bluuebunny/crossref_metadata_2025 huggingface dataset:
X-Ray of Excised Cancerous Breast Tissue Does Not Affect Clinical Biomarker Expression
Authors: Lloyd Isaac E. , Welm Alana L. , DeRose Yoko , Neumayer Leigh A. , Kohan Jessica L. , Malmberg Elisabeth M. , Salama Mohamed E. , Factor Rachel E.
Published: February 2017

Context:

College of American Pathologists (CAP) and the American Society of Clinical Oncology have emphasized the need to reduce preanalytic variables for evaluating predictive biomarker expression in breast cancer. Postoperative x-ray of excised breast tissue is commonplace, yet is a variable that has not been investigated previously. We asked whether such radiation affects expression of relevant biomarkers.

Design:

A previous study found that human breast cancers grown in mice demonstrate the same immunohistochemical and molecular profiles as the original tumors. Thirteen patient-derived xenografts were harvested fresh and divided for specimen radiography and a matched nonirradiated control, while following CAP/ASCO guidelines for cold ischemia time and fixation. Samples were processed in a tissue microarray for immunohistochemistry. Estrogen receptor (ER), progesterone receptor (PR), p53, and Ki67 staining was evaluated using an optimized scoring algorithm performed on digitally scanned slides. Samples were also scored manually by a blinded pathologist using the H-score method, and HER2 by the CAP/ASCO 2013 protocol. Histologic scores were compared by analysis of variance.

Results:

There was no significant difference in quantity or intensity of staining between irradiated and nonirradiated samples for estrogen receptor (P=0.28), p53 (P=0.96), and Ki67 (P=0.94). A small but statistically significant difference was observed for PR (P=0.0058). HER2 staining was similarly unchanged in the 1 tumor exhibiting 3+ staining.

Conclusions:

Our study demonstrates that x-ray of breast carcinomas does not significantly affect the expression of predictive biomarkers, with the exception of PR for unclear reasons. It also highlights the utility of the patient-derived xenograft model for biomarker studies.
Evolution of Quality Assurance for Clinical Immunohistochemistry in the Era of Precision Medicine. Part 3: Technical Validation of Immunohistochemistry (IHC) Assays in Clinical IHC Laboratories
Authors: Torlakovic Emina E. , Cheung Carol C. , D’Arrigo Corrado , Dietel Manfred , Francis Glenn D. , Gilks C. Blake , Hall Jacqueline A. , Hornick Jason L. , Ibrahim Merdol , Marchetti Antonio , Miller Keith , van Krieken J. Han , Nielsen Soren , Swanson Paul E. , Vyberg Mogens , Zhou Xiaoge , Taylor Clive R.
Published: February 2017

Validation of immunohistochemistry (IHC) assays is a subject that is of great importance to clinical practice as well as basic research and clinical trials. When applied to clinical practice and focused on patient safety, validation of IHC assays creates objective evidence that IHC assays used for patient care are “fit-for-purpose.” Validation of IHC assays needs to be properly informed by and modeled to assess the purpose of the IHC assay, which will further determine what sphere of validation is required, as well as the scope, type, and tier of technical validation. These concepts will be defined in this review, part 3 of the 4-part series “Evolution of Quality Assurance for Clinical Immunohistochemistry in the Era of Precision Medicine.”
PD-L1 Expression and Intratumoral Heterogeneity Across Breast Cancer Subtypes and Stages
Authors: Dill Erik A. , Gru Alejandro A. , Atkins Kristen A. , Friedman Lisa A. , Moore Margaret E. , Bullock Timothy N. , Cross Janet V. , Dillon Patrick M. , Mills Anne M.
Published: February 2017

Tumor expression of programmed cell death ligand 1 (PD-L1) is associated with immune evasion in a variety of malignancies, including a subset of triple-negative breast carcinomas, and may mark cancers as susceptible to PD-1/PD-L1 inhibitor therapies. We herein characterize PD-L1 expression in breast cancers across the full range of histomorphologies and investigate its intratumoral heterogeneity and fidelity across primaries and metastases. A total of 245 primary and 40 metastatic (20 nodal, 20 distant) breast carcinomas were evaluated with PD-L1 immunohistochemistry on tissue microarray. Tumor PD-L1 staining was seen in 12% of all primaries including 32% of triple-negative cancers. Staining was common in ductal cancers with medullary (54%), apocrine (27%), and metaplastic features (40%). However, diffuse (>50%) staining was rare (2% of all cancers and 5% of triple negatives). Immune staining was seen in 29% of all primaries and 61% of triple negatives. Tumor expression of PD-L1 was conserved in 94% of matched primary/metastasis pairs, while immune staining showed fidelity in 71%; the remaining cases acquired PD-L1 immune cell expression in the metastasis. Only half of cases with positive tumor staining showed concordance across all analyzed cores. These data demonstrate that PD-L1 expression is prevalent among high-grade, hormone receptor–negative breast cancers with a range of histomorphologies and shows fidelity between primary and metastatic sites in treatment-naive cancers, although acquisition of immune PD-L1 staining in metastases is not uncommon. There is considerable intratumoral heterogeneity in PD-L1 expression, undermining the suitability of core biopsy in the determination of PD-L1 status. Clinical trials are needed to determine PD-L1 staining thresholds required for therapeutic response, as diffuse staining is rare.
Improved Clinical Performance and Teamwork of Pediatric Interprofessional Resuscitation Teams With a Simulation-Based Educational Intervention*
Authors: Gilfoyle Elaine , Koot Deanna A. , Annear John C. , Bhanji Farhan , Cheng Adam , Duff Jonathan P. , Grant Vincent J. , St. George-Hyslop Cecilia E. , Delaloye Nicole J. , Kotsakis Afrothite , McCoy Carolyn D. , Ramsay Christa E. , Weiss Matthew J. , Gottesman Ronald D.
Published: February 2017

Objectives:

To measure the effect of a 1-day team training course for pediatric interprofessional resuscitation team members on adherence to Pediatric Advanced Life Support guidelines, team efficiency, and teamwork in a simulated clinical environment.

Design:

Multicenter prospective interventional study.

Setting:

Four tertiary-care children’s hospitals in Canada from June 2011 to January 2015.

Subjects:

Interprofessional pediatric resuscitation teams including resident physicians, ICU nurse practitioners, registered nurses, and registered respiratory therapists (n = 300; 51 teams).

Interventions:

A 1-day simulation-based team training course was delivered, involving an interactive lecture, group discussions, and four simulated resuscitation scenarios, each followed by a debriefing. The first scenario of the day (PRE) was conducted prior to any team training. The final scenario of the day (POST) was the same scenario, with a slightly modified patient history. All scenarios included standardized distractors designed to elicit and challenge specific teamwork behaviors.

Measurements and Main Results:

Primary outcome measure was change (before and after training) in adherence to Pediatric Advanced Life Support guidelines, as measured by the Clinical Performance Tool. Secondary outcome measures were as follows: 1) change in times to initiation of chest compressions and defibrillation and 2) teamwork performance, as measured by the Clinical Teamwork Scale. Correlation between Clinical Performance Tool and Clinical Teamwork Scale scores was also analyzed. Teams significantly improved Clinical Performance Tool scores (67.3–79.6%; p < 0.0001), time to initiation of chest compressions (60.8–27.1 s; p < 0.0001), time to defibrillation (164.8–122.0 s; p < 0.0001), and Clinical Teamwork Scale scores (56.0–71.8%; p < 0.0001). A positive correlation was found between Clinical Performance Tool and Clinical Teamwork Scale (R
2 = 0.281; p < 0.0001).

Conclusions:

Participation in a simulation-based team training educational intervention significantly improved surrogate measures of clinical performance, time to initiation of key clinical tasks, and teamwork during simulated pediatric resuscitation. A positive correlation between clinical and teamwork performance suggests that effective teamwork improves clinical performance of resuscitation teams.
Loss to Follow-up Trends in HIV-Positive Patients Receiving Antiretroviral Treatment in Asia From 2003 to 2013
Authors: De La Mata Nicole L. , Ly Penh S. , Nguyen Kinh V. , Merati Tuti P. , Pham Thuy T. , Lee Man P. , Choi Jun Y. , Ross Jeremy , Law Matthew G. , Ng Oon T.
Published: February 2017

Introduction:

Over time, there has been a substantial improvement in antiretroviral treatment (ART) programs, including expansion of services and increased patient engagement. We describe time trends in, and factors associated with, loss to follow-up (LTFU) in HIV-positive patients receiving ART in Asia.

Methods:

Analysis included HIV-positive adults initiating ART in 2003–2013 at 7 ART programs in Asia. Patients LTFU had not attended the clinic for ≥180 days, had not died, or transferred to another clinic. Patients were censored at recent clinic visit, follow-up to January 2014. We used cumulative incidence to compare LTFU and mortality between years of ART initiation. Factors associated with LTFU were evaluated using a competing risks regression model, adjusted for clinical site.

Results:

A total of 8305 patients were included. There were 743 patients LTFU and 352 deaths over 26,217 person-years (pys), a crude LTFU, and mortality rate of 2.83 (2.64–3.05) per 100 pys and 1.34 (1.21–1.49) per 100 pys, respectively. At 24 months, the cumulative LTFU incidence increased from 4.3% (2.9%–6.1%) in 2003–05 to 8.1% (7.1%–9.2%) in 2006–09 and then decreased to 6.7% (5.9%–7.5%) in 2010–13. Concurrently, the cumulative mortality incidence decreased from 6.2% (4.5%–8.2%) in 2003–05 to 3.3% (2.8%–3.9%) in 2010–13. The risk of LTFU reduced in 2010–13 compared with 2006–09 (adjusted subhazard ratio = 0.73, 0.69–0.99).

Conclusions:

LTFU rates in HIV-positive patients receiving ART in our clinical sites have varied by the year of ART initiation, with rates declining in recent years whereas mortality rates have remained stable. Further increases in site-level resources are likely to contribute to additional reductions in LTFU for patients initiating in subsequent years.
Regionally Specific Brain Volumetric and Cortical Thickness Changes in HIV-Infected Patients in the HAART Era
Authors: Sanford Ryan , Fernandez Cruz Ana Lucia , Scott Susan C. , Mayo Nancy E. , Fellows Lesley K. , Ances Beau M. , Collins D. Louis
Published: February 2017

Background:

Cognitive impairment still occurs in a substantial subset of HIV-infected patients, despite effective viral suppression with highly active antiretroviral therapy (HAART). Structural brain changes may provide clues about the underlying pathophysiology. This study provides a detailed spatial characterization of the pattern and extent of brain volume changes associated with HIV and relates these brain measures to cognitive ability and clinical variables.

Methods:

Multiple novel neuroimaging techniques (deformation-based morphometry, voxel-based morphometry, and cortical modeling) were used to assess regional brain volumes in 125 HIV-infected patients and 62 HIV-uninfected individuals. Ninety percent of the HIV-infected patients were on stable HAART with most of them (75%) having plasma viral suppression. Brain volumetrics and cortical thickness estimates were compared between the HIV-infected and uninfected groups, and the relationships between these measures of brain volume and indices of current and past infection severity, central nervous system penetration of HAART, and cognitive performance were assessed.

Results:

Regionally specific patterns of reduced thalamic and brainstem volumes and reduced cortical thickness in the orbitofrontal cortex, cingulate gyrus, primary motor and sensory cortex, temporal, and frontal lobes were seen in HIV-infected patients compared to HIV-uninfected participants. Observed white matter loss and subcortical atrophy were associated with lower nadir CD4 cell counts, while reduction in cortical thickness was related to worse cognitive performance.

Conclusions:

Our findings suggest that distinct mechanisms may underlie cortical and subcortical injury in people with HIV and argues for the potential importance of early initiation of HAART to protect long-term brain health.
Brief Report: Pharmacokinetics of Crushed Elvitegravir Combination Tablet Given With or Without Enteral Nutrition
Authors: Jongbloed-de Hoon Mieke , Colbers Angela , Velthoven-Graafland Kirsten , Duisenberg-van Essenberg Marjolijn , Kruijssen Martine , Abbink Evertine , van Crevel Reinout , Burger David
Published: February 2017

We investigated whether a fixed-dose combination tablet of elvitegravir, cobicistat, emtricitabine, and tenofovirDF (Stribild) can be crushed and combined with enteral nutrition without influencing pharmacokinetics. This was an open-label, 3-period, single-dose, randomized, crossover trial in 24 healthy volunteers. Subjects received Stribild whole tablet with breakfast (reference), crushed/suspended Stribild + breakfast, crushed/suspended Stribild + enteral nutrition. Crushed/suspended Stribild + enteral nutrition was bioequivalent (90% confidence interval between 80% and 125%) with a whole Stribild tablet. Crushed/suspended Stribild + breakfast showed bioequivalence for the area under the curve (AUC0–32), but not for maximum concentration (Cmax) (considered not clinically relevant). Patients with swallowing difficulties or an enteral feeding tube can use crushed and suspended Stribild tablets.
Effect of Pregnancy on Interferon Gamma Release Assay and Tuberculin Skin Test Detection of Latent TB Infection Among HIV-Infected Women in a High Burden Setting
Authors: LaCourse Sylvia M. , Cranmer Lisa M. , Matemo Daniel , Kinuthia John , Richardson Barbra A. , Horne David J. , John-Stewart Grace
Published: February 2017

Background:

Peripartum immunologic changes may affect latent tuberculosis infection (LTBI) diagnostic performance among HIV-infected women.

Methods:

HIV-infected women were serially tested with tuberculin skin test (TST) and interferon gamma release assay [QuantiFERON TB Gold In-tube (QFT)] in pregnancy and 6 weeks postpartum in Kenya. Prevalence, sensitivity and agreement, and correlates of QFT/TST positivity were assessed. Quantitative QFT mitogen and Mycobacterium tuberculosis antigen (Mtb-Ag) responses were compared by peripartum stage. Incidence of test conversion at 6 weeks postpartum was evaluated in baseline TST−/QFT− women.

Results:

Among 100 HIV-infected women, median age was 26 years, median CD4 was 555 cells per cubic millimeter, and 88% were on antiretrovirals. More women were QFT+ than TST+ in both pregnancy (35.4% vs. 13.5%, P = 0.001) and postpartum (29.6% vs. 14.8%, P < 0.001). Among 18 consistently QFT+ women, 8 (44%) converted from TST− to TST+, with improved test agreement postpartum (56.9%, κ = 0.20 to 82.4%, κ = 0.60). Three initially QFT−/TST− women had test conversion (TST+ and/or QFT+), suggesting new infection (incidence 13.4/100 person-years). Mean QFT mitogen (4.46 vs. 7.64 IU/mL, P < 0.001) and Mtb-Ag (1.03 vs. 1.54 IU/mL, P = 0.03) responses were lower among all women retested in pregnancy vs. postpartum, and specifically among persistently QFT+ women (Mtb-Ag: 3.46 vs. 4.48 IU/mL, P = 0.007). QFT indeterminate rate was higher in pregnancy (16%) compared with postpartum (0%) because of lower mitogen response.

Conclusions:

QFT identified >2-fold more women with LTBI compared with TST in pregnancy and postpartum. Lower QFT Mtb-Ag and mitogen responses in pregnancy compared with postpartum suggest that pregnancy-associated immunologic changes may influence LTBI test performance.
Expanded HIV Testing Strategy Leveraging the Electronic Medical Record Uncovers Undiagnosed Infection Among Hospitalized Patients
Authors: Felsen Uriel R. , Cunningham Chinazo O. , Heo Moonseong , Futterman Donna C. , Weiss Jeffrey M. , Zingman Barry S.
Published: February 2017

Background:

Routine HIV testing of hospitalized patients is recommended, but few strategies to expand testing in the hospital setting have been described. We assessed the impact of an electronic medical record (EMR) prompt on HIV testing for hospitalized patients.

Methods:

We performed a pre–post study at 3 hospitals in the Bronx, NY. We compared the proportion of admissions of patients 21–64 years old with an HIV test performed, characteristics of patients tested, and rate of new HIV diagnoses made by screening while an EMR prompt recommending HIV testing was inactive vs. active. The prompt appeared for patients with no previous HIV test or a high-risk diagnosis after their last HIV test.

Results:

Among 36,610 admissions while the prompt was inactive, 9.5% had an HIV test performed. Among 18,943 admissions while the prompt was active, 21.8% had an HIV test performed. Admission while the prompt was active was associated with increased HIV testing among total admissions [adjusted odds ratio (aOR) 2.78, 95% confidence interval (CI): 2.62 to 2.96], those without a previous HIV test (aOR 4.03, 95% CI: 3.70 to 4.40), and those with a previous negative test (aOR 1.52, 95% CI: 1.37 to 1.68) (P < 0.0001 for all). Although the prompt was active, testing increased across all patient characteristics. New HIV diagnoses made by screening increased from 8.2/100,000 admissions to 37.0/100,000 admissions while the prompt was inactive and active, respectively (OR 4.51 95% CI: 1.17 to 17.45, P = 0.03).

Conclusions:

An EMR prompt for hospitalized patients was associated with a large increase in HIV testing, a diversification of patients tested, and an increase in diagnoses made by screening.
Gastrointestinal Symptom Distress is Associated With Worse Mental and Physical Health-Related Quality of Life
Authors: O'Neill Tyler J. , Raboud Janet M. , Tinmouth Jill , Rourke Sean B. , Rueda Sergio , Hart Trevor A. , Cooper Curtis , Rachlis Anita , Burchell Ann N. ,   the OHTN Cohort Study Team
Published: February 2017

Background:

The prevalence of self-reported gastrointestinal (GI) symptoms and distress is high, but few studies have quantified their impact on health-related quality of life (HRQoL).

Methods:

We conducted a prospective cohort study of patients with HIV in care in Ontario, Canada (2007–2014). General linear mixed models were used to assess the impact of GI symptoms (diarrhea/soft stool, nausea/vomiting, bloating/painful abdomen, loss of appetite, weight loss/wasting) and distress (range: 0–4) on physical and mental HRQoL summary scores (range: 0–100) measured by the Medical Outcomes Survey SF-36.

Results:

A total of 1787 participants completed one or more questionnaires {median 3 [interquartile range (IQR): 1–4]}. At baseline, 59.0% were men who had sex with men, 53.7% white, median age 45 (IQR: 38–52), median CD4+ count 457 (IQR: 315–622), and 71.0% had undetectable HIV viremia. The mean (standard deviation [SD]) mental and physical HRQoL scores were 49.2 (8.6) and 45.3 (13.0), respectively. In adjusted models, compared with those reporting no symptoms, all GI symptom distress scores from 2 (“have symptom, bothers me a little”) to 4 (“have symptom, bothers a lot”) were associated with lower mental HRQoL. Loss of appetite distress scores ≥ 1; scores ≥ 2 for diarrhea, nausea/vomiting, and bloating; and a score ≥ 3 for weight loss were independently associated with lower physical HRQoL scores (P < 0.0001). Increasing GI symptom distress is associated with impaired mental and physical HRQoL (P < 0.0001).

Conclusions:

Increasing GI symptom distress is associated with impaired mental and physical HRQoL. Identifying, treating, and preventing GI symptoms may reduce overall symptom burden and improve HRQoL for patients with HIV.
Can Ultrasound With Contrast Enhancement Replace Nonenhanced Computed Tomography Scans in Patients With Contraindication to Computed Tomography Contrast Agents?
Authors: Sawhney Summit , Wilson Stephanie R.
Published: February 2017

Purpose

Our purpose is to determine the efficacy of ultrasound (US), with the addition of contrast enhancement (CEUS), in the identification and characterization of abdominal pathology compared with nonenhanced computed tomography (CT) scan (NECT).

Methods

This prospective cohort study recruited 197 patients with NECT, the majority with renal failure, to have US, with addition of CEUS, if focal pathology was detected, occurring in 145 patients. Nonenhanced CT scan, US, and CEUS images/video files were presented to 2 blinded readers, in anonymous order. Examination quality and positive observations were recorded. True diagnosis was determined with pathology, follow-up imaging, and clinical notes. Data analysis showed sensitivity of NECT and US in the identification and characterization of pathology and sensitivity of CEUS to characterize abnormalities.

Results

Most pathology involved liver (n = 87), kidney (n = 35), and peritoneum (n = 13). Ultrasound alone was superior to NECT in the identification of hepatic and renal pathology, with both performing poorly at characterization. With addition of CEUS, characterization of hepatic and renal pathology reached 100%. Nonenhanced CT is superior to US in identification of peritoneal pathology, especially in large patients. Further solid and hollow organ pathology identified and characterized was of insufficient size to draw conclusions.

Conclusions

Nonenhanced CT has limited ability to identify and characterize solid and hollow organ pathology. Ultrasound with the benefit of CEUS is superior to NECT in the characterization of focal liver, kidney, and peritoneal pathology. Contrast-enhanced ultrasound outperforms NECT in evaluation of suspect abdominal pathology in those with renal failure.
Sex Differences in Civilian Injury in Baghdad From 2003 to 2014
Authors: Shaak Kyle , Lafta Riyadh , Stewart Barclay T. , Fowler Thomas R. , Al-Shatari Sahar A. Esa , Burnham Gilbert , Cherewick Megan , Wren Sherry M. , Groen Reinou S. , Kushner Adam L.
Published: February 2017

Objective:

To examine sex differences in injury mechanisms, injury-related death, injury-related disability, and associated financial consequences in Baghdad since the 2003 invasion of Iraq to inform prevention initiatives, health policy, and relief planning.

Background:

Reliable estimates of injury burden among civilians during conflict are lacking, particularly among vulnerable subpopulations, such as women.

Methods:

A 2-stage, cluster randomized, community-based household survey was conducted in May 2014 to determine the civilian burden of injury in Baghdad since 2003. Households were surveyed regarding injury mechanisms, healthcare required, disability, deaths, connection to conflict, and resultant financial hardship.

Results:

We surveyed 900 households (5148 individuals), reporting 553 injuries, 162 (29%) of which were injuries among women. The mean age of injury was higher among women compared with men (34 ± 21.3 vs 27 ± 16.5 years; P < 0.001). More women than men were injured while in the home [104 (64%) vs 82 (21%); P < 0.001]. Fewer women than men died from injuries [11 (6.8%) vs 77 (20%); P < 0.001]; however, women were more likely than men to live with reduced function [101 (63%) vs 192 (49%); P = 0.005]. Of intentional injuries, women had higher rates of injury by shell fragments (41% vs 26%); more men were injured by gunshots [76 (41%) vs 6 (17.6%); P = .011).

Conclusions:

Women experienced fewer injuries than men in postinvasion Baghdad, but were more likely to suffer disability after injury. Efforts to improve conditions for injured women should focus on mitigating financial and provisional hardships, providing counseling services, and ensuring access to rehabilitation services.
Real-time Navigation for Liver Surgery Using Projection Mapping With Indocyanine Green Fluorescence
Authors: Nishino Hiroto , Hatano Etsuro , Seo Satoru , Nitta Takashi , Saito Tomoyuki , Nakamura Masaaki , Hattori Kayo , Takatani Muneo , Fuji Hiroaki , Taura Kojiro , Uemoto Shinji
Published: February 2017

Objective:

The aim of the present study was to evaluate the usefulness of a new imaging device, the Medical Imaging Projection System (MIPS), which uses the indocyanine green emission signal and active projection mapping, for liver resection.

Background:

During anatomic liver resection, surgeons cannot completely view the intraparenchymal structure. Although a fluorescent imaging technique using indocyanine green has recently been developed for hepatobiliary surgery, limitations in its application for real-time navigation persist.

Methods:

We conducted a retrospective review of surgical and clinical outcomes for 23 patients who underwent anatomic hepatectomy using the MIPS and 29 patients who underwent the procedure without MIPS guidance, between September 2014 and September 2015.

Results:

Preoperative characteristics were comparable between the 2 groups. No significant between-group differences were identified with regard to surgical and clinical outcomes. The demarcation lines were clearly projected by the MIPS in 21 patients; however, the boundary line was undetectable in 2 patients.

Conclusions:

We developed the MIPS to address limitations in current intraoperative imaging methods. Our retrospective analysis provides evidence of the feasibility and clinical utility of the MIPS to identify anatomical landmarks for parenchymal dissection. The MIPS holds promise as a novel real-time navigation system for liver resection.
The Privilege of Induction Avoidance and Calcineurin Inhibitors Withdrawal in 2 Haplotype HLA Matched White Kidney Transplantation
Authors: Brifkani Zaid , Brennan Daniel C. , Lentine Krista L. , Horwedel Timothy A. , Malone Andrew F. , Delos Santos Rowena , Maw Thin Thin , Alhamad Tarek
Published: February 2017

Background

White recipients of 2-haplotype HLA-matched living kidney transplants are perceived to be of low immunologic risk. Little is known about the safety of induction avoidance and calcineurin inhibitor withdrawal in these patients.

Methods

We reviewed our experience at a single center and compared it to Organ Procurement and Transplantation Network (OPTN) registry data and only included 2-haplotype HLA-matched white living kidney transplants recipients between 2000 and 2013.

Results

There were 56 recipients in a single center (where no induction was given) and 2976 recipients in the OPTN. Among the OPTN recipients, 1285 received no induction, 903 basiliximab, 608 thymoglobulin, and 180 alemtuzumab. First-year acute rejection rates were similar after induction-free transplantation among the center and induced groups nationally. Compared with induction-free transplantation in the national data, there was no decrease in graft failure risk over 13 years with use of basiliximab (adjusted hazard ratio [aHR], 0.86; confidence interval [CI], 0.68-1.08), Thymoglobulin (aHR, 0.92; CI, 0.7-1.21) or alemtuzumab (aHR, 1.18; CI, 0.72-1.93). Among induction-free recipients at the center, calcineurin inhibitor withdrawal at 1 year (n = 27) did not significantly impact graft failure risk (HR,1.62; CI, 0.38-6.89).

Conclusions

This study may serve as a foundation for further studies to provide personalized, tailored, immunosuppression for this very low-risk population of kidney transplant patients.
Tex19.1Restricts LINE-1 Mobilisation in Mouse Embryonic Stem Cells
Authors: MacLennan Marie , García-Cañadas Marta , Reichmann Judith , Khazina Elena , Salvador-Palomeque Carmen , Mann Abigail R. , Peressini Paula , Sanchez Laura , Playfoot Christopher J. , Read David , Hung Chao-Chun , Eskeland Ragnhild , Meehan Richard R. , Weichenrieder Oliver , GarcíaPérez Jose Luis , Adams Ian R.
Published: February 2017

Mobilisation of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution. In humans, retrotransposon mobilisation is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilise in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilisation. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, we show that loss ofTex19.1increases L1-ORF1p levels and mobilisation of L1 reporters in pluripotent mouse embryonic stem cells implying thatTex19.1prevents new retrotransposition-mediated mutations from arising in the germline genome. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in the epigenetically dynamic developing mammalian germline.
Integrative analysis and refined design of CRISPR knockout screens
Authors: Chen Chen-Hao , Li Wei , Xiao Tengfei , Xu Han , Jiang Peng , Meyer Clifford A. , Brown Myles , Liu X. Shirley
Published: February 2017

Genome-wide CRISPR-Cas9 screen has been widely used to interrogate gene functions. However, the analysis remains challenging and rules to design better libraries beg further refinement. Here we present MAGeCK-NEST, which integrates protein-protein interaction (PPI), improves the inference accuracy when fewer guide-RNAs (sgRNAs) are available, and assesses screen qualities using information on PPI. MAGeCK-NEST also adopts a maximum-likelihood approach to remove sgRNA outliers, which are characterized with higher G-nucleotide counts, especially in regions distal from the PAM motif. Using MAGeCK-NEST, we found that choosing non-targeting sgRNAs as negative controls lead to strong bias, which can be mitigated by sgRNAs targeting the “safe harbor” regions. Custom-designed screens confirmed our findings, and further revealed that 19nt sgRNAs consistently gave the best signal-to-noise separation. Collectively, our method enabled robust calling of CRISPR screen hits and motivated the design of an improved genome-wide CRISPR screen library.
Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1
Authors: Elnatan Daniel , Betegon Miguel , Liu Yanxin , Ramelot Theresa , Kennedy Michael A. , Agard David A.
Published: February 2017

Hsp90 is a homodimeric ATP-dependent molecular chaperone that remodels its substrate “client” proteins, facilitating their folding and activating them for biological function. Despite decades of research, the mechanism connecting ATP hydrolysis and chaperone function remains elusive. Particularly puzzling has been the apparent lack of cooperativity in hydrolysis of the ATP in each protomer. A crystal structure of the mitochondrial Hsp90, TRAP1, revealed that the catalytically active state is closed in a highly-strained asymmetric conformation. This asymmetry, unobserved in other Hsp90 homologs, is due to buckling of one of the protomers and is most pronounced at the broadly conserved client-binding region. Here, we show that rather than being cooperative or independent, ATP hydrolysis on the two protomers is sequential and deterministic. Moreover, dimer asymmetry sets up differential hydrolysis rates for each protomer, such that the buckled conformation favors ATP hydrolysis. Remarkably, after the first hydrolysis, the dimer undergoes a flip in the asymmetry while remaining in a closed state for the second hydrolysis. From these results, we propose a model where direct coupling of ATP hydrolysis and conformational flipping rearranges client-binding sites, providing a paradigm of how energy from ATP hydrolysis can be used for client remodeling.
Evidence for time division multiplexing: Single neurons may encode simultaneous stimuli by switching between activity patterns
Authors: Caruso Valeria C. , Mohl Jeff T. , Glynn Christopher , Lee Jungah , Willett Shawn M. , Zaman Azeem , Ebihara Akinori F. , Estrada Rolando , Freiwald Winrich A. , Tokdar Surya T. , Groh Jennifer M.
Published: February 2017

How the brain preserves information about multiple simultaneous items is poorly understood. We report that single neurons can represent multiple different stimuli by interleaving different signals across time. We record single units in an auditory region, the inferior colliculus, while monkeys localize 1 or 2 simultaneous sounds. During dual-sound trials, we find that some neurons fluctuate between firing rates observed for each single sound, either on a whole-trial or on a sub-trial timescale. These fluctuations are correlated in pairs of neurons, can be predicted by the state of local field potentials prior to sound onset, and, in one monkey, can predict which sound will be reported first. We find corroborating evidence of fluctuating activity patterns in a separate data set involving responses of inferotemporal cortex neurons to multiple visual stimuli. Alternation between activity patterns corresponding to each of multiple items may therefore be a general strategy to enhance the brain processing capacity, potentially linking such disparate phenomena as variable neural firing, neural oscillations, and limits in attentional/memory capacity.
Evolutionary and functional data power search for obsessive-compulsive disorder genes
Authors: Noh Hyun Ji , Tang Ruqi , Flannick Jason , O’Dushlaine Colm , Swofford Ross , Howrigan Daniel , Genereux Diane P. , Johnson Jeremy , van Grootheest Gerard , Grünblatt Edna , Andersson Erik , Djurfeldt Diana R. , Patel Paresh D. , Koltookian Michele , Hultman Christina , Pato Michele T. , Pato Carlos N. , Rasmussen Steven A. , Jenike Michael A. , Hanna Gregory L. , Stewart S. Evelyn , Knowles James A. , Ruhrmann Stephan , Grabe Hans-Jörgen , Wagner Michael , Rück Christian , Mathews Carol A. , Walitza Susanne , Cath Daniëlle C. , Feng Guoping , Karlsson Elinor K. , Lindblad-Toh Kerstin
Published: February 2017

Obsessive-compulsive disorder (OCD) is a severe psychiatric disorder linked to abnormalities in the cortico-striatal circuit and in glutamate signaling. We sequenced coding and regulatory elements for 608 genes implicated in OCD from humans and two animal models (mouse and dog). Using a new method, PolyStrat, which prioritizes variants disrupting evolutionarily conserved, functional regions, we found four strongly associated genes when comparing 592 cases to 560 controls. These results were validated in a second, larger cohort.NRXN1andHTR2Aare enriched for coding variants altering postsynaptic protein-binding domains, whileCTTNBP2(synapse maintenance) andREEP3(vesicle trafficking) are enriched for regulatory variants. The rare coding variant burden inNRXN1achieves genomewide significance (p=6.37×10−11) when we include public data for 33,370 controls. Of 17 regulatory variants identified inCTTNBP2andREEP3, we show that at least six alter transcription factor-DNA binding in human neuroblastoma cells. Our findings suggest synaptic adhesion as a key function in compulsive behaviors across three species, and demonstrate how combining targeted sequencing with functional annotations can identify potentially causative variants in both coding and noncoding regions, even when genomic data is limited.
MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia
Authors: Brown Fiona C. , Still Eric , Cifani Paolo , Takao Sumiko , Reed Casie , Ficarro Scott B. , Koche Richard P. , Romanienko Peter , Mark Willie , O’Donnell Conor , Spitzer Barbara , Stutzke Crystal , Krivtsov Andrei V. , Pouliot Gayle , Gray Nathanael , Marto Jarrod A. , Armstrong Scott , Kentsis Alex
Published: February 2017

HIGHLIGHTS

MEF2C S222 phosphorylation is a specific marker of chemotherapy resistance in diagnostic AML patient specimens.

MEF2C S222 phosphorylation is dispensable for normal hematopoiesis in mice, as established using genome editing in vivo, but is required for MLL-AF9 induced leukemogenesis.

MARK kinases specifically phosphorylate MEF2C S222, potentiating its transcriptional activity.

Chemical inhibition of MARK-induced MEF2C phosphorylation overcomes chemotherapy resistance of and exhibits selectivity toxicity against MEF2C-activated human AML cells.

In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that Mef2cS222A/S222A knock-in mutant mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. MEF2C phosphorylation was required for leukemia stem cell maintenance, and induced by MARK kinases in cells. Treatment with the selective MARK inhibitor MRT199665 caused apoptosis of MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C phosphorylation. These findings identify kinase-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.
Dynamic Functional Connectivity between Order and Randomness and its Evolution across the Human Adult Lifespan
Authors: Battaglia Demian , Boudou Thomas , Hansen Enrique C. A. , Lombardo Diego , Chettouf Sabrina , Daffertshofer Andreas , McIntosh Anthony R. , Zimmermann Joelle , Ritter Petra , Jirsa Viktor
Published: February 2017

Functional Connectivity (FC) during resting-state or task conditions is not fixed but inherently dynamic. Yet, there is no consensus on whether fluctuations in FC may resemble isolated transitions between discrete FC states rather than continuous changes. This quarrel hampers advancing the study of dynamic FC. This is unfortunate as the structure of fluctuations in FC can certainly provide more information about developmental changes, aging, and progression of pathologies. We merge the two perspectives and consider dynamic FC as an ongoing network reconfiguration, including a stochastic exploration of the space of possible steady FC states. The statistical properties of this random walk deviate both from a purely “order-driven” dynamics, in which the mean FC is preserved, and from a purely “randomness-driven” scenario, in which fluctuations of FC remain uncorrelated over time. Instead, dynamic FC has a complex structure endowed with long-range sequential correlations that give rise to transient slowing and acceleration epochs in the continuous flow of reconfiguration. Our analysis for fMRI data in healthy elderly revealed that dynamic FC tends to slow down and becomes less complex as well as more random with increasing age. These effects appear to be strongly associated with age-related changes in behavioural and cognitive performance.

Highlights

Dynamic Functional Connectivity (dFC) at rest and during cognitive task performs a “complex” (anomalous) random walk.

Speed of dFC slows down with aging.

Resting dFC replaces complexity by randomness with aging.

Task performance correlates with the speed and complexity of dFC.
Between semelparity and iteroparity: empirical evidence for a continuum of modes of parity
Authors: Hughes P. William
Published: February 2017

The number of times an organism reproduces (i.e. its mode of parity) is a fundamental life-history character, and evolutionary and ecological models that compare the relative fitness of strategies are common in life history theory and theoretical biology. Despite the success of mathematical models designed to compare intrinsic rates of increase between annual-semelparous and perennial-iteroparous reproductive schedules, there is widespread evidence that variation in reproductive allocation among semelparous and iteroparous organisms alike is continuous. This paper reviews the ecological and molecular evidence for the continuity and plasticity of modes of parity––that is, the idea that annual-semelparous and perennial-iteroparous life histories are better understood as endpoints along a continuum of possible strategies. I conclude that parity should be understood as a continuum of different modes of parity, which differ by the degree to which they disperse or concentrate reproductive effort in time. I further argue that there are three main implications of this conclusion: (1) That seasonality should not be conflated with parity; (2) that mathematical models purporting to explain the evolution of semelparous life histories from iteroparous ones (or vice versa) should not assume that organisms can only display either an annual-semelparous life history or a perennial-iteroparous one; and (3) that evolutionary ecologists should examine the physiological or molecular basis of traits underlying different modes of parity, in order to obtain a general understanding of how different life history strategies can evolve from one another.
On the relationship between indenation hardness and modulus, and the damage resistance of biological materials
Authors: Labonte David , Lenz Anne-Kristin , Oyen Michelle L.
Published: February 2017

The remarkable mechanical performance of biological materials is based on intricate structure-function relationships. Nanoindentation has become the primary tool for characterising biological materials, as it allows to relate structural changes to variations in mechanical properties on small scales. However, the respective theoretical background and associated interpretation of the parameters measured via indentation derives largely from research on ‘traditional’ engineering materials such as metals or ceramics. Here, we discuss the functional relevance of indentation hardness in biological materials by presenting a meta-analysis of its relationship with indentation modulus. Across seven orders of magnitude, indentation hardness was directly proportional to indentation modulus, illustrating that hardness is not an independent material property. Using a lumped parameter model to deconvolute indentation hardness into components arising from reversible and irreversible deformation, we establish criteria which allow to interpret differences in indentation hardness across or within biological materials. The ratio between hardness and modulus arises as a key parameter, which is a proxy for the ratio between irreversible and reversible deformation during indentation, and the material’s yield strength. Indentation hardness generally increases upon material dehydration, however to a larger extend than expected from accompanying changes in indentation modulus, indicating that water acts as a ‘plasticiser’. A detailed discussion of the role of indentation hardness, modulus and toughness in damage control during sharp or blunt indentation yields comprehensive guidelines for a performance-based ranking of biological materials, and suggests that quasi-plastic deformation is a frequent yet poorly understood damage mode, highlighting an important area of future research.
Functional Bias and Demographic History Obscure Patterns of Selection among Single-Copy Genes in a Fungal Species Complex
Authors: Sánchez-Ramírez Santiago , Moncalvo Jean-Marc
Published: February 2017

Many different evolutionary processes may be responsible for explaining natural variation within genomes, some of which include natural selection at the molecular level and changes in population size. Fungi are highly adaptable organisms, and their relatively small genomes and short generation times make them pliable for evolutionary genomic studies. However, adaptation in wild populations has been relatively less documented compared to experimental or clinical studies. Here, we analyzed DNA sequences from 502 putative single-copy orthologous genes in 63 samples that represent seven recently diverged North AmericanAmanita(jacksonii-complex) lineages. For each gene and each species, we measured the genealogical sorting index (gsi) and infinite-site-based summary statistics, such as,andDTajin coding and intron regions. MKT-based approaches and likelihood-ratio-testKn/Ksmodels were used to measure natural selection in all coding sequences. Multi-locus (Extended) Bayesian Skyline Plots (eBSP) were used to model intraspecific demographic changes through time based on unlinked, putative neutral regions (introns). Most genes show evidence of long-term purifying selection, likely reflecting a functional bias implicit in single-copy genes. We find that two species have strongly negatively skewed Tajima’sD, while three other have a positive skew, corresponding well with patterns of demographic expansion and contraction. Standard MKT analyses resulted in a high incidence of near-zero α with a tendency towards negative values. In contrast, α estimates based on the distribution of fitness effects (DFE), which accounts for demographic effects and slightly deleterious mutations, suggest a higher proportion of sites fixed by positive selection. The difference was more notorious in species with expansion signatures or with historically low population sizes, evidencing the concealing effects of specific demographic histories. Finally, we attempt to mitigate Gene Ontology term overrepresentation, highlighting the potential adaptive or ecological roles of some genes under positive selection.
Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells
Authors: Kumar Sandeep , Peng Xiangdong , Daley James M. , Yang Lin , Shen Jianfeng , Nguyen Nghi , Bae Goeun , Niu Hengyao , Peng Yang , Hsieh Hui-Ju , Wang Lulu , Rao Chinthalapally , Stephan Clifford C. , Sung Patrick , Ira Grzegorz , Peng Guang
Published: February 2017

Replication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. Our studies showed that DNA2 nuclease is an evolutionarily conserved essential component of HR repair machinery. Here we demonstrate that DNA2 is indeed overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90%-95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anti-cancer drugs by targeting druggable nuclease DNA2. We 4, 16. In propose DNA2 inhibition as new strategy in cancer therapy by targeting replication stress, a molecular property of cancer cells that is acquired as a result of oncogene activation instead of targeting undruggable oncoprotein itself such as KRAS.