bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance
Authors: Das Kalyan , Martinez Sergio E. , Arnold Eddy 
Published: April 2017

ABSTRACT
HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in patients failing therapies with dideoxynucleosides (didanosine [ddI], zalcitabine [ddC]) and/or zidovudine (AZT). The cluster of the five mutations is referred to as the Q151M complex (Q151Mc), and an RT or virus containing Q151Mc exhibits resistance to multiple NRTIs. To understand the structural basis for Q151M and Q151Mc resistance, we systematically determined the crystal structures of the wild-type RT/double-stranded DNA (dsDNA)/dATP (complex I), wild-type RT/dsDNA/ddATP (complex II), Q151M RT/dsDNA/dATP (complex III), Q151Mc RT/dsDNA/dATP (complex IV), and Q151Mc RT/dsDNA/ddATP (complex V) ternary complexes. The structures revealed that the deoxyribose rings of dATP and ddATP have 3′-endo and 3′-exo conformations, respectively. The single mutation Q151M introduces conformational perturbation at the deoxynucleoside triphosphate (dNTP)-binding pocket, and the mutated pocket may exist in multiple conformations. The compensatory set of mutations in Q151Mc, particularly F116Y, restricts the side chain flexibility of M151 and helps restore the DNA polymerization efficiency of the enzyme. The altered dNTP-binding pocket in Q151Mc RT has the Q151-R72 hydrogen bond removed and has a switched conformation for the key conserved residue R72 compared to that in wild-type RT. On the basis of a modeled structure of hepatitis B virus (HBV) polymerase, the residues R72, Y116, M151, and M184 in Q151Mc HIV-1 RT are conserved in wild-type HBV polymerase as residues R41, Y89, M171, and M204, respectively; functionally, both Q151Mc HIV-1 and wild-type HBV are resistant to dideoxynucleoside analogs.
Synthetic (p)ppGpp Analogue Is an Inhibitor of Stringent Response in Mycobacteria
Authors: Syal Kirtimaan , Flentie Kelly , Bhardwaj Neerupma , Maiti Krishnagopal , Jayaraman Narayanaswamy , Stallings Christina L. , Chatterji Dipankar 
Published: April 2017

ABSTRACT

Bacteria elicit an adaptive response against hostile conditions such as starvation and other kinds of stresses. Their ability to survive such conditions depends, in part, on stringent response pathways. (p)ppGpp, considered to be the master regulator of the stringent response, is a novel target for inhibiting the survival of bacteria. In mycobacteria, the (p)ppGpp synthetase activity of bifunctional Rel is critical for stress response and persistence inside a host. Our aim was to design an inhibitor of (p)ppGpp synthesis, monitor its efficiency using enzyme kinetics, and assess its phenotypic effects in mycobacteria. As such, new sets of inhibitors targeting (p)ppGpp synthesis were synthesized and characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. We observed significant inhibition of (p)ppGpp synthesis by Rel
Msm
in the presence of designed inhibitors in a dose-dependent manner, which we further confirmed by monitoring the enzyme kinetics. The Rel enzyme inhibitor binding kinetics were investigated by isothermal titration calorimetry. Subsequently, the effects of the compounds on long-term persistence, biofilm formation, and biofilm disruption were assayed in
Mycobacterium smegmatis
, where inhibition in each case was observed.
In vivo
, (p)ppGpp levels were found to be downregulated in
M. smegmatis
treated with the synthetic inhibitors. The compounds reported here also inhibited biofilm formation by the pathogen
Mycobacterium tuberculosis
. The compounds were tested for toxicity by using an MTT assay with H460 cells and a hemolysis assay with human red blood cells, for which they were found to be nontoxic. The permeability of compounds across the cell membrane of human lung epithelial cells was also confirmed by mass spectrometry.
Specific
bla
CTX-M-8
/IncI1 Plasmid Transfer among Genetically Diverse Escherichia coli Isolates between Humans and Chickens
Authors: Norizuki Chihiro , Wachino Jun-ichi , Suzuki Masahiro , Kawamura Kumiko , Nagano Noriyuki , Kimura Kouji , Arakawa Yoshichika 
Published: April 2017

ABSTRACT

We investigated the genetic backbones of 14
bla
CTX-M-8
-positive
Escherichia coli
isolates recovered from human stool samples and chicken meat. All isolates carried IncI1 plasmids with
bla
CTX-M-8
(
bla
CTX-M-8
/IncI1), and most (9/14) belonged to a specific genetic lineage, namely, plasmid sequence type 113 (pST113). The genetic contexts of the nine
bla
CTX-M-8
/IncI1 pST113 plasmids were similar, regardless of the source. These results suggest the probable local transfer of
bla
CTX-M-8
/IncI1 between humans and chickens with genetically diverse
E. coli
.
Highly Tigecycline-Resistant Klebsiella pneumoniae Sequence Type 11 (ST11) and ST147 Isolates from Companion Animals
Authors: Ovejero Cristina M. , Escudero Jose Antonio , Thomas-Lopez Daniel , Hoefer Andreas , Moyano Gabriel , Montero Natalia , Martin-Espada Carmen , Gonzalez-Zorn Bruno 
Published: April 2017

ABSTRACT

In this study, we characterized two tigecycline-resistant
Klebsiella pneumoniae
isolates from dog urine samples. The isolates were genetically unrelated, belonging to sequence type 11 (ST11) and ST147, both classically related to human isolates. To the best of our knowledge, this is the first identification of tigecycline-resistant isolates from animals. We unveil here the worrisome circulation among animals of bacterial clones resistant to this last-resort antibiotic.
Giardia Alters Commensal Microbial Diversity throughout the Murine Gut
Authors: Barash N. R. , Maloney J. G. , Singer S. M. , Dawson S. C. 
Published: April 2017

ABSTRACT

Giardia lamblia
is the most frequently identified protozoan cause of intestinal infection. Over 200 million people are estimated to have acute or chronic giardiasis, with infection rates approaching 90% in areas where
Giardia
is endemic. Despite its significance in global health, the mechanisms of pathogenesis associated with giardiasis remain unclear, as the parasite neither produces a known toxin nor induces a robust inflammatory response.
Giardia
colonization and proliferation in the small intestine of the host may, however, disrupt the ecological homeostasis of gastrointestinal commensal microbes and contribute to diarrheal disease associated with giardiasis. To evaluate the impact of
Giardia
infection on the host microbiota, we used culture-independent methods to quantify shifts in the diversity of commensal microbes throughout the gastrointestinal tract in mice infected with
Giardia
. We discovered that
Giardia
's colonization of the small intestine causes a systemic dysbiosis of aerobic and anaerobic commensal bacteria. Specifically,
Giardia
colonization is typified by both expansions in aerobic
Proteobacteria
and decreases in anaerobic
Firmicutes
and
Melainabacteria
in the murine foregut and hindgut. Based on these shifts, we created a quantitative index of murine
Giardia
-induced microbial dysbiosis. This index increased at all gut regions during the duration of infection, including both the proximal small intestine and the colon. Giardiasis could be an ecological disease, and the observed dysbiosis may be mediated directly via the parasite's unique anaerobic fermentative metabolism or indirectly via parasite induction of gut inflammation. This systemic alteration of murine gut commensal diversity may be the cause or the consequence of inflammatory and metabolic changes throughout the gut. Shifts in the commensal microbiota may explain observed variations in giardiasis between hosts with respect to host pathology, degree of parasite colonization, infection initiation, and eventual clearance.
Transperineal aggressive angiomyxoma
Authors: Pereira Pedro , Melo Abreu Elisa , Cunha Teresa Margarida , Rolim Inês 
Published: April 2017

A 45-year-old woman with a history of total hysterectomy with adnexal preservation for uterine leiomyomas presented to our hospital with a right gluteal palpable mass, which she first noticed 6 months before and had progressively enlarged since then.Radiological studies revealed a 14 cm lesion with translevator growth that displaced rather than invaded adjacent structures, with a peculiar whorled pattern on T2-weighted MRI, which enhanced following gadolinium administration. CT-guided biopsy was performed, and in conjunction with imaging features the diagnosis of an aggressive angiomyxoma was assumed and confirmed following surgical excision.
Predictors and clinical implication of high-sensitivity cardiac troponin-I elevation following diagnostic cardiac catheterisations
Authors: Hamaya Rikuta , Yonetsu Taishi , Murai Tadashi , Kanaji Yoshihisa , Usui Eisuke , Matsuda Junji , Hoshino Masahiro , Araki Makoto , Hada Masahiro , Niida Takayuki , Ichijo Sadamitsu , Kanno Yoshinori , Kakuta Tsunekazu 
Published: April 2017

ObjectivesAlthough diagnostic coronary angiography (CAG) is performed worldwide, procedure-related myocardial necrosis (PMN) following diagnostic catheter-based procedures has not been well investigated. The aim of this study was to determine clinical and procedural factors associated with PMN, using a high-sensitivity cardiac troponin I (hs-cTnI) assay, and to investigate the clinical implications of PMN.MethodsAmong 697 patients undergoing elective CAG and pre- and post-procedural hs-cTnI (pre-TnI, post-TnI, respectively) measurements, a total of 538 patients (124 female) were evaluated, with 2.2% lost during follow-up. Minor PMN was defined as post-TnI above the sex-specific upper reference limit (URL), with a 20% increase from the pre-TnI level. Major PMN was defined as post-TnI above 5x the URL. Clinical and procedural factors predicting PMN and the association between PMN and major adverse cardiac events (MACE) following CAG were examined.ResultsPMN of any type was detected in 178 patients (33.0%), while major PMN was observed in 32 patients (5.9%). Female sex, estimated glomerular filtration rate, procedural time, left ventricular end-diastolic pressure (LVEDP) and fractional flow reserve measurement independently predicted any PMN; whereas, only LVEDP and log-transformed N-terminal pro-brain natriuretic peptide independently predicted major PMN. The incidence of MACE was significantly associated with major PMN. Cox proportional-hazards models revealed that major PMN, pre-TnI, and the absence of statin use were independently associated with MACE.ConclusionsDiagnostic cardiac catheteriation may highlight cardiomyocyte susceptibility to stress in patients with or without CAD. CAG-related major myocardial injury might be associated with future adverse cardiac events independently of the presence or absence of functional stenosis.
Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer
Authors: Hanker Ariella B. , Estrada Mónica Valeria , Bianchini Giampaolo , Moore Preston D. , Zhao Junfei , Cheng Feixiong , Koch James P. , Gianni Luca , Tyson Darren R. , Sánchez Violeta , Rexer Brent N. , Sanders Melinda E. , Zhao Zhongming , Stricker Thomas P. , Arteaga Carlos L. 
Published: April 2017

Abstract
PIK3CA mutations are associated with resistance to HER2-targeted therapies. We previously showed that HER2+/PIK3CAH1047R transgenic mammary tumors are resistant to the HER2 antibodies trastuzumab and pertuzumab but respond to PI3K inhibitor buparlisib (TPB). In this study, we identified mechanisms of resistance to combined inhibition of HER2 and PI3K. TPB-resistant tumors were generated by treating HER2+/PIK3CAH1047R tumor-bearing mice long term with the drug combination. RNA sequencing of TPB-resistant tumors revealed that extracellular matrix and cell adhesion genes, including collagen II (Col2a1), were markedly upregulated, accompanied by activation of integrin β1/Src. Cells derived from drug-resistant tumors were sensitive to TBP when grown in vitro, but exhibited resistance when plated on collagen or when reintroduced into mice. Drug resistance was partially reversed by the collagen synthesis inhibitor ethyl-3,4-dihydroxybenzoate. Inhibition of integrin β1/Src blocked collagen-induced resistance to TPB and inhibited growth of drug-resistant tumors. High collagen II expression was associated with significantly lower clinical response to neoadjuvant anti-HER2 therapy in HER2+ breast cancer patients. Overall, these data suggest that upregulation of collagen/integrin/Src signaling contributes to resistance to combinatorial HER2 and PI3K inhibition. Cancer Res; 77(12); 3280–92. ©2017 AACR.
LncRNA GAS5 Inhibits Cellular Proliferation by Targeting P27Kip1
Authors: Luo Gang , Liu Dong , Huang Chao , Wang Miao , Xiao Xingyuan , Zeng Fuqing , Wang Liang , Jiang Guosong 
Published: April 2017

Abstract
Recent studies have demonstrated that long noncoding RNAs (lncRNA) have important roles in cancer biology, and that the downregulation of lncRNA growth arrest–specific transcript 5 (GAS5) has been reported in a variety of human cancers. However, its role in prostate cancer is largely unknown. This study aims to investigate the biological role and underlying mechanism of GAS5 on proliferation in prostate cancer. The results demonstrate that GAS5 expression is significantly decreased in prostate cancer cells compared with prostate epithelial cells. Ectopic expression of GAS5 inhibited cell proliferation and induced a cell-cycle arrest in G0–G1 phase, whereas GAS5 knockdown promoted the G1–S phase transition. Subsequent analysis demonstrated that P27Kip1, a known regulator of cell cycle, was positively regulated by GAS5 and upregulation of GAS5 increased its promoter activity. E2F1, an important transcription factor, was shown to bind directly to and activate the P27Kip1 promoter. In addition, GAS5 interacted with E2F1 and enhanced the binding of E2F1 to the P27Kip1 promoter. Collectively, these findings determine that GAS5 functions as a tumor suppressor in prostate cancer development and progression via targeting P27Kip1.
Implications: This study reveals a molecular pathway involving lncRNA GAS5/E2F1/P27Kip1 which regulates cell proliferation and could be a potential therapeutic target in prostate cancer. Mol Cancer Res; 15(7); 789–99. ©2017 AACR.
Percutaneous Pericardial Resection
Authors: Borlaug Barry A. , Carter Rickey E. , Melenovsky Vojtech , DeSimone Christopher V. , Gaba Prakriti , Killu Ammar , Naksuk Niyada , Lerman Lilach , Asirvatham Samuel J. 
Published: April 2017

Background—
People with heart failure and preserved ejection fraction develop increases in left ventricular (LV) end-diastolic pressures during exercise that contribute to dyspnea. In normal open-chest animal preparations, the pericardium restrains LV filling when central blood volume increases. We hypothesized that resection of the pericardium using a minimally invasive epicardial approach would mitigate the increase in LV end-diastolic pressure that develops during volume loading in normal and diseased hearts with the chest intact.

Methods and Results—

Invasive hemodynamic assessment was performed at baseline and after saline load before and after pericardial resection in normal canines with open (n=3) and closed chest (n=5) and in a pig model with features of human heart failure and preserved ejection fraction with sternum intact (n=4). In closed-chest animals, pericardiotomy was performed using a novel subxiphoid procedure. In both experimental preparations of normal dogs, pericardiotomy blunted the increase in LV end-diastolic pressure with saline infusion, while enhancing the saline-mediated increase in LV end-diastolic volume. With chest intact in the pig model, percutaneous pericardial resection again blunted the increase in LV end-diastolic pressure secondary to volume expansion (+4±3 versus +13±5 mm Hg;
P
=0.014), while enhancing the saline-mediated increase in LV end-diastolic volume (+17±1 versus +10±2 mL;
P
=0.016).

Conclusions—
This proof of concept study demonstrates that pericardial resection through a minimally invasive percutaneous approach mitigates the elevation in LV filling pressures with volume loading in both normal animals and a pig model with diastolic dysfunction. Further study is warranted to determine whether this method is safe and produces similar acute and chronic hemodynamic benefits in people with heart failure and preserved ejection fraction.
A Novel Patient Safety Event Reporting Tool in Otolaryngology
Authors: Vila Peter M. , Lewis Sean , Cunningham Gene , Brereton Jean , Espinel Alexandra G. , Roberson David W. , Shah Rahul K. 
Published: April 2017

ObjectiveTo report the results of a preliminary analysis of a quality improvement initiative aimed to identify potential latent systems defects.MethodsA pilot study of an anonymous, voluntary, event reporting system made available to all members of the American Academy of Otolaryngology—Head and Neck Surgery was performed. The National Coordinating Council for Medication Error Reporting and Prevention (NCC MERP) index was used to classify error types. Descriptive statistics were used to summarize submissions to the database.ResultsIn the 53 cases reported to the database over 22 months, the majority involved errors that had resulted in harm (n = 34, 64%), followed by errors that occurred and did not result in harm (n = 7, 13%). Errors occurred predominantly in the hospital (n = 23, 44%) and operating room (n = 19, 35%). Most entries were classified as either technical (n = 21, 39%) or related to postoperative care (n = 15, 30%).DiscussionThis preliminary descriptive analysis of a novel otolaryngology patient safety event reporting tool shows that this platform brings unique value to the identification of errors and adverse events in our specialty. Most reported events were classified as errors resulting in harm. The most common type of reported event was a technical error, most often resulting in a nerve injury.Implications for PracticeThis reporting tool will likely allow for identification and prioritization of improvement opportunities. This example may serve as a guide for other societies to create similar platforms as we strive for a standardized process for event reporting.
Very Severe Obstructive Sleep Apnea in Children: Outcomes of Adenotonsillectomy and Risk Factors for Persistence
Authors: Isaiah Amal , Hamdan Hisham , Johnson Romaine F. , Naqvi Kamal , Mitchell Ron B. 
Published: April 2017

Objectives(1) To describe the clinical, demographic and polysomnographic (PSG) characteristics of children with very severe obstructive sleep apnea (OSA) without significant comorbidities; (2) to assess the outcomes following tonsillectomy and adenoidectomy (T&A); and (3) to determine predictors of persistence of OSA after T&A.Study DesignCase series with chart review.SettingTertiary‐level freestanding children’s hospital.Subjects and MethodsSeventy‐four children aged 2 to 12 years who underwent T&A for very severe OSA (obstructive apnea‐hypopnea index [AHI] >30) were included. Children with significant comorbidities were excluded. PSG variables were compared pre‐ and post‐T&A using statistical tests. Factors affecting OSA resolution and persistence were studied.ResultsThe mean (95% confidence interval) age was 4.3 (3.8‐4.7) years with the majority black or Hispanic (64/74, 86%). The mean decrease in AHI after T&A was 49 (43‐58) (P <. 001). Complete resolution of OSA, defined by an AHI <1, or an AHI <5 was seen in 32% (24/74) and 80% (59/74), respectively. Total sleep time (TST) greater than 5 minutes with end‐tidal CO2 >50 mm Hg was strongly associated with persistent OSA. The decrease in AHI post‐T&A was best predicted by higher preoperative oxygen saturation (SpO2) nadir and lower TST with SpO2 <90% (R
2 = 0.24, P <. 001).ConclusionsT&A is associated with a significant improvement but not resolution of very severe OSA. The severity of baseline hypercapnia and hypoxemia may best predict persistent OSA after T&A. The study supports obtaining routine post‐T&A PSG in children with very severe OSA.
Immunohistochemistry Analysis of CD44, EGFR, and p16 in Oral Cavity and Oropharyngeal Squamous Cell Carcinoma
Authors: Cohen Erin R. , Reis Isildinha M. , Gomez Carmen , Pereira Lutecia , Freiser Monika E. , Hoosien Gia , Franzmann Elizabeth J. 
Published: April 2017

ObjectivesWe analyze the relationship between CD44, epidermal growth factor receptor (EGFR), and p16 expression in oral cavity and oropharyngeal cancers in a diverse population. We also describe whether particular patterns of staining are associated with progression‐free survival and overall survival.Study DesignProspective study, single‐blind to pathologist and laboratory technologist.SettingHospital based.Subjects and MethodsImmunohistochemistry, comprising gross staining and cellular expression, was performed and interpreted in a blinded fashion on 24 lip/oral cavity and 40 oropharyngeal cancer specimens collected between 2007 and 2012 from participants of a larger study. Information on overall survival and progression‐free survival was obtained from medical records.ResultsNineteen cases were clinically p16 positive, 16 of which were oropharyngeal. Oral cavity lesions were more likely to exhibit strong CD44 membrane staining (P =. 0002). Strong CD44 membrane and strong EGFR membrane and/or cytoplasmic staining were more common in p16‐negative cancers (P =. 006). Peripheral/mixed gross p16 staining pattern was associated with worse survival than the universal staining on univariate and multivariate analyses (P =. 006, P =. 030). This held true when combining gross and cellular localization for p16. For CD44, universal gross staining demonstrated poorer overall survival compared with the peripheral/mixed group (P =. 039). CD44 peripheral/mixed group alone and when combined with universal p16 demonstrated the best survival on multivariate analysis (P =. 010).ConclusionIn a diverse population, systematic analysis applying p16, CD44, and EGFR gross staining and cellular localization on immunohistochemistry demonstrates distinct patterns that may have prognostic potential exceeding current methods. Larger studies are warranted to investigate these findings further.