tbuckley/cabot-search huggingface dataset:
Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome
Authors: Pia S. Pannaraj, Fan Li, Chiara Cerini, Jeffrey M. Bender, Shangxin Yang, Adrienne Rollie, Helty Adisetiyo, Sara Zabih, Pamela J. Lincez, Kyle Bittinger, Aubrey Bailey, Frederic D. Bushman, John W. Sleasman, Grace M. Aldrovandi
Journal: JAMA Pediatrics (2017)

<h3>Importance</h3> Establishment of the infant microbiome has lifelong implications on health and immunity. Gut microbiota of breastfed compared with nonbreastfed individuals differ during infancy as well as into adulthood. Breast milk contains a diverse population of bacteria, but little is known about the vertical transfer of bacteria from mother to infant by breastfeeding. <h3>Objective</h3> To determine the association between the maternal breast milk and areolar skin and infant gut bacterial communities. <h3>Design, Setting, and Participants</h3> In a prospective, longitudinal study, bacterial composition was identified with sequencing of the 16S ribosomal RNA gene in breast milk, areolar skin, and infant stool samples of 107 healthy mother-infant pairs. The study was conducted in Los Angeles, California, and St Petersburg, Florida, between January 1, 2010, and February 28, 2015. <h3>Exposures</h3> Amount and duration of daily breastfeeding and timing of solid food introduction. <h3>Main Outcomes and Measures</h3> Bacterial composition in maternal breast milk, areolar skin, and infant stool by sequencing of the 16S ribosomal RNA gene. <h3>Results</h3> In the 107 healthy mother and infant pairs (median age at the time of specimen collection, 40 days; range, 1-331 days), 52 (43.0%) of the infants were male. Bacterial communities were distinct in milk, areolar skin, and stool, differing in both composition and diversity. The infant gut microbial communities were more closely related to an infant's mother's milk and skin compared with a random mother (mean difference in Bray-Curtis distances, 0.012 and 0.014, respectively;<i>P</i> &lt; .001 for both). Source tracking analysis was used to estimate the contribution of the breast milk and areolar skin microbiomes to the infant gut microbiome. During the first 30 days of life, infants who breastfed to obtain 75% or more of their daily milk intake received a mean (SD) of 27.7% (15.2%) of the bacteria from breast milk and 10.3% (6.0%) from areolar skin. Bacterial diversity (Faith phylogenetic diversity,<i>P</i> = .003) and composition changes were associated with the proportion of daily breast milk intake in a dose-dependent manner, even after the introduction of solid foods. <h3>Conclusions and Relevance</h3> The results of this study indicate that bacteria in mother's breast milk seed the infant gut, underscoring the importance of breastfeeding in the development of the infant gut microbiome.
The macrophage activation marker, soluble CD163 is associated with hepatic inflammation and fibrosis in chronic viral hepatitis C and declines during effective direct-acting antiviral therapy
Authors: T.L. Laursen, C. Siggaard, K. Kazankov, T. Sandahl, H.J. Møller, J. George, A. Ong, M.W. Douglas, A.L. Laursen, P. Leutscher, A. Hiramatsu, T. Nakahara, K. Chayama, H. Grønbæk
Journal: Journal of Hepatology (2017)
Molecular Profiling of High-Risk Pediatric Acute Myeloid Leukemia
Authors: Lianna J Marks, Jennifer A Oberg, Julia L Glade-Bender, Susan J Hsiao, Danielle Pendrick, Anthony N Sireci, Stuart J Andrews, Mahesh M Mansukhani, Andrew L. Kung, Maria Luisa Sulis
Journal: Blood (2016)
Real-World Use of Pomalidomide and Dexamethasone in Double Refractory Multiple Myeloma: A Multicentre UK Experience
Authors: Nicola Maciocia, Andrew Melville, Paul Michael Maciocia, Simon Cheesman, Faye Sharpley, Karthik Ramasamy, Matthew Streetly, Matthew W Jenner, Reuben Benjamin, Stephen A Schey, Rakesh Popat, Shirley D'Sa, Ali Rismani, Kwee L Yong, Neil Rabin
Journal: Blood (2016)
A new HDV mouse model showing important features of human infection and identifying MAVS as a key player in IFN-β induction
Authors: C. Usai, L. Suarez-Amaran, M. Di Scala, C. Godoy, Y. Ni, M. Hommel, L. Palomo, V. Segura, C. Olagüe, A. Vales, E. Salido, J. Prieto, S. Urban, F. Rodriguez-Frias, R. Aldabe, G. Gonzalez-Aseguinolaza
Journal: Journal of Hepatology (2017)
The Mechanism By Which Mutant Nucleophosmin (NPM1) Creates Leukemic Self-Renewal Is Readily Reversed
Authors: Xiaorong Gu, Reda Z. Mahfouz, Quteba Ebrahem, Francis Enane, Tomas Radivoyevitch, Michael J. Clemente, Bartlomiej P Przychodzen, Zhenbo Hu, Ramesh Balusu, Claudiu V. Cotta, David N. Wald, Yosef Landesman, Maria Paola Martelli, Brunangelo Falini, Jaroslaw P Maciejewski, Yogenthiran Saunthararajah
Journal: Blood (2016)
Incidence and prevalence of psoriatic arthritis in Denmark: a nationwide register linkage study
Authors: Alexander Egeberg, Lars Erik Kristensen, Jacob P Thyssen, Gunnar Hilmar Gislason, Alice B Gottlieb, Laura C Coates, Denis Jullien, Paolo Gisondi, Dafna D Gladman, Lone Skov, Lotus Mallbris
Journal: Annals of the Rheumatic Diseases (2017)

To examine the incidence and temporal trends of psoriatic arthritis (PsA) in the general population in Denmark.Using nationwide registry data, we estimated the number of patients with incident PsA within each 1-year period between 1997 and 2011 and calculated the rate of PsA cases within gender and age subgroups. Incidence rates were presented per 100 000 person-years.There was a female predominance ranging from 50.3% (1998) to 59.2% (2010), and the mean age at time of diagnosis was 47-50 years. We identified a total of 12 719 patients with PsA (prevalence=0.22%), including 9034 patients where the PsA diagnosis was made by a rheumatologist (prevalence=0.16%). Incidence rates of PsA (per 100 000 person-years) increased from 7.3 in 1997 to a peak incidence of 27.3 in 2010. Incidence rates were highest for women and patients aged 50-59 years, respectively. The use of systemic non-biologic agents, that is, methotrexate, leflunomide, ciclosporin or sulfasalazine increased over the 15-year study course and were used in 66.3% of all patients. Biologic agents (etanercept, infliximab, adalimumab, certolizumab pegol, golimumab or ustekinumab) were used in 17.7% of patients with PsA.We found a clear trend of rising PsA incidence on a national level. While the cause remains unclear, our findings might be explained by increased attention by patients and physicians.
Rationality in prophylactic central neck dissection in clinically node-negative (cN0) papillary thyroid carcinoma: Is there anything more to say? A decade experience in a single-center
Authors: C. Dobrinja, M. Troian, T. Cipolat Mis, G. Rebez, S. Bernardi, B. Fabris, L. Piscopello, P. Makovac, F. Di Gregorio, N. de Manzini
Journal: International Journal of Surgery (2017)
Correlation between vitamin D as measured by 25(OH) choleciferol and PSA in veterans with prostate cancer.
Authors: Nancy S. Vander Velde, Lizheng Shi, Krishnarao Moparty, Hui Shao
Journal: Journal of Clinical Oncology (2015)

e16004 Background: Several observation and epidemiologic studies have suggested that the incidence of prostate cancer seems to be lower in relation to ultraviolet light exposure and distance from the equator, which has led to theories that vitamin D may play a role in the prevention of cancer. This study seeks to determine if a correlation exists between vitamin D levels in the serum as measured by 25 (OH) cholecalciferol and serum PSA in male veterans with prostate cancer. Methods: Veterans with prostate cancer seen in the urology or oncology clinic at the Southeast Louisiana Veterans Affairs Healthcare system were identified using ICD 9 codes. After informed consent, serum 25(OH) hydroxyvitamin D levels and PSA were drawn. 119 patients were enrolled on the study from 1/16/13 to 11/15/13. Demographic data such as age, ethnicity, cancer stage, use of vitamin D supplements, gleason score, and treatment were examined. Pearson’s correlation analysis was performed. Results: 91 of the participants were African American; 61 of these had low vitamin D and 30 had normal levels. 27 were white; 15 had low vitamin D, 12 were normal. There were no Hispanic or Asian patients participating. There was one patient self-identified as other who had vitamin D in the normal range. The mean age of the veteran population was 66.27, and 38.66% (46) of the patients had underwent prostatectomy. There were 24 patients (20.17%) who were taking vitamin D supplements. We conducted correlation analysis on both the whole sample and multiple subgroups. We found the correlation coefficient for vitamin D and PSA in the subgroup of veterans with high PSAs and no prostatectomy was -0.38 (p = 0.133). Conclusions: There was no significant correlation between vitamin D and PSA in veterans with prostate cancer. There was a trend for correlation in the subgroup of veterans with high PSAs who did not undergo prostatectomy.
Capecitabine-gemcitabine in thymic epithelial tumors.
Authors: Giovannella Palmieri, Carlo Buonerba, Giuseppe Di Lorenzo, Piera Federico, Lucia Nappi, Pasquale Rescigno, Filomena Calabrese, Margaret Ottaviano, Sabino De Placido, Vincenzo Damiano
Journal: Journal of Clinical Oncology (2013)

e18536 Background: Thymic epithelial tumors (TET) are a rare disease. Once loco-regional treatments have failed, platinum-based chemotherapy is employed to prolong survival and palliate symptoms. In November 2005, we started prospective multi-center trial to test capecitabine-gemcitabine in pretreated TET. Mature results are awaited. We here retrospectively review all patients with TET treated at our Institution with this schedule. Methods: Patients with pathologically confirmed TET receiving at least one cycle of capecitabine-gemcitabine were included in this analysis. Descriptive statistics and frequency counts were used to summarize characteristics of the study population. Median numbers were presented with interquartile ranges. Results: Twenty-three patients were included in this single-center analysis. Six patients had a thymic carcinoma, while three, eight, two and four patients had a B1, B2, B2/B3 and B3 TET, respectively. Median age was 52 years (47-58).Eleven patients were female. Gemcitabine was delivered at the dose of 800-1,000 mg/m2 by 30-minute infusion on days 1 and 8 every 3 weeks along with oral capecitabine at the dose of 500-650 mg/m2 twice daily on days 1 to 14. Fourteen patients had an ECOG performance status of 0, one of 2, the remaining of 1. Seven patients had an IV a tumor, while the remaining had a IVb tumor. All patients, except for three for whom capecitabine-gemcitabine was the first line of therapy, had received a platinum-based regimen. Only one patient was primary refractory, while a complete response was obtained in 2 patients, a partial response in four patients, and the remaining had stable disease. Median PFS was 7 months (range, 4-9). Median survival was 12 months (6-20). Treatment was well tolerated. Twelve patients showed grade 3/4 toxicity, of whom two patients showed severe anemia, six severe neutropenia, four severe thrombocytopenia, two severe diarrhea and one severe fatigue. Conclusions: In this retrospective analysis, gemcitabine-capecitabine was confirmed to have a high activity in TET. Mature results from the ongoing multicenter trial are awaited.
A phase I/II trial of the combination of romidepsin and lenalidomide in patients with relapsed/refractory lymphoma and myeloma: Phase I results.
Authors: Matthew Alexander Lunning, Jia Ruan, Sumithra Nair, Adam M. Boruchov, Regina Byrne, John F. Gerecitano, Paul A. Hamlin, Beth Inserra, John Leonard, Peggy Lynch, Matthew J. Matasar, Alison J. Moskowitz, Craig Moskowitz, Patricia L. Myskowski, Patrick Nolan, Maria Lia Palomba, Christiane Quefeld, David J. Straus, Andrew David Zelenetz, Steven M. Horwitz
Journal: Journal of Clinical Oncology (2014)

8582 Background: Epigenetic manipulation and immunomodulation are therapeutic strategies in hematologic malignancies. Romidepsin (Romi), a histone deacetylase inhibitor, and lenalidomide (Len), an immunomodulatory agent, both have efficacy and lack cumulative toxicity in relapsed/refractory (rel/ref) lymphoma and myeloma. We report the phase I results from an ongoing phase I/II study. Methods: The phase I portion evaluated toxicity (tox), maximum tolerated dose (MTD) and clinical activity of Romi-Len. Romi was given IV on days 1, 8, and 15 and Len was given orally on days 1-21 of a 28-day cycle. A standard 3+3 dose escalation schema was followed and 4 cohorts were planned: 1) Romi 8 mg/m2-Len 15 mg, 2) Romi 8 mg/m2-Len 25 mg, 3) Romi 10 mg/m2-Len 25 mg, 4) Romi 14 mg/m2-Len 25 mg. Dose-limiting tox (DLT) was defined as any of the following in cycle 1: ≥ grade 3 non-heme tox, ≥ grade 4 heme tox or grade 3 heme tox resulting in a significant delay of treatment. Tumor response was based on disease-specific criteria. Patients (pts) could be treated to progression or intolerance. Results: Nineteen pts with rel/ref lymphoma have been enrolled with 15 pts evaluable for DLT (13 pts for response). Three pts progressed prior to study drug and 1 pt progressed in cycle 1; all were replaced for DLT assessment. Two DLTs have occurred to date: cohort 2, 1/7 pts had grade 4 pneumonia; cohort 4, 1/3 pts had grade 3 thrombocytopenia delaying therapy. One grade 3 neutropenic fever has been seen post cycle 1. Of the 13 pts evaluable for response, the overall response rate is 54% (7/13) with complete response in 15% (2/13) and partial response in 39% (5/13). Four responses are ongoing at 4-13 cycles. Responses by subtype include B-cell 50% (2/4), T-cell 67% (4/6), and Hodgkin 33% (1/3). No cumulative tox has been seen. Conclusions: The combination of Romi-Len appears to be well tolerated without unexpected tox up to standard single agent doses of each drug. Responses have been seen across multiple lymphoma subtypes. Disease specific phase II cohorts will include B-cell lymphomas, T-cell lymphomas, and multiple myeloma. Final phase 1 safety and efficacy data will be presented. Clinical trial information: NCT#01755975.
An open-label phase 3b/4 safety trial of flat-dose nivolumab plus ipilimumab in patients with advanced non-small cell lung cancer (NSCLC)
Authors: L. Paz-Ares, B. Lash, I. Albert, G. Gagnon, C. Chakmakjian, N. Ready, W. Hu, L. Krug, J. Fairchild, R.N. Pillai
Journal: Annals of Oncology (2017)
Assessment of the variability of and effect of hormone therapy on circulating tumor cell numbers and androgen receptor expression in patients with prostate cancer.
Authors: Noel W Clarke, Sarah E Marley, Andrew M. Hughes, Anthony F Nash, Michael D Malone, Jim W Growcott, Darren R Hodgson, Robert Sloane, David J Moore, Tim H Ward, P. Anthony Elliott, Caroline Dive
Journal: Journal of Clinical Oncology (2012)

e15141 Background: In prostate cancer (PC) CTC number and character may offer a means of assessing disease load and target engagement. However, capture platforms differ, presenting challenges to enumeration and molecular characterisation. We report the findings of a pilot study assessing the intra- and inter-patient variability of 2 different platforms, and the feasibility of measuring CTC-androgen receptor (AR) expression by immunohistochemistry (IHC) in a single platform. Methods: Following ethical approval, 4 PC cohorts (n = 12, 12, 10, and 6 respectively) were recruited; #1 localised, no hormonal therapy; #2 and #3: castrate-resistant, receiving LHRHa or LHRHa and bicalutamide, respectively; #4: newly diagnosed locally advanced, no hormonal therapy. Blood (2 x 10 mL, 2 visits #1-3; 2 x 10 mL,1 visit #4) was taken and CTCs isolated using either the Cell Search CTC Test (Veridex) or Isolation by Size of Epithelial Cells Technique (ISET) for enumeration, and ISET for AR expression (H-score [(% 1*1+) + (% 2*2+) + (% 3*3+)]). Results: There was no correlation between Veridex and ISET for detection of CTCs (Veridex enumeration:14%, 63%, 53% and 0% of samples in #1 - 4, respectively, vs ISET enumeration: 100% of samples across all cohorts) with the latter platform detecting a significantly higher number of CTCs/4mls from patients in cohort #4 vs #1 (GLS Means 119 vs 46, p=0.0135). For both platforms there was no evidence of a systematic change in the counts at two separate visits 2 weeks apart. AR was detectable in approximately 25-35% CTCs from all cohorts and there were no significant differences in the H-score between the cohorts, although the number of AR-positive cells/4mls was significantly higher in #4 vs #1, and #2 (GLS Means 25 vs 14, 15, p= 0.0197, 0.0398, respectively). Conclusions: Populations of CTCs detected by Veridex and ISET appear stable over short durations (2 weeks) and AR was detected in a proportion of CTCs by ISET using IHC. Further work is required to find alternative methodologies with greater specificity.
Hepatocyte nuclear factor 4α played a different role in lipotoxicity and bile acid toxicity in non-alcoholic fatty liver disease model
Authors: J.S. Lee, D.W. Jun, S.B. Ahn, W.K. Saeed, Y.J. Chae, J.Y. Jeong, H.T. Kang, J.H. Sohn, E.C. Jang, B.-K. Kang
Journal: Journal of Hepatology (2017)
Metabolic syndrome and obesity are the cornerstones of liver fibrosis in HIV-monoinfected patients
Authors: M. Lemoine, K. Lacombe, J.-P. Bastard, L. Fonquernie, M. Sébire, S. Fellahi, N. Valin, J. Capeau, P.-M. Girard, J.-L. Meynard
Journal: Journal of Hepatology (2017)
Abstract B02: A regulatory role for codon bias in KRAS-driven tumor progression and therapeutic resistance
Authors: Erin Kaltenbrun, Moiez Ali, Sarah Jo Stephens, Christopher Counter, Kris Wood
Journal: Cancer Research (2017)

Abstract The RAS genes HRAS, NRAS, and KRAS are mutated in a quarter of all human cancers to drive the initiation and maintenance of cancer. While all three genes encode nearly identical proteins, KRAS is highly enriched, compared to the other isoforms, in rare codons. These rare codons impede translation and subsequent protein expression. Despite this, increased KRAS expression and signaling is associated with malignancy and cancer progression, and KRAS mutations have been implicated as drivers of resistance to diverse targeted therapies. Using a pathway-activating genetic screen in a panel of human cancer cell lines, we find that mutant HRAS actually has greater resistance conferring potential than mutant KRAS. This differential resistance is governed by codon bias, suggesting that KRAS-driven resistance is limited by inefficient protein expression. We hypothesized that KRAS-driven cancer progression and primary resistance to a targeted therapeutic, such as an EGFR inhibitor, is dependent upon both the presence of a KRAS mutation as well as the ability of cancer cells to overcome this translational barrier. Indeed, we find that KRAS-mutant cancer cells globally upregulate translation, which results in enhanced expression of mutant KRAS and the formation of a translationally primed state that can be therapeutically exploited using inhibitors of protein translation. Collectively, these findings reveal a critical regulatory role for codon bias in mediating KRAS-driven therapeutic resistance and cancer progression. Ongoing work seeks to more precisely define the mechanisms governing KRAS translation in the setting of cancer and therapeutic resistance to obtain more specific approaches to target these tumors. Citation Format: Erin Kaltenbrun, Moiez Ali, Sarah Jo Stephens, Christopher Counter, Kris Wood. A regulatory role for codon bias in KRAS-driven tumor progression and therapeutic resistance. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B02.
Sarcopenia is associated with increased hospital expenditure in patients undergoing major cancer surgery of the alimentary tract
Authors: J. Van Vugt, S. Buettner, S. Levolger, R.C. van den Braak, M. Suker, M. Gaspersz, R. de Bruin, C. Verhoef, C. van Eijck, N. Bossche, B.G. Koerkamp, J. IJzermans
Journal: Journal of Hepatology (2017)
Myeloid Sarcoma: The Mayo Clinic Experience of Ninety Six Case Series
Authors: Jennifer Yui, Mythri Mudireddy, Mrinal M Patnaik, Naseema Gangat, Aref Al-Kali, Michelle Elliott, William J. Hogan, C. Christopher Hook, Alexandra P Wolanskyj, Mark R. Litzow, Matthew T Howard, Curtis A. Hanson, Rhett P. Ketterling, Animesh D. Pardanani, Ayalew Tefferi, Kebede H. Begna
Journal: Blood (2016)
Role of Acquired Cardiovascular Disease in Tetralogy of Fallot Patients &gt;50 Years of Age
Authors: Jouke P. Bokma, Michiel M. Winter, Joey M. Kuijpers, Monique R. Jongbloed, Anthonie L. Duijnhouwer, Elke S. Hoendermis, Gert-Jan T. Sieswerda, Martijn C. Post, Barbara J.M. Mulder, Berto J. Bouma
Journal: Journal of the American College of Cardiology (2017)
Hepatitis B virus-specific T cell receptors with high functional avidity redirect T cells to eliminate HBV
Authors: K. Wisskirchen, J. Kah, K. Metzger, L. Weigand, W. Uckert, M. Schiemann, T. Volz, A. Krackhardt, M. Dandri, U. Protzer
Journal: Journal of Hepatology (2017)
An algorythm including quantitave HBsAg and HBcrAg is useful for discrimation between hepatitis B virus inactive carriers and patients with active chronic hepatitis B HBeAg negative
Authors: M.R. Barciela, A. Ruiz, D. Tabernero, M. Bes, M.T. Salcedo, S. Sauleda, L. Nieto, F. Rodríguez-Frías, R. Esteban, M. Buti
Journal: Journal of Hepatology (2017)
Outcome of leiomyosarcoma of bone: A single center experience.
Authors: Rajeev Rajendra, Seth Pollack, Eve T. Rodler, Ernest U. Conrad, Darin J Davidson, Xiaoyu Chai, Robin Lewis Jones
Journal: Journal of Clinical Oncology (2013)

e21502 Background: Leiomyosarcoma (LMS) of bone is a very rare sarcoma subtype. These tumors are managed akin to osteosarcoma, with neoadjuvant chemotherapy followed by surgery. The precise role of chemotherapy remains to be defined. Methods: Patients treated with primary bone LMS at the University of Washington between 2002 and 2012 were included. Patients with high grade tumors were treated with neoadjuvant chemotherapy and surgery; whereas those with low grade tumors were treated with surgical resection alone. Chemotherapy consisted of doxorubicin and ifosfamide x 2 cycles. Treatment details included: initial treatment (surgery versus chemo), surgical and pathological margins, and timing of chemotherapy. Follow-up data included: time to local recurrence, time to metastasis, time to last follow up if alive, or time to death. Results: Ten patients were identified, 4 male and 6 female. Median age at diagnosis: 52 years (range 29 - 91). The primary site was the distal femur in 5 patients, and the hemipelvis, acetabulum, proximal femur, distal clavicle and mid-shaft of femur in 1 patient each. Median tumor size at diagnosis was 8 cm. Five were high-grade tumors; 3 were intermediate and 2 were low grade. Four of 10 patients received neoadjuvant chemotherapy, with the following histological response; 70%, 30%, 15% and &lt;5%. None of these patients had a dimensional radiological response to chemotherapy. Of the patients treated with surgery alone, one developed a local recurrence and another developed metastatic disease. Of the patients treated with chemotherapy and surgery, 1 died from an unrelated cause. Median follow-up was 9 months (range 0 - 83). Median DFS was 9 months (range 0 - 83). OS has not yet been reached. Conclusions: Surgical resection remains the mainstay of management of LMS of bone. The role of neoadjuvant chemotherapy requires further evaluation. Larger collaborative studies and biomarker analyses are essential to evaluate optimal treatment strategies for this rare disease.
Dual proteotoxic stress promotes liver tumorigenesis via autophagy overload and activation of p62-mTOR-Nrf2 axis
Authors: D. Kuscuoglu, K. Wenzel, K. Levada, G.K. Ensari, N.G. Schwarzl, J. Haybaeck, K. Hittatiya, H.-P. Fischer, C. Trautwein, P. Strnad
Journal: Journal of Hepatology (2017)