bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass-Observation, Left Intellectuals and the Politics of Everyday Life
Authors: Campsie Alexandre
Published: February 2016

This article examines the careers of a number of left thinkers who broke with the Communist Party of Great Britain in the late 1930s, committing themselves instead to a ‘politics of everyday life’ based on social investigation. Central to this moment was the social research organisation Mass-Observation, the sociologists of which argued that democracy should be built around the vibrancy and irreverence they identified in ordinary culture. This ambition gained its fullest application during the 1940s, as a number of former M-O researchers became influential in the social reconstruction effort, in Labour Party policy circles and, later, in post-war academic sociology. By tracing the sociological arguments of unaligned left intellectuals from the 1930s to the 1950s, this article emphasises the rich plurality of influences at play within British progressive thought in the mid-twentieth century—influences which spanned the worlds of far-left activism, literature, art, the social sciences, town planning and parliamentary politics. It also helps us to reassess the genesis of the first ‘New Left’ in 1956. This is often hailed as the moment when British socialists first started to appreciate ordinary culture, freed from political dogmatism. In fact, left intellectuals had been engaging with the politics of everyday life for at least two decades previously. Indeed, the nostalgic accent which some New Left writers placed on the traditional working-class group was but one facet of a more heterogeneous political tradition—one concerned to think beyond ‘class’ altogether, and to examine how culture operated at the level of the individual.
Star Wars: Response to Simonson, Winer/Fader, and Kozinets
Authors: de Langhe Bart , Fernbach Philip M. , Lichtenstein Donald R.
Published: February 2016

In de Langhe, Fernbach, and Lichtenstein (2016), we argue that consumers trust average user ratings as indicators of objective product performance much more than they should. This simple idea has provoked passionate commentaries from eminent researchers across three subdisciplines of marketing: experimental consumer research, modeling, and qualitative consumer research. Simonson challenges the premise of our research, asking whether objective performance even matters. We think it does and explain why in our response. Winer and Fader argue that our results are neither insightful nor important. We believe that their reaction is due to a fundamental misunderstanding of our goals, and we show that their criticisms do not hold up to scrutiny. Finally, Kozinets points out how narrow a slice of consumer experience our article covers. We agree, and build on his observations to reflect on some big-picture issues about the nature of research and the interaction between the subdisciplines.
Evolution of dispersion in the cosmic deuterium abundance
Authors: Dvorkin Irina , Vangioni Elisabeth , Silk Joseph , Petitjean Patrick , Olive Keith A.
Published: February 2016

Deuterium is created during big bang nucleosynthesis, and, in contrast to the other light stable nuclei, can only be destroyed thereafter by fusion in stellar interiors. In this Letter, we study the cosmic evolution of the deuterium abundance in the interstellar medium (ISM) and its dispersion using realistic galaxy evolution models. We find that models that reproduce the observed metal abundance are compatible with observations of the deuterium abundance in the local ISM and z ∼ 3 absorption line systems. In particular, we reproduce the low astration factor which we attribute to a low global star formation efficiency. We calculate the dispersion in deuterium abundance arising from different structure formation histories in different parts of the Universe. Our model also predicts a tight correlation between deuterium and metal abundances which could be used to measure the primordial deuterium abundance.
Long-Term Control of Human Immunodeficiency Virus-1 Replication Despite Extensive Resistance to Current Antiretroviral Regimens: Clonal Analysis of Resistance Mutations in Proviral Deoxyribonucleic Acid
Authors: Stella-Ascariz Natalia , Montejano Rocio , Martin-Vicente María , Mingorance Jesús , Pérez-Valero Ignacio , Bernardino José I. , Arribas Jose R.
Published: February 2016

Archived resistance mutations compromise antiretroviral treatment. We have investigated 3 selected aviremic patients who had extensive historical resistance to their current regimen. All 3 patients underwent unstructured treatment interruptions associated to the re-emergence of wild-type virus before starting their current suppressive regimes. Almost all historical resistance mutations detected in plasma were found in circulating proviral deoxyribonucleic acid. None of the clones analyzed was fully resistant to the current antiretroviral regimen.
Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease
Authors: Galloway-Peña Jessica , Clement Meredith E. , Sharma Kuinkel Batu K. , Ruffin Felicia , Flores Anthony R. , Levinson Howard , Shelburne Samuel A. , Moore Zack , Fowler Vance G.
Published: February 2016

Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.
Absence of Pneumocystis jirovecii Colonization in Human Immunodeficiency Virus-Infected Individuals With and Without Airway Obstruction and With Undetectable Viral Load
Authors: Ronit Andreas , Klitbo Ditte Marie , Kildemoes Anna Overgaard , Benfield Thomas , Gerstoft Jan , Vestbo Jørgen , Jensen Jørgen Skov , Kurtzhals Jørgen , Nielsen Susanne Dam
Published: February 2016

Pneumocystis jirovecii colonization has been associated with non-acquired immune deficiency syndrome (AIDS) pulmonary comorbidity. We used spirometry to measure pulmonary function and analyzed oral wash specimens by quantitative polymerase chain reaction (PCR), targeting the large mitochondrial ribosomal subunit. For sensitivity control, a blinded subsample was subjected to touch-down PCRs, targeting both large and small ribosomal subunits and the major surface glycoprotein. Pneumocystis jirovecii deoxyribonucleic acid (DNA) was detected in 1 of 156 (95% confidence interval, .1%–3.5%) virologically suppressed human immunodeficiency virus (HIV)-infected individuals confirmed by all PCR methods. Thus, prevalence of P jirovecii colonization was low and unlikely to be a major cause of pulmonary comorbidity in this group of well treated HIV-infected individuals.
The Effects of Acoustic Bandwidth on Simulated Bimodal Benefit in Children and Adults with Normal Hearing
Authors: Sheffield Sterling W. , Simha Michelle , Jahn Kelly N. , Gifford René H.
Published: February 2016

Objectives:

The primary purpose of this study was to examine the effect of acoustic bandwidth on bimodal benefit for speech recognition in normal-hearing children with a cochlear implant (CI) simulation in one ear and low-pass filtered stimuli in the contralateral ear. The effect of acoustic bandwidth on bimodal benefit in children was compared with the pattern of adults with normal hearing. Our hypothesis was that children would require a wider acoustic bandwidth than adults to (1) derive bimodal benefit, and (2) obtain asymptotic bimodal benefit.

Design:

Nineteen children (6 to 12 years) and 10 adults with normal hearing participated in the study. Speech recognition was assessed via recorded sentences presented in a 20-talker babble. The AzBio female-talker sentences were used for the adults and the pediatric AzBio sentences (BabyBio) were used for the children. A CI simulation was presented to the right ear and low-pass filtered stimuli were presented to the left ear with the following cutoff frequencies: 250, 500, 750, 1000, and 1500 Hz.

Results:

The primary findings were (1) adults achieved higher performance than children when presented with only low-pass filtered acoustic stimuli, (2) adults and children performed similarly in all the simulated CI and bimodal conditions, (3) children gained significant bimodal benefit with the addition of low-pass filtered speech at 250 Hz, and (4) unlike previous studies completed with adult bimodal patients, adults and children with normal hearing gained additional significant bimodal benefit with cutoff frequencies up to 1500 Hz with most of the additional benefit gained with energy below 750 Hz.

Conclusions:

Acoustic bandwidth effects on simulated bimodal benefit were similar in children and adults with normal hearing. Should the current results generalize to children with CIs, these results suggest pediatric CI recipients may derive significant benefit from minimal acoustic hearing (<250 Hz) in the nonimplanted ear and increasing benefit with broader bandwidth. Knowledge of the effect of acoustic bandwidth on bimodal benefit in children may help direct clinical decisions regarding a second CI, continued bimodal hearing, and even optimizing acoustic amplification for the nonimplanted ear.
The Prevalence and the Incidence of Diagnosed Open-Angle Glaucoma and Diagnosed Angle-Closure Glaucoma: Changes From 2001 to 2010
Authors: Chiu Shin-Lin , Chu Chiao-Lee , Muo Chih-Hsin , Chen Chiu-Liang , Lan Shou-Jen
Published: February 2016

Purpose:

To explore the trends in diagnosed open-angle glaucoma (OAG) and diagnosed angle-closure glaucoma (ACG) in Taiwan during the period of 2001 to 2010.

Materials and Methods:

Data were sourced from the National Longitudinal Health Insurance Database 2000 (LHID2000). The study population comprised all patients with a diagnosis of OAG or ACG (International Classification of Diseases, 9th Revision, Clinical Modification codes 365). Patients were stratified by their sex and age; differences in standardized incidence rates were compared between the stratified groups.

Results:

Throughout the study period, the prevalence of diagnosed OAG (slope=0.18, P<0.0001) and ACG (slope=0.09, P<0.0001) increased. Before 2005, the prevalence of ACG was higher than that of OAG; however, from 2005 to 2010, the prevalence of OAG was higher than that of ACG. The standardized incidence of diagnosed OAG increased insignificantly (slope=1.06, P=0.18), and that of diagnosed ACG decreased significantly (slope=−1.17, P=0.009). The prevalence and the incidence of OAG and ACG were the highest among people of advanced age. Women had higher standardized incidence rates of ACG during the study period. Men had higher standardized incidence rates of OAG in every year of the study with the exception of 2007.

Conclusions:

In Taiwan, ACG was more prevalent in women and OAG might be more prevalent in men. The prevalence of ACG was higher than that of OAG before 2005, but the prevalence of OAG has been higher than that of ACG since 2005.
Evaluation of Retinal Nerve Fiber Layer and Ganglion Cell Complex Thickness in Unilateral Exfoliation Syndrome Using Optical Coherence Tomography
Authors: Aydin Damla , Kusbeci Tuncay , Uzunel Umut D. , Orsel Tumay , Yuksel Bora
Published: February 2016

Purpose:

To evaluate retinal nerve fiber layer (RNFL) and ganglion cell complex (GCC) thickness by using optical coherence tomography in unilateral exfoliation syndrome (XFS) and to assess whether exfoliation itself is an independent risk factor for glaucomatous optic nerve damage.

Materials and Methods:

Thirty exfoliative eyes of unilateral XFS cases, 30 fellow eyes of unilateral exfoliation, and 30 eyes of healthy subjects were enrolled the study. Peripapillary RNFL and macular GCC thickness measurements by Cirrus HD OCT (Carl Zeiss Meditec, Dublin, CA) were performed on all subjects.

Results:

RNFL thickness in superior quadrant was significantly different between groups (P=0.025) and it was thinner in XFS than healthy subjects (P=0.020). All GCC parameters except GCC thickness in inferior quadrant were significantly different between groups (P=0.110 for inferior quadrant, P<0.046 for other GCC parameters). GCC were thinner in XFS than healthy subjects except inferior and inferonasal quadrants (P=0.091, 0.051 for inferior and inferonasal quadrants, respectively, P<0.039 for other GCC parameters). Minimum GCC thickness, GCC thicknesses in superior, and inferonasal quadrants were significantly thinner in fellow eyes than healthy subjects (P=0.011, 0.013, 0.047, respectively).

Conclusions:

XFS is related with thinner RNFL and GCC even in normal intraocular pressure values, similar optic disc parameters and visual field results. XFS may be an independent risk factor for glaucomatous optic nerve damage. So, further studies are needed to evaluate whether exfoliation itself is an independent risk factor for optic nerve damage.
Repeatability of Spectral Domain Optical Coherence Tomography Measurements in High Myopia
Authors: Rao Harsha L. , Kumar Addepalli U. , Bonala Sampath R. , Yogesh Kadam , Lakshmi Bodduluri
Published: February 2016

Purpose:

The purpose of this study was to compare the repeatability of spectral domain optical coherence tomography (SDOCT) parameters in high-myopic and emmetropic healthy subjects, and to evaluate the influence of axial length on the repeatability of SDOCT parameters in high myopia.

Methods:

In a prospective study, 93 eyes of 63 high-myopic subjects (spherical refractive error, −6 to −12 D; median age, 25 y) and 28 eyes of 14 emmetropic (spherical refractive error, 0 D; median age, 30 y) subjects underwent optic nerve head, retinal nerve fiber layer (RNFL), and ganglion cell complex imaging with SDOCT. For the repeatability analysis, 31 eyes of 31 high-myopic subjects and 14 eyes of 14 emmetropic subjects underwent 3 repeated scans in the same session.

Results:

Among the optic nerve head parameters, within-subject coefficient of variation (CVw) measurements of the disc area (0.6% vs. 0.2%), rim area (8.7 vs. 2.8), and rim volume (16.7 vs. 8.9) were significantly larger (worse) in high-myopic compared with the emmetropic subjects. CVw measurements of all RNFL (range, 1.7 to 22.4) and ganglion cell complex (range, 1.8 to 2.5) parameters in high-myopic subjects were comparable to that in emmetropic subjects (2.4 to 24.0 and 1.7 to 2.0, respectively). Axial length significantly affected the CVw of nasal (coefficient, 0.01; P=0.04) and average RNFL (coefficient, 0.004; P=0.001) parameters but not that of the other SDOCT parameters.

Conclusions:

Repeatabilities of most of the SDOCT parameters in high-myopic subjects were good and comparable to that of emmetropic subjects. This suggests that SDOCT can be useful for following up high-myopic glaucoma patients to detect progression.
A New 35-mm Short Intra-aortic Balloon Catheter: A Suitable Option also for Non-Small-Sized Patients?
Authors: Gelsomino Sandro , Lozekoot Pieter Willem , Lorusso Roberto , de Jong Monique Maria , Parise Orlando , Matteucci Francesco , Lucà Fabiana , Kumar Narendra , Dehkord Eshan Sadeghian , Romano Salvatore Mario , Gensini Gian Franco , La Meir Mark , Maessen Josephus Gregorius
Published: February 2016

Objective

Visceral ischemia can be a potentially life-threatening complication of intra-aortic balloon pump (IABP) support. A shorter IABP catheter might lead to a reduction of visceral complications. In this animal study, we evaluate the effects of a 35-mL short catheter in comparison with a 40-mL standard-sized catheter.

Methods

Eighteen healthy swine underwent 120-minute ligation of the left anterior descending coronary artery followed by 6 hours of reperfusion being supported by either a short IABP catheter (short group) (n = 6) or a long IABP catheter (long group) (n = 6) or with no assistance (controls) (n = 6). Hemodynamics, visceral and coronary flows, as well as biochemical markers were evaluated throughout the different phases of the protocol.

Results

Mesenteric flows increased significantly at reperfusion (P < 0.001 both) remaining constant afterward (all, P > 0.05) in the short group, while remaining significantly lower in the long group at the start of reperfusion, remaining constantly lower than the short group and controls (P < 0.001 vs short, P < 0.003 vs controls). In both long and short groups, catheters improved renal flows at reperfusion (P < 0.001 both) without any further variation (P < 0.05). In the short group, the flows were higher during the whole of reperfusion (all, P < 0.05). Intra-aortic balloon pump support improved hemodynamic indices and coronary blood flows during reperfusion to a similar extent in both the small and the long group (P > 0.05).

Conclusions

The short IABP catheter proved to be as effective as the standard-sized catheter in supporting hemodynamics and coronary circulation. Furthermore, it even improves visceral flows in comparison with conventional IABP catheters.
External Saphenous Vein Support Mesh Does Not Interfere with Transit-Time Flow Measurement on Venous Coronary Bypass Conduit: Clinical Confirmation
Authors: Mootoosamy Parmeseeven , Jolou Jalal , Myers Patrick O. , Walpoth Beat H. , Kalangos Afksendiyos , Cikirikcioglu Mustafa
Published: February 2016

A 65-year-old patient underwent double coronary artery bypass grafting using the left internal thoracic artery on the left anterior descending coronary artery and nitinol alloy mesh [external Saphenous Vein Support (eSVS)]–covered saphenous vein graft to the right posterior descending coronary artery. Transit-time flow measurements (TTFMs) were obtained on meshed and bare parts of the vein graft. There was no difference in TTFM parameters (flow, pulsatility index, and diastolic fraction values) obtained from the eSVS mesh-covered and the uncovered parts of the venous graft. This observation confirms that eSVS mesh does not interfere with TTFM on venous coronary bypass conduits.
Preoperative pain mechanisms assessed by cuff algometry are associated with chronic postoperative pain relief after total knee replacement
Authors: Petersen Kristian Kjær , Graven-Nielsen Thomas , Simonsen Ole , Laursen Mogens Berg , Arendt-Nielsen Lars
Published: February 2016

Chronic postoperative pain after total knee replacement (TKR) in knee osteoarthritis (KOA) implies clinical challenges. Widespread hyperalgesia, facilitated temporal summation of pain (TSP), and impaired conditioned pain modulation (CPM) have been found in painful KOA. This exploratory study investigated postoperative pain relief 12 months after TKR in 4 subgroups of patients preoperatively profiled by mechanistic quantitative sensory testing. In 103 patients with KOA, pressure pain detection threshold (PDT) and tolerance thresholds (PTT) were assessed at the lower leg using cuff algometry. Temporal summation of pain was measured as an increase in pain intensity scores during 10 repeated (2 seconds intervals) painful cuff stimuli. Conditioned pain modulation was calculated as the relative increase in PDT during painful conditioning stimulation. The grand averages of TSP and CPM were calculated and values below or above were used for subgrouping: facilitated TSP/impaired CPM (group A, N = 16), facilitated TSP/normal CPM (group B, N = 15), normal TSP/impaired CPM (group C, N = 44), and normal TSP/normal CPM (group D, N = 28). Clinical VAS pain intensity scores were collected before and 12 months after TKR surgery and the pain relief calculated. Less pain relief was found in group A (52.0% ± 14.0% pain relief) than in group B (81.1% ± 3.5%,P= 0.023) and group C (79.6% ± 4.4%,P= 0.007), but not group D (69.4% ± 7.9%,P= 0.087). Low preoperative PDT was associated with a less postoperative pain relief (R= −0.222,P= 0.034), whereas TSP or CPM alone showed no associations with postoperative pain relief. This explorative study indicated that patients with osteoarthritis with facilitated TSP together with impaired CPM are more vulnerable to experience less pain relief after TKR.
Lower sex hormone levels are associated with more chronic musculoskeletal pain in community-dwelling elderly women
Authors: de Kruijf Marjolein , Stolk Lisette , Zillikens M. Carola , de Rijke Yolanda B. , Bierma-Zeinstra Sita M.A. , Hofman Albert , Huygen Frank J.P.M. , Uitterlinden Andre G. , van Meurs Joyce B.J.
Published: February 2016

Chronic pain is more prevalent in women than in men, with increasing differences between sexes in advanced age. This could be caused by differences in sex hormone levels. We therefore studied the relationship between sex hormones and the prevalence and incidence of chronic pain. The association between sex hormone levels and chronic pain was examined in 9717 participants aged 45 years and older from the Rotterdam Study, a population-based study. Chronic pain was defined as pain in the lower back, hands, knees and/or hips for at least 3 months. Sex hormone levels included estrogen, testosterone, androstenedione, and 17-hydroxyprogesterone. Relationships between hormones and prevalent and new onset chronic pain were analyzed using linear and logistic regression, stratified by gender. Women with androstenedione or estradiol levels in the lowest tertile had more chronic pain (odds ratio, 1.20; 95% CI, 1.03-1.39 and odds ratio, 1.27; 95% CI, 1.10-1.48, respectively). Mean estradiol levels were lower among men with chronic pain (mean difference −3.88 pmol/L; P = 0.005). Lowest tertile 17-hydroxyprogesterone in women was associated with 38% more new onset pain. All these associations were independent from age, body mass index, health and lifestyle factors, and osteoarthritis. Lower sex hormone levels are associated with chronic musculoskeletal pain, independent from lifestyle and health-related factors, in community-dwelling elderly women. These results suggest that sex hormones play a role in chronic pain and should be taken into account when a patient presents with chronic pain. Therefore, sex hormones may be a potential treatment target for these patients.
Demoralization in Cancer Patients and Related Factors in Taiwan
Authors: Li Yu-Chi , Ho Chung-Han , Wang Hsiu-Hung
Published: February 2016

Background:

Demoralization frequently occurs in hospice, cancer, and critically ill patients. Severe demoralization can lead to suicidal ideation, making this issue of great import to healthcare providers.

Objective:

The aim of this study is to inform nursing professionals of the risk factors of demoralization in cancer patients via investigating its relationship with cancer patients’ demographic data and disease characteristics.

Methods:

This is a cross-sectional descriptive study using a structured questionnaire including assessments of demographic data and disease characteristics, as well as the Demoralization Scale Mandarin version. Univariate logistic regression was used to explore the relations between demoralization and these other variables.

Results:

The mean (SD) Demoralization Scale Mandarin version score was 30.08 (13.68) (range, 0–73). Demoralization was significantly related to age (r = 0.1, P = .050), marital status (r = 0.11, P = .034), education (r = 0.17, P < .001), monthly income (r = 0.22, P < .001), disease status (r = 0.10, P = .050), and treatment type (r = 0.12, P = .014).

Conclusions:

This study demonstrates the factors influencing demoralization among cancer patients. Future studies might expand to include patients with other chronic or critical illnesses or disadvantaged groups to better understand the prevalence of demoralization. This would help draw more attention from clinical healthcare providers, healthcare institutions, and other healthcare authorities to demoralization.

Implications or Practice:

The results provide reference data for nursing professionals about the care of cancer patients.
BAP1 Immunohistochemistry and p16 FISH in the Diagnosis of Sarcomatous and Desmoplastic Mesotheliomas
Authors: Hwang Harry C. , Pyott Shawna , Rodriguez Stephanie , Cindric Ashlie , Carr April , Michelsen Carmen , Thompson Kim , Tse Christopher H. , Gown Allen M. , Churg Andrew
Published: February 2016

The separation of sarcomatous and desmoplastic mesotheliomas from benign organizing pleuritis can be morphologically very difficult. Deletion of p16 (CDKN2A) by fluorescence in situ hybridization (FISH) testing appears to be a reliable marker of malignancy in mesothelial proliferations, and more recently it has been reported that, in this setting, loss of BAP1 by immunohistochemistry is only seen in malignant mesotheliomas. To determine how useful these tests are with sarcomatous and desmoplastic mesotheliomas, we examined 20 such tumors. Loss of BAP1 was seen in 3/20 (15%) and deletion of p16 by FISH was seen in 16/20 (80%) cases. Loss of one or the other marker was observed in 17/20 (85%). We also examined 13 sarcomatoid carcinomas, an important differential diagnosis of sarcomatoid mesotheliomas, and found that BAP1 was never lost, but p16 was deleted in 3/11 (27%). We conclude that: (1) BAP1 immunohistochemistry is relatively insensitive in the context of sarcomatous and desmoplastic mesotheliomas, but as a matter of time and cost efficiency may nonetheless be a useful first approach to the problem; (2) deletion of p16 by FISH is considerably more sensitive, but there remain a proportion of cases in which p16 is not deleted; (3) a small improvement in sensitivity can be achieved by using both markers; (4) in the context of a spindle cell malignant tumor in the pleura or peritoneum, which morphologically might be a metastatic sarcomatoid carcinoma or a mesothelioma, the finding of BAP1 loss favors mesothelioma, but p16 FISH cannot be used to separate sarcomatous mesotheliomas from sarcomatoid carcinomas.
Fumarate Hydratase–deficient Renal Cell Carcinoma Is Strongly Correlated With Fumarate Hydratase Mutation and Hereditary Leiomyomatosis and Renal Cell Carcinoma Syndrome
Authors: Trpkov Kiril , Hes Ondrej , Agaimy Abbas , Bonert Michael , Martinek Petr , Magi-Galluzzi Cristina , Kristiansen Glen , Lüders Christine , Nesi Gabriella , Compérat Eva , Sibony Mathilde , Berney Daniel M. , Mehra Rohit , Brimo Fadi , Hartmann Arndt , Husain Arjumand , Frizzell Norma , Hills Kirsten , Maclean Fiona , Srinivasan Bhuvana , Gill Anthony J.
Published: February 2016

Hereditary leiomyomatosis and renal cell carcinoma syndrome–associated renal cell carcinomas (RCC) are difficult to diagnose prospectively. We used immunohistochemistry (IHC) to identify fumarate hydratase (FH)-deficient tumors (defined as FH negative, 2-succinocysteine [2SC] positive) in cases diagnosed as “unclassified RCC, high grade or with papillary pattern,” or “papillary RCC type 2,” from multiple institutions. A total of 124 tumors (from 118 patients) were evaluated by IHC for FH and 2SC. An FH deficiency was found in 24/124 (19%) cases. An indeterminate result (only 1 marker abnormal) was found in 27/124 (22%) cases. In a tissue microarray of 776 RCCs of different types, only 2 (0.5%) tumors, initially considered papillary type 2, were FH deficient. FH mutations were found in 19/21 FH-deficient tumors (with confirmed germline mutations in 9 of 9 tumors in which germline status could be assessed) and in 1/26 FH-indeterminate tumors identified by IHC. No FH mutations were found in 2/21 FH-deficient RCCs, 25/26 FH-indeterminate RCCs, and 10/10 RCCs demonstrating FH expression by IHC. Patients with FH-deficient RCC had a median age of 44 years (range, 21 to 65 y). Average tumor size was 8.2 cm (range, 0.9 to 18 cm). FH-deficient RCCs were characterized by at least focal macronucleoli and demonstrated 2 or more growth patterns in 93% cases. Papillary was the most common (74%) and dominant (59%) pattern, whereas other common patterns included: solid (44%), tubulocystic (41%), cribriform (41%), and cystic (33%). At presentation, 57% were stage ≥pT3, 52% had positive nodes, and 19% had distant metastases. After a mean follow-up of 27 months (range, 1 to 114 mo), 39% of patients were dead of disease, and 26% had disease progression. We conclude that FH and 2SC are useful IHC ancillary tools, which allow recognition of FH-deficient RCC.
Spectrum of Cystic Epithelial Tumors of the Prostate
Authors: Paner Gladell P. , Lopez-Beltran Antonio , So Jeffrey S. , Antic Tatjana , Tsuzuki Toyonori , McKenney Jesse K.
Published: February 2016

Cystic epithelial tumors arising from the prostate are rare, and their full histologic spectrum has yet to be defined. Herein, we present 8 examples of prostatic cystic tumors including 1 giant multilocular cystadenoma and 7 cystadenocarcinomas. We divided the cystadenocarcinomas into “giant multilocular” cystadenocarcinoma (3) and “microscopic” cystadenocarcinoma (4) because of their differing clinical presentations with clinically apparent cystic masses in the former. The cystadenoma was an 11 cm multilocular cystic pelvic tumor in a 55-year-old man who presented with lower urinary tract symptoms. The cystadenoma was lined predominantly by benign acinar cells and had a distinct basal cell layer. No recurrence occurred 3 months after resection. The 3 patients with giant multilocular cystadenocarcinomas were 62 to 82 years old, had large pelvic cystic masses (up to 16 cm), and 2 presented with obstructive urinary and lower intestinal tract symptoms. One giant multilocular cystadenocarcinoma had a markedly high cystic fluid prostate-specific antigen at >80,000 ng/mL. All 3 giant multilocular cystadenocarcinomas were ductal adenocarcinoma with exuberant intracystic papillary formations. One tumor was associated with a high-grade noncystic conventional (acinar) adenocarcinoma (Gleason score 9 [ISUP grade group 5]). Follow-up on the 3 giant multilocular cystadenocarcinoma cases (7 to 21 mo) showed multiple metastases in 1 patient but was attributed to the high-grade conventional adenocarcinoma component. In addition, we described 4 examples of microscopic cystadenocarcinomas that were small (≤1 cm) solitary or multiple cystic tumors identified on pathologic examination of the prostate. In 3 of 4 microscopic cystadenocarcinomas the lining was ductal adenocarcinoma with occasional to exuberant papillae and appeared similar to the smaller cysts in the giant multilocular cystadenocarcinomas. One of the 4 microscopic cystadenocarcinomas had an acinar adenocarcinoma lining with occasional papillae and was associated with a conventional adenocarcinoma. Follow-up of the 4 patients with microscopic cystadenocarcinoma (1 to 14 mo) showed no evidence of disease. Review of literature highlighted similarities between the findings in our cases and previously published prostatic cystadenocarcinomas, including the markedly high cystic fluid prostate-specific antigen level in giant multilocular cystadenocarcinomas and the typical ductal adenocarcinoma morphology with intracystic papillary pattern. In conclusion, cystic epithelial tumors of the prostate exhibit unique clinicopathologic features. Cystadenocarcinomas, whether the clinically apparent giant multilocular form or the incidentally identified microscopic type, represent a rare underrecognized pattern of prostatic adenocarcinoma mostly within the histologic spectrum of the ductal variant.
Developing Normal Turns–Amplitude Clouds for Upper and Lower Limbs
Authors: Jabre Joe F. , Nikolayev Sergey G. , Babayev Michael B. , Chindilov Denis V. , Muravyov Anatoly Y.
Published: February 2016

Purpose:

Turns and amplitude analysis (T&A) is a frequently used method for automatic EMG interference pattern analysis. The T&A normal values have only been developed for a limited number of muscles. Our objective was to obtain normal T&A clouds for upper and lower extremity muscles for which no normal values exist in the literature.

Methods:

The T&A normative data using concentric needle electrodes were obtained from 68 men and 56 women aged 20 to 60 years.

Results:

Normal upper and lower extremity T&A clouds were obtained and presented in this article.

Conclusion:

The T&A normal values collected in this study maybe used to detect neurogenic and myopathic abnormalities in men and women at low-to-moderate muscle contractions. The effect of turns–amplitude data obtained at high force level of muscle contraction and its potential to falsely show neurogenic abnormalities are discussed.
Evaluation of Techniques for Performing Cellular Isolation and Preservation during Microgravity Conditions
Authors: Rizzardi Lindsay F. , Kunz Hawley , Rubins Kathleen , Chouker Alexander , Quiriarte Heather , Sams Clarence , Crucian Brian E. , Feinberg Andrew P.
Published: February 2016

Genomic and epigenomic studies require the precise transfer of small volumes from one container to another. Epigenomic and transcriptional analysis require separation of purified cell types, and long term preservation of cells requires their isolation and transfer into appropriate freezing media. There are currently no protocols for these procedures on the ISS. Currently samples are either frozen as mixed cell populations, with poor yield, or returned under ambient conditions, requiring timing with Soyuz missions. Here, we evaluate the feasibility of translating terrestrial cell purification techniques to the ISS. Our evaluations were performed in microgravity conditions during parabolic atmospheric flight. The pipetting of open liquids in microgravity was evaluated using analog blood fluids and several types of pipette hardware. The best performing pipettes were used to evaluate the pipetting steps required for peripheral blood mononuclear cell (PBMC) isolation via density gradient centrifugation (DGC). Evaluation of actual blood products was performed for both the overlay of diluted blood, and the extraction of isolated PBMCs. We also validated magnetic purification of cells. We found that positive displacement pipettes avoided air bubbles, and the tips allowed the strong surface tension of water, glycerol and blood to maintain a patent meniscus and withstand robust pipetting in microgravity. These procedures will greatly increase the breadth of research that can be performed onboard the ISS, and allow improvised experimentation on extraterrestrial missions.
variancePartition: Interpreting drivers of variation in complex gene expression studies
Authors: Hoffman Gabriel E. , Schadt Eric E.
Published: February 2016

As genomics studies become more complex and consider multiple sources of biological and technical variation, characterizing these drivers of variation becomes essential to understanding disease biology and regulatory genetics. We describe a statistical and visualization framework, variancePartition, to prioritize drivers of variation with a genome-wide summary, and identify genes that deviate from the genome-wide trend. variancePartition enables rapid interpretation of complex gene expression studies and is applicable to many genomics assays.
Sentinel versus passive surveillance for measuring changes in dengue incidence: Evidence from three concurrent surveillance systems in Iquitos, Peru
Authors: Olkowski Sandra , Stoddard Steven T. , Halsey Eric S. , Morrison Amy C. , Barker Christopher M. , Scott Thomas W.
Published: February 2016

Monitoring changes in infectious disease incidence is fundamental to outbreak detection and response, intervention outcome monitoring, and identifying environmental correlates of transmission. In the case of dengue, little is known about how consistently surveillance data track disease burden in a population over time. Here we use four years of monthly dengue incidence data from three sources – population-based (‘passive’) surveillance including suspected cases, ‘sentinel’ surveillance with 100% laboratory confirmation and complete reporting, and door-to-door (‘cohort’) surveillance conducted three times per week - in Iquitos, Peru, to quantify their relative consistency and timeliness. Data consistency was evaluated using annual and monthly expansion factors (EFs) as cohort incidence divided by incidence in each surveillance system, to assess their reliability for estimating disease burden (annual) and monitoring disease trends (monthly). Annually, passive surveillance data more closely estimated cohort incidence (average annual EF=5) than did data from sentinel surveillance (average annual EF=19). Monthly passive surveillance data generally were more consistent (ratio of sentinel/passive EF standard deviations=2.2) but overestimated incidence in 26% (11/43) of months, most often during the second half of the annual high season as dengue incidence typically wanes from its annual peak. Increases in sentinel surveillance incidence were correlated temporally (correlation coefficient = 0.86) with increases in the cohort, while passive surveillance data were significantly correlated at both zero-lag and a one-month lag (0.63 and 0.44, respectively). Together these results suggest that, rather than relying on a single data stream, a clearer picture of changes in infectious disease incidence might be achieved by combining the timeliness of sentinel surveillance with the representativeness of passive surveillance.
Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction
Authors: Shurtleff Matthew , Karfilis Kate V. , Temoche-Diaz Morayma , Ri Sayaka , Schekman Randy
Published: February 2016

Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of microRNAs that are highly enriched with respect to their cellular levels. To explore the biochemical requirements for exosome biogenesis and RNA packaging, we devised a cell-free reaction that recapitulates the species-selective enclosure of miR-223 in isolated membranes supplemented with cytosol. We found that the RNA-binding protein Y-box protein I (YBX1) binds to and is required for the sorting of miR-223 in the cell-free reaction. Furthermore, YBX1 serves an important role in the secretion of miRNAs in exosomes by HEK293T cells.
A universal model for carbon dioxide uptake by plants
Authors: Wang Han , Prentice I. Colin , Cornwell William K. , Keenan Trevor F. , Davis Tyler W. , Wright Ian J. , Evans Bradley J. , Peng Changhui
Published: February 2016

The rate of carbon uptake by land plants depends on the ratio of leaf-internal to ambient carbon dioxide partial pressures1, here termedχ. This quantity is a key determinant of both primary production and transpiration and the relationship between them. But current models forχare empirical and incomplete, contributing to the many uncertainties afflicting model estimates and future projections of terrestrial carbon uptake2,3. Here we show that a simple evolutionary optimality hypothesis4,5generates functional relationships betweenχand growth temperature, vapour pressure deficit and elevation that are precisely and quantitatively consistent with empiricalχvalues from a worldwide data set containing > 3500 stable carbon isotope measurements. A single global equation embodying these relationships then unifies the empirical light use efficiency model with the standard model of C3photosynthesis1, and successfully predicts gross primary production as measured at flux sites. This achievement is notable because of the equation′s simplicity (with just two parameters, both independently estimated) and applicability across biomes and plant functional types. Thereby it provides a theoretical underpinning, grounded in eco-evolutionary principles, for large-scale analysis of the CO2and water exchanges between atmosphere and land.
Comparative assessment of fluorescent proteins forin vivoimaging in an animal model system
Authors: Heppert Jennifer K , Dickinson Daniel J , Pani Ariel M , Higgins Christopher D , Steward Annette , Ahringer Julie , Kuhn Jeffrey R , Goldstein Bob
Published: February 2016

Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamicsin vivo. Recent advances in genome editing have enabled precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential ofin vivoimaging experiments, and they facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been madein vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap we quantitatively assessed fluorescent protein propertiesin vivoin an animal model system. We generated transgenicC. elegansstrains expressing green, yellow, or red fluorescent proteins in embryos, and we imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not brightin vivoas predicted based onin vitrodata, but that mNeonGreen is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imagingin vivoinC. elegansembryos, and they suggest good candidate fluorescent proteins to test in other animal model systems.
C. elegansparaoxonase-like proteins control the functional expression of DEG/ENaC mechanosensory proteins
Authors: Chen Yushu , Bharill Shashank , Altun Zeynep , O'Hagan Robert , Coblitz Brian , Isacoff Ehud I. , Chalfie Martin
Published: February 2016

Caenorhabditis eleganssenses gentle touch via a mechanotransduction channel formed from the DEG/ENaC proteins MEC-4 and MEC-10. An additional protein, the paraoxonase-like protein MEC-6, is essential for transduction, and previous work suggested that MEC-6 was part of the transduction complex. We found that MEC-6 and a similar protein, POML-1, reside primarily in the endoplasmic reticulum and do not colocalize with MEC-4 on the plasma membrane in vivo. As with MEC-6, POML-1 is needed for touch sensitivity, for the neurodegeneration caused by themec-4(d)mutation, and for the expression and distribution of MEC-4 in vivo. Both proteins are likely needed for the proper folding or assembly of MEC-4 channels in vivo as measured by FRET. MEC-6 detectably increases the rate of MEC-4 accumulation on theXenopusoocyte plasma membrane. These results suggest that MEC-6 and POML-1 interact with MEC-4 to facilitate expression and localization of MEC-4 on the cell surface. Thus, MEC-6 and POML-1 act more like chaperones for MEC-4 than channel components.
Kronos: a workflow assembler for genome analytics and informatics
Authors: Taghiyar M Jafar , Rosner Jamie , Grewal Diljot , Grande Bruno , Aniba Rad , Grewal Jasleen , Boutros Paul C , Morin Ryan D , Bashashati Ali , Shah Sohrab P
Published: February 2016

Background

The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into ‘best practices’ for automated analysis of NGS datasets) still requires significant programming investment and expertise.

Results

We presentKronos, a software platform for automating the development and execution of reproducible, auditable and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. Resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications which can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, promoting and facilitating reproducible research and comparative analyses. We introduce a framework for building Kronos components which function as shareable, modular nodes in Kronos workflows.

Conclusion

The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon AWS machine images. It is free, open source and available through PyPI (Python Package Index) andhttps://github.com/jtaghiyar/kronos.
Metaproteomics reveals biomarkers of system collapse in a dynamic aquatic ecosystem
Authors: Northrop Amanda C. , Brooks Rachel , Ellison Aaron M. , Gotelli Nicholas J. , Ballif Bryan A.
Published: February 2016

Forecasting and preventing rapid ecosystem state changes is important but hard to achieve without functionally relevant early warning indicators. Here we use metaproteomic analysis to identify protein biomarkers indicating a state change in an aquatic ecosystem resulting from detrital enrichment. In a 14-day field experiment, we used detritus (arthropod prey) to enrich replicate aquatic ecosystems formed in the water-filled pitcher-shaped leaves of the northern pitcher plant,Sarracenia purpurea. Shotgun metaproteomics using a translated, custom metagenomic database identified proteins, molecular pathways, and microbial taxa that differentiated control oligotrophic ecosystems that captured only ambient prey from eutrophic ecosystems that were experimentally enriched. The number of microbial taxa was comparable between treatments; however, taxonomic evenness was higher in the oligotrophic controls. Aerobic and facultatively anaerobic bacteria dominated control and enriched ecosystems, respectively. The molecular pathways and taxa identified in the enriched treatments were similar to those found in a wide range of enriched or polluted aquatic ecosystems and are derived from microbial processes that occur at the base of most detrital food webs. We encourage the use of metaproteomic pipelines to identify better early-warning indicators of impending changes from oligotrophic to eutrophic states in aquatic and other detrital-based ecosystems.
Dermoscopy of Grover's disease: Variability according to histological subtype
Authors: Errichetti Enzo , De Francesco Vincenzo , Pegolo Enrico , Stinco Giuseppe
Published: February 2016

Distinguishing Grover's disease from other papular dermatoses is often a troublesome task. According to two relatively recent case reports, dermoscopy may be useful in assisting the diagnosis of such a disorder by showing a peculiar pattern. The aim of this study was to evaluate the dermoscopic features of Grover's disease in a larger series of patients and correlate dermoscopy with histopathological findings. Seven patients with histopathologically confirmed Grover's disease were included in the study, with three of them displaying a Darier‐like histology and the remaining four cases having a spongiotic histological pattern. The results of our study suggest that Grover's disease may display different features according to the histological subtype, with a central star‐shaped/branched polygonal/roundish‐oval brownish area surrounded by a whitish halo being characteristic of the Darier‐like histological subtype and whitish scales over a reddish‐yellowish background being characteristic of the spongiotic histological subtype.