foci in the absence of any infectious agent in the eye. We describe an antituberculous treatment for patients with granulomatous uveitis non-responsive to other treatments in this prospective study. In this clinical trial, 50 patients (32 women, 18 men) with granulomatous uveitis (2 granulomatous uveitis and coroiditis, 2 intermediate uveitis, 1 anterior scleritis and granulomatous uveitis, 1 multifocal uveitis, 1 multifocal uveitis and bilateral panuveitis, 43 granulomatous uveitis) were studied. Mean age of the patients was 45.34±13.71. Patients (7.1%) had been previously treated due to pulmonary tuberculosis. 9 (21.4%) of the patients had a history of tuberculosis contact. Tuberculine skin test (TST) was positive in 45 patients (96%) and Quantiferon – GOLD test was positive in 43 patients (89%). 41 (82%) patients with latent tuberculosis who were non-responsive to all treatments were considered as tuberculosis and treated with antituberculous agents. 19 patients (46%) responded well to anti tuberculous treatment. 15 patients (37%) were non-responsive to the treatment and in follow-up granulamatous uveitis recurred. 5 patients were out of follow-up.  This study indicates that antituberculous treatment is an option which must be considered for patients with latent tuberculous who were determined to be granulomatous uveitis and also who were non-responsive to other treatments.
Primary ciliary aplasia as a cause of recurrent respiratory infections in an infertile young man
Authors: Mario Canciani, Sara Bortolato, Gioia N. Canciani, Margherita De Santi
Journal: European Respiratory Journal (2011)

We present a case of primary ciliary aplasia (PCA) a rare form of primary ciliary dyskinesia, characterised by the total absence of cilia in respiratory and sperm cells.  B.A. was born to healthy, first-degree related parents (first cousins). A few hours following birth, the patient developed the first of recurrent upper and lower respiratory tract infections. Cystic fibrosis, major immune deficiencies and allergic sensitization were excluded. Chest CT showed diffuse bronchiectasis of both middle lobes. Nasal and bronchial mucosa samples on transmission electron microscopy revealed total lack of cilia and basal bodies on columnar epithelial cells, despite displaying the morphological features of ciliated cells. At puberty, testicular volume and serum hormone levels were normal. Seminal fluid analysis revealed: ejaculate volume of 0.6 ml; pH 8; low sperm concentration (0.5-0.7 million of spermatozoa/ml); and asthenospermia-terathospermia (immotile spermatozoa > 75%). Ultrastructural examination showed a high prevalence of spermatozoa with normal nuclei and well structured acrosomes but a high percentage of spermatozoa (>80%) totally lacked the neck region; this region was embedded in a wide cytoplasm in the remaining 20%. No tails were detected in any samples. As the respiratory mucosa and seminal fluid analyses showed the same morphological features, the diagnosis of PCA was made. The clinical presentation at birth and the parents9 consanguinity make it unlikely that these changes are the result of infection or exposure to pollutants, thus supporting the hypothesis that PCA can be an inherited disorder.
Dose-dependent efficacy of daratumumab (DARA) as monotherapy in patients with relapsed or refractory multiple myeloma (RR MM).
Authors: Henk M. Lokhorst, Jacob Laubach, Hareth Nahi, Torben Plesner, Peter Gimsing, Markus Hansson, Monique Minnema, Ulrik Niels Lassen, Jakub Krejcik, Tahamtan Ahmadi, Steen Lisby, Linda Basse, Nikolai C. Brun, Paul G. Richardson
Journal: Journal of Clinical Oncology (2014)

8513 Background: Pts with RR MM received DARA for 9 wks in doses of 0.005-24mg/kg in the GEN501 dose-escalation part (Lokhorst: EHA 2013 abstract S576). The purpose of the GEN501 expansion part, which has completed enrollment, was to evaluate safety and efficacy of 2 doses of DARA for up to 24 mths using alternate dose schedules. Methods: Pts ≥18 yrs, RR to at least 2 prior lines of therapy, incl. IMiDs and proteasome inhibitors, and ineligible for ASCT were enrolled at 2 dose levels: A: 8mg/kg +/- pre-dose (10mg) wkly for the first 8 infusions.B: 16mg/kg without pre-dose with a 3-wk washout period between the first 2 doses followed by 7 wkly doses. Then all pts were dosed every 2nd wk for 16 wks followed by dosing every 4th wk until disease progression, toxicity or for max 24 mths. Results: Data from 30 pts in the 8mg/kg cohort and 15 pts in the 16mg/kg cohort recruited into the GEN501 expansion part are presented. Median age was 58.2 (35.1-76.9) and 64.1 (50.5-75.0) years, prior treatment lines were 5 (3-11), and 4 (2-8) and time since diagnosis was 5.5 (2.1-15.2) and 7.1 (0.4-13.3) years, respectively. Median number of DARA infusions was 10.5 vs 7.0, reflecting the more recent initiation of the 16mg/kg cohort. Infusion times were 3.5 vs 3.4 hours in the 8 and 16mg/kg groups, respectively. Safety: No dose-related increase in adverse events (AEs) was observed. Most common AEs reported (in ≥20% of all pts) were pyrexia, allergic rhinitis, fatigue, upper respiratory tract infection, diarrhea, dyspnea and cough. Only mild (Gr 1 and 2) infusion-related reactions (IRRs) were reported with 27% in the 16mg/kg group vs 20% in the 8mg/kg group. 2 SAEs, 1 in each group, were assessed as related to DARA (1 thrombocytopenia, 1 lymphocytopenia). One pt was withdrawn after 1st full dose due to thrombocytopenia Gr 3. Omission of the pre-dose increased neither the incidence nor the severity of IRRs. Conclusions: DARA monotherapy in RR MM pts resulted in high single agent activity when administered at 16 mg/kg (46% ORR). The safety profile was manageable. Full response data will be presented at the meeting incl. bone marrow assessments. Clinical trial information: NCT00574288. PD SD MR PR VGPR ORRA 8 mg/kg n=30 9 14 5 2 0 7% 16 mg/kg n=13B 3 3 1 3 3 46% A PR or better. B 2 pts only had 1st dose at data cutoff.
Evaluation and treatment of patients receiving radiation for cancer of the rectum or sigmoid colon in the United States: results of the 1988-1989 Patterns of Care Study process survey.
Authors: L Coia, M Wizenberg, A Hanlon, L Gunderson, D Haller, J Hoffman, R Kline, M Mohiuddin, A Russell, J Tepper
Journal: Journal of Clinical Oncology (1994)

PURPOSE For the first time, a Patterns of Care Study (PCS) was conducted in 1989 to determine the national practice standards of radiation oncologists in evaluating and treating adenocarcinoma of the rectum and sigmoid colon. MATERIALS AND METHODS A national survey of 73 institutions using two-stage cluster sampling was conducted, and specific information on 408 patients from 69 facilities with adenocarcinoma of the rectum and sigmoid colon who received radiation as part of definitive or adjuvant management was collected. RESULTS Using the modified Astler-Coller (MAC) pathologic staging system, the stage distribution was as follows: A, 0.5%; B1, 4.4%; B2, 23.5%; B3, 5.1%; C1, 8.9%; C2, 30.2%; and C3, 6.6%. Preoperative radiation was used in 29% of patients, but the total dose was greater than 40 Gy in only 20%. Seventy-three percent of patients received postoperative radiation, with approximately 4% receiving combined preoperative and postoperative radiation. Chemotherapy was administered to 44% of patients overall, representing 55% of patients with disease through the bowel wall and/or involving lymph nodes. Only 37% of all patients received chemotherapy concurrent with radiation. An abdominoperineal resection was used in 43%; a low anterior resection was used in 43% as well, while 5% underwent other types of bowel resection. Approximately 8% of patients were treated with a local curative procedure less than bowel resection (eg, local excision, endoscopic resection, fulguration, or contact radiation). At least one third of patients had interruption in their pelvic irradiation of greater than 3 days. There was no statistically significant difference in the frequency of treatment interruptions by dose per fraction or whether chemotherapy was given concurrent with radiation. There was no significant difference in total dose delivered to patients staged B2 and higher treated without chemotherapy compared with concurrent chemotherapy and radiation. Also, there was no significant difference in total dose delivered to patients with B1 and B2, or C1 and C2 versus B3 or C3 cancer. CONCLUSION This study was conducted on patients treated just before the 1990 National Institutes of Health consensus guidelines issued on the management of colon and rectal cancer. This study indicates that the minority of patients treated with radiation in 1988 and 1989 received concurrent chemoradiation, as currently recommended. Additionally, insofar as present studies are investigating important issues such as the use of sphincter-sparing procedures, preoperative radiation and chemotherapy, and the importance of radiation dose and scheduling with chemotherapy, the information provided by this study will serve as a useful baseline to track future changes in rectal cancer evaluation and management.
Understanding globin regulation in -thalassemia: it's as simple as , , , 
Authors: A. Bank
Journal: Journal of Clinical Investigation (2005)

A vast excess of α-globin production and inadequate γ-globin compensation lead to the development of severe anemia in human β-thalassemia. Newly identified modifiers of α- and γ-globin synthesis and insights into the mechanisms of globin regulation provide the tools for potential new approaches to treating this and other red blood cell disorders. In the study by Han and colleagues in this issue of the JCI, the activity of a heme-regulated protein, HRI, is shown to modulate the accumulation of excess α-globin chains in murine β-thalassemia and to decrease the severity of the disease.
Rejection of a Transplantable Marek's Disease Lymphoma in Normal Versus Immunologically Deficient Chickens 2 3
Authors: B. W. Calnek, J. Fabricant, K. A. Schat, K. K. Murthy
Journal: JNCI Journal of the National Cancer Institute (1978)

Normal and immunosuppressed N-line chickens were challenged at 7 days of age with a transplantable Marek's disease (MD) lymphoma. They were subjected to immunosuppressive treatments that included embryonal bursectomy (BX), neonatal thymectomy (TX), cyclophosphamide (CY) administration, a combination of BX and TX or TX and CY administration, or neonatal infection with virulent MD virus. The transplant cells were of N-line origin. In all normal intact chicks, progressively growing palpable tumors at the inoculation site appeared, usually by 6-8 days; these regressed in most birds between 14 and 18 days post inoculation. Many birds in which transplanted tumors regressed later developed visceral lymphomas. Transplanted tumor grow1h and rejection were unaffected by TX or CY treatments, but the combined TX and CY treatment and prior MD virus infection significantly delayed tumor rejection. Bursectomized chicks developed fewer palpable tumors and, when they developed tumors, those tumors regressed more rapidly than did those in intact birds. Both BX and CY treatments markedly reduced the incidence of MD through 10 weeks. The enhanced transplant rejection in bursectomlzed chicks could have been due to “blocking antibody,” but the rejection pattern was not altered by repeated injections of sera from chicks with tumors or from chicks with tumors that regressed. injections of convalescent sera from MD virus-exposed birds enhanced the rejection of transplants in intact birds.
Meta-analysis on nocturnal non-invasive positive pressure ventilation for stable COPD; an update
Authors: Fransien Struik, Yves Lacasse, Huib Kerstjens, Peter Wijkstra
Journal: European Respiratory Journal (2012)

Introduction   Nocturnal non-invasive positive pressure ventilation (NIPPV) might be beneficial in stable hypercapnic patients with COPD. However, evidence remains conflicting.   Aim    To determine the effect of NIPPV in patients with stable hypercapnic COPD.   Methods   This meta-analysis gathered individual patient data from randomized controlled trials (RCTs) comparing NIPPV plus standard therapy with standard therapy alone. The current analyses are limited to gas exchange parameters.   Results   Our older Cochrane review and 3 new studies were identified, totaling 5 short-term and 2 long-term RCTs. After 3 months (n=162; age 66 yrs; FEV 1  0.78L; IPAP 15.4(10-22); EPAP 3.4) we found a significant change in PaCO2 (mean difference= -3.56 (95% CI=-4.93;-2.18 mmHg)) and PaO2 (1.84 (95% CI=0.24; 3.45 mmHg)) but no significant changes after 12 months of NIPPV (n=118).   Conclusions   With the newer studies, this update now finds a significant decrease in PaCO2 and increase in PaO2 in stable hypercapnic COPD patients after 3 months of NIPPV, but not after a year. There was considerable variation in settings; notably inspiratory pressures.
Phase I study of high-dose piroxantrone with granulocyte colony-stimulating factor.
Authors: D M Savarese, A M Denicoff, S L Berg, M Hillig, S P Baker, J A O'Shaughnessy, C Chow, G A Otterson, F M Balis, D G Poplack
Journal: Journal of Clinical Oncology (1993)

We performed a phase I trial of piroxantrone with and without granulocyte colony-stimulating factor (G-CSF) to determine whether the use of this cytokine would enable us to increase the dose-intensity of piroxantrone.Thirty-eight patients received 121 courses of piroxantrone administered once every 21 days. Initial patient cohorts received piroxantrone alone starting at 150 mg/m2 and the dose was escalated in subsequent patients until dose-limiting toxicity (DLT) was reached. Patient cohorts then received escalating doses of piroxantrone starting at 185 mg/m2 administered with G-CSF beginning day 2.Dose-limiting neutropenia occurred in three of six patients treated with 185 mg/m2 piroxantrone; the maximum-tolerated dose (MTD) of piroxantrone alone was 150 mg/m2. Three of six patients treated with piroxantrone and G-CSF exhibited dose-limiting thrombocytopenia at 445 mg/m2; the MTD of piroxantrone with G-CSF was thus 355 mg/m2. Seven patients developed symptomatic congestive heart failure (CHF) at cumulative piroxantrone doses ranging from 855 to 2,475 mg/m2 and two have died of cardiotoxicity. Of these patients, six of seven had previously received doxorubicin. Other nonhematologic toxicity was mild.The use of G-CSF results in a more than twofold increase in the MTD of piroxantrone. However, symptomatic cardiotoxicity is prominent, especially in patients who have received prior treatment with anthracyclines.
Seborrhoeic keratoses and carcinoma of the large bowel.
Authors: K. LIDDELL, J.E. WHITE, I.W. CALDWELL
Journal: British Journal of Dermatology (1975)

Journal Article Seborrhoeic keratoses and carcinoma of the large bowel: THREE CASES EXHIBITING THE SIGN OF LESER‐TRÉLAT Get access K. LIDDELL, K. LIDDELL Southampton University Hospital Group Search for other works by this author on: Oxford Academic Google Scholar J.E. WHITE, J.E. WHITE Southampton University Hospital Group Search for other works by this author on: Oxford Academic Google Scholar I.W. CALDWELL I.W. CALDWELL Southampton University Hospital Group Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 92, Issue 4, 1 April 1975, Pages 449–452, https://doi.org/10.1111/j.1365-2133.1975.tb03107.x Published: 01 April 1975 Article history Accepted: 26 July 1974 Published: 01 April 1975
Discontinuation of empirical antibiotic therapy in neutropenic acute myeloid leukaemia patients with fever of unknown origin: is it ethical?
Authors: J.-B. Micol, C. Chahine, P.-L. Woerther, D. Ghez, F. Netzer, C. Dufour, M. Merad, F. Blot, E. Chachaty, S. de Botton, B. Gachot
Journal: Clinical Microbiology and Infection (2013)
Fractional exhaled nitrogen oxide (FeNO), asthma, respiratory symptoms and self-reported allergy among high school students in Penang, Malaysia
Authors: Jamal Hisham, Gunilla Wieslander, Zailina Hashim, Vinoshini Rao, Dan Norback
Journal: European Respiratory Journal (2013)

Background : We investigated the association between FeNO and respiratory symptoms, asthma and allergy among high school students in Penang, Malaysia.

Methods : Eight high schools were randomly selected in Penang. In each school, 4 classes were randomly selected, and 20 students were randomly selected from each class. A total of 368 pupils (58%) answered the questionnaire and 348 participated in the FeNO measurements using a NIOX-MINO. FeNO was adjusted for gender, race, smoking and parental asthma or allergy.

Results : The median FeNO was 17ppb (IQR 10-39), with 45% of the students reporting levels above 20 ppb. Boys had higher FeNO (p=0.001). Prevalence of respiratory symptoms in the last 12 month was 14% for wheeze, 9% for wheeze with breathlessness, 38% for daytime and 11% for night time attacks of breathlessness, while 13% ever had asthma, 11% had doctor’s diagnosed asthma and 37% had any respiratory infection in the last 3 months. Moreover, 9% reported pollen allergy, 8% cat allergy, 3% dog allergy, 5% mould allergy, 19% any food allergy/intolerance and 14% seafood allergy. FeNO was higher in students with wheeze (p=0.004), wheeze with breathlessness (p=0.04), ever asthma (p<0.001), doctor’s diagnosed asthma (p=0.002), cat allergy (p=0.01), food allergy/intolerance (p<0.001) and seafood allergy (p=0.001). Moreover, FeNO was higher in students with rhinitis symptoms in the last 3 months (p<0.001 for runny nose and p=0.002 for nasal congestion).

Discussion : Median FeNO was associated with wheeze, doctor’s diagnosed asthma, rhinitis symptoms and self-reported allergy to cat and seafood.
The Mammalian Blood-Testis Barrier: Its Biology and Regulation
Authors: Dolores D. Mruk, C. Yan Cheng
Journal: Endocrine Reviews (2015)

Spermatogenesis is the cellular process by which spermatogonia develop into mature spermatids within seminiferous tubules, the functional unit of the mammalian testis, under the structural and nutritional support of Sertoli cells and the precise regulation of endocrine factors. As germ cells develop, they traverse the seminiferous epithelium, a process that involves restructuring of Sertoli-germ cell junctions, as well as Sertoli-Sertoli cell junctions at the blood-testis barrier. The blood-testis barrier, one of the tightest tissue barriers in the mammalian body, divides the seminiferous epithelium into 2 compartments, basal and adluminal. The blood-testis barrier is different from most other tissue barriers in that it is not only comprised of tight junctions. Instead, tight junctions coexist and cofunction with ectoplasmic specializations, desmosomes, and gap junctions to create a unique microenvironment for the completion of meiosis and the subsequent development of spermatids into spermatozoa via spermiogenesis. Studies from the past decade or so have identified the key structural, scaffolding, and signaling proteins of the blood-testis barrier. More recent studies have defined the regulatory mechanisms that underlie blood-testis barrier function. We review here the biology and regulation of the mammalian blood-testis barrier and highlight research areas that should be expanded in future studies.
Fc Gamma Receptor 3A and 2A Polymorphisms Do Not Predict Response to Rituximab in Follicular Lymphoma
Authors: Vaishalee P. Kenkre, Fangxin Hong, James R. Cerhan, Marcia Lewis, Leslie Sullivan, Michael E. Williams, Randy D. Gascoyne, Sandra J. Horning, Brad S. Kahl
Journal: Clinical Cancer Research (2015)

Preclinical studies suggest that SNPs in the Fc gamma receptor (FCGR) genes influence response to rituximab, but the clinical relevance of this is uncertain.We prospectively obtained specimens for genotyping in the rituximab extended schedule or re-treatment trial (RESORT) study, in which 408 previously untreated, low tumor burden follicular lymphoma (FL) patients were treated with single agent rituximab. Patients received rituximab in 4 weekly doses and responders were randomized to rituximab re-treatment (RR) upon progression versus maintenance rituximab (MR). SNP genotyping was performed in 321 consenting patients.Response rates to initial therapy and response duration were correlated with the FCGR3A SNP at position 158 (rs396991) and the FCGR2A SNP at position 131 (rs1801274). The response rate to initial rituximab was 71%. No FCGR genotypes or grouping of genotypes were predictive of initial response. A total of 289 patients were randomized to RR (n = 143) or to MR (n = 146). With a median follow-up of 5.5 years, the 3-year response duration in the RR arm and the MR arm was 50% and 78%, respectively. Genotyping was available in 235 of 289 randomized patients. In patients receiving RR (n = 115) or MR (n = 120), response duration was not associated with any FCGR genotypes or genotype combinations.Based on this analysis of treatment-naïve, low tumor burden FL, we conclude that the FCGR3A and FCGR2A SNPs do not confer differential responsiveness to rituximab.