bluuebunny/crossref_metadata_2025 huggingface dataset:
A journal is a club: a new economic model for scholarly publishing
Authors: Potts Jason , Hartley John , Montgomery Lucy , Neylon Cameron , Rennie Ellie
Published: October 2017

A new economic model for the analysis of scholarly publishing – journal publishing in particular – is proposed that draws on club theory. The standard approach builds on market failure in the private production (by research scholars) of a public good (new scholarly knowledge). In this model, publishing is communication, as the dissemination of information. But a club model views publishing differently: namely as group formation, where members form groups in order to confer externalities on each other, subject to congestion. A journal is a self-constituted group, endeavouring to create new knowledge. In this sense, a journal is a club. The knowledge club model of a journal seeks to balance the positive externalities of a shared resource (readers, citations, referees) against the negative externalities of crowding (decreased prospect of publishing in that journal). A new economic model of a journal as a knowledge club is elaborated. We suggest some consequences for the management of journals and financial models that might be developed to support them.
Was the Missing 2013 WASDE Missed?
Authors: Adjemian Michael K , Johansson Robert , McKenzie Andrew , Thomsen Michael
Published: October 2017

Government crop data have been shown to contribute to the efficient operation of agricultural commodity markets. In 2013, the USDA curtailed its crop report publication for the first time in decades due to an appropriations lapse, thereby offering the chance to study the impact on markets of missing government data. As expected, derivatives markets for corn and soybeans did not display characteristic short‐run patterns in terms of uncertainty resolution and price changes that are normally observed around scheduled USDA release times. We are unable to detect evidence of a prolonged period of heightened uncertainty, realized volatility around the missing report, or abnormal pricing errors in the absence of government data. However, an unsurprisingly large 2013 corn and soybean crop could confound that attempt.
FunImageJ: a Lisp framework for scientific image processing
Authors: Harrington Kyle I S , Rueden Curtis T , Eliceiri Kevin W
Published: October 2017

FunImageJ is a Lisp framework for scientific image processing built upon the ImageJ software ecosystem. The framework provides a natural functional-style for programming, while accounting for the performance requirements necessary in big data processing commonly encountered in biological image analysis.

Availability and implementation

Freely available plugin to Fiji (http://fiji.sc/#download). Installation and use instructions available at http://imagej.net/FunImageJ.

Supplementary information

Supplementary data are available at Bioinformatics online.
Influence of decreased biomass on the ogive of sex change of northern shrimp (Pandalus borealis)
Authors: Jónsdóttir Ingibjörg G , Thórarinsdóttir Gudrún G , Jonasson Jónas P
Published: October 2017

Northern shrimp (Pandalus borealis) are protandrous hermaphrodites that reproduce first as males, go through a transition phase and transform to females, and then spawn as such for the rest of their lives. No clear consensus exists as to which factors influence the activation of the sex change process, but one possible factor is population density. Here, we investigate whether changes in stock size can influence the ogive of sex change, and use a 26-year time series (i.e. 1990–2015) of survey data on shrimp biomass from three different stocks in Iceland as a test case. Two of the stocks experienced periods of high biomass during the 1990 s, with a pronounced and prolonged depletion observed after 2000. In contrast, stock biomass of the third stock decreased only slightly during the time series. We found that the ogives of sex change of the two stocks where the biomass decreased to very low levels have changed significantly, and that shrimp now change sex at a lower size compared to earlier. Furthermore, Lmax has decreased significantly.
Outcomes of Bleb Repair for Delayed Bleb Leaks and Sweating Blebs
Authors: Senthil Sirisha , Basia Arpita , Rao Harsha L. , Choudhari Nikhil , Dikshit Siddharth , Mandal Anil K. , Garudadri Chandra Sekhar
Published: October 2017

Purpose:

To report the outcomes of bleb repair for delayed onset leaking blebs and sweating blebs following glaucoma filtering surgery.

Materials and Methods:

Medical records of 76 eyes of 76 subjects that underwent bleb repair for either leaking bleb or sweating bleb between 1990 and 2015 were reviewed. Complete success was resolution of bleb leak and or hypotony with intraocular pressure ≥5 and ≤21 mm Hg with no antiglaucoma medication.

Results:

There were 45 eyes with leaking bleb and 31 eyes with sweating bleb that underwent bleb repair by either conjunctival autograft or conjunctival advancement (P=0.11). Before bleb repair, complications like blebitis and hypotony maculopathy were significantly higher in sweating bleb group (13/31) compared with bleb leak group (5/45) (P=0.002). Median follow-up after bleb repair was >2 years in both groups (P=0.69). After repair, eyes in leaking bleb group had higher immediate (P=0.01) and long-term intraocular pressure elevation (P=0.06) compared with sweating bleb group. Complete success probability in sweating bleb group was significantly better (88%, 78%, and 71%) compared with leaking bleb group (54%, 45%, and 40%) at 1, 3, and 6 years, respectively (P=0.01). One eye in each group had blebitis, 2 eyes in leaking bleb group and 1 eye in sweating bleb group needed repeat glaucoma intervention.

Conclusions:

Higher complication rate before bleb repair in eyes with sweating bleb warrants early bleb repair. Bleb repair helped retain bleb function in majority of the eyes with sweating blebs, strengthening our recommendation.
Pertussis in California: A Tale of 2 Epidemics
Authors: Winter Kathleen , Zipprich Jennifer , Harriman Kathleen
Published: October 2017

Introduction:

California experienced pertussis epidemics in 2010 and 2014, with more than 9000 and 11,000 reported cases, respectively. Using an ecologic study design, we compared age-specific pertussis incidence for persons ≤20 years of age in California in 2010 and 2014 to describe any changes in disease burden that may be attributable to changes in pertussis vaccination policy that occurred during interepidemic years.

Methods:

We evaluated California pertussis surveillance data for reported pertussis cases 20 years of age and younger with disease onset from January 1, 2010 to December 31, 2010 or from January 1, 2014 to December 31, 2014. Age-specific pertussis rates were calculated for each of the epidemic years. Characteristics of each age group were compared across epidemic years and age-specific rate ratios (RRs) and associated 95% confidence intervals (CIs) were calculated.

Results:

In both years, the highest disease rate was reported in infants <6 months of age; however, the incidence of pertussis declined significantly among infants <6 months of age in 2014 compared with 2010 (RR 0.58, 95% CI: 0.53–0.63). Incidence remained stable among infants ≥6 months of age, children and adolescents <12 years of age (RR 1.1, 95% CI: 0.5–1.3). Adolescents 12–18 years of age had significantly higher rates of pertussis in 2014 compared with 2010, with the highest rates observed among 14- to 16-year-olds (RR 6.5, 95% CI: 5.4–7.8).

Conclusions:

A 42% reduction (53%–63%) in pertussis incidence among infants <6 months of age in 2014 after the routine prenatal Tdap vaccination recommendation suggested that an increase in prenatal Tdap coverage has been having some impact on infant pertussis. The excess number of cases observed in 2014 compared with 2010 occurred almost exclusively among the 12- to 17-year-old age group. Among older children, the peak age of pertussis is shifting, consistent with aging of the acellular pertussis vaccine cohort.
Annual Versus Biannual Mass Azithromycin Distribution and Malaria Parasitemia During the Peak Transmission Season Among Children in Niger
Authors: Oldenburg Catherine E. , Amza Abdou , Kadri Boubacar , Nassirou Beido , Cotter Sun Y. , Stoller Nicole E. , West Sheila K. , Bailey Robin L. , Porco Travis C. , Keenan Jeremy D. , Lietman Thomas M. , Gaynor Bruce D.
Published: October 2017

Background:

Azithromycin has modest efficacy against malaria, and previous cluster randomized trials have suggested that mass azithromycin distribution for trachoma control may play a role in malaria control. We evaluated the effect of annual versus biannual mass azithromycin distribution over a 3-year period on malaria prevalence during the peak transmission season in a region with seasonal malaria transmission in Niger.

Methods:

Twenty-four communities in Matameye, Niger, were randomized to annual mass azithromycin distribution (3 distributions to the entire community during the peak transmission season) or biannual-targeted azithromycin distribution (6 distributions to children <12 years of age, including 3 in the peak transmission season and 3 in the low transmission season). Malaria indices were evaluated at 36 months during the high transmission season.

Results:

Parasitemia prevalence was 42.6% (95% confidence interval: 31.7%–53.6%) in the biannual distribution arm compared with 50.6% (95% confidence interval: 40.3%–60.8%) in the annual distribution arm (P = 0.29). There was no difference in parasite density or hemoglobin concentration in the 2 treatment arms.

Conclusions:

Additional rounds of mass azithromycin distribution during low transmission may not have a significant impact on malaria parasitemia measured during the peak transmission season.
MRI to Arthroscopy Correlations in SLAP Lesions and Long Head Biceps Pathology
Authors: Welton K. Linnea , Bartley Justin H. , Major Nancy M. , McCarty Eric C.
Published: October 2017

Superior labral anterior and posterior lesions and long head biceps injury are 2 common sources of shoulder pain. The presenting complaints and physical examination findings for these etiologies are often nonspecific, making diagnosis challenging. Further complicating their diagnoses, these 2 pathologies often cooccur together or with other shoulder pathologies such as subacromial bursitis, rotator cuff tear, and shoulder instability. However, with advancement in magnetic resonance imaging and shoulder arthroscopy techniques the ability to diagnose and treat these pathologies has vastly improved over the past 30 years. This review provides a case-based description of the correlation between magnetic resonance imaging and arthroscopic findings in common superior labral anterior and posterior and long head biceps injury, accompanied with current management strategies.
MRI and Arthroscopic Correlation of the Wrist
Authors: Nacey Nicholas C. , Boatright Jeffrey D. , Freilich Aaron M.
Published: October 2017

Since its introduction in 1979, the practice of and indications for wrist arthroscopy in the diagnosis and treatment of pathologic conditions in the wrist continues to grow. Magnetic resonance imaging (MRI) is another commonly used tool to noninvasively examine the anatomy and pathology of the wrist joint. Here, we review the normal wrist anatomy as seen arthroscopically and through MRI. We then examine the various common pathologic entities and define both the arthroscopic findings and correlated MRI findings in each of these states.
Racial Disparities in the Presentation and Treatment of Colorectal Cancer
Authors: Rodriguez Eduardo A. , Tamariz Leonardo , Palacio Ana , Li Hua , Sussman Daniel A.
Published: October 2017

Background:

Non-Hispanic blacks (NHB) and Hispanics often present with advanced colorectal cancer (CRC). The aim of the study was to characterize CRC differences among Hispanics, NHB, and non-Hispanic whites (NHW).

Methods:

A cross-sectional analysis and logistic regression of 2009 Florida Agency for Healthcare Administration Hospital Admission Database data for CRC using the International Classification of Diseases, 9th Revision, Clinical Modification codes was performed. Outcomes included CRC location, frequency of metastasis and colectomy rates. Each minority group was compared with NHW.

Results:

A total of 34,577 patients were NHW, 5190 were NHB, and 5033 were Hispanic. NHB had more proximal CRC [odds ratio (OR), 1.17; 95% confidence interval (CI), 1.09-1.25; P<0.0001]; Hispanics had more distal CRC (OR, 0.90; 95% CI, 0.83-0.96; P=0.0024). Hispanics had increased metastases (OR, 1.11; 95% CI, 1.02-1.22; P=0.04). NHB and Hispanics underwent fewer colectomies [(OR, 0.93; 95% CI, 0.86-0.99; P=0.03) and (OR, 0.9; 95% CI, 0.84-0.97; P=0.001), respectively].

Conclusions:

Disparities in CRC metastases and colectomy rates exist among these racial groups in Florida. This work should serve as a foundation to study potential causes and to design culture-specific interventions.
A Web-based Multimedia Program Before Colonoscopy Increased Knowledge and Decreased Anxiety, Sedation Requirement, and Procedure Time
Authors: Parker Siddhartha , Zipursky Jonathan , Ma Helen , Baumblatt Geri-Lynn , Siegel Corey A.
Published: October 2017

Goals:

Assess the impact of a web-based multimedia patient engagement program on patient anxiety, perception and knowledge about the colonoscopy in addition to procedure outcomes.

Background:

The success of patients coming for a colonoscopy for colorectal cancer screening is dependent in part on patients’ understanding of the preparation and of the procedure. Patients were randomized to use either our institution’s standard preprocedure colonoscopy packet or a web-based multimedia patient engagement program (Emmi Solutions) before their scheduled procedure. On the day of colonoscopy, all participants completed a survey including questions to assess knowledge and perception of colonoscopy, in addition to the State Trait Anxiety Inventory. We also collected procedure data including medication doses and procedure time.

Study Results:

Patients in the experimental group correctly answered knowledge questions (82%) more often than the control group (74%) (P=0.0003). More than half (58%) of patients in the experimental group felt this intervention reduced their anxiety about the procedure, and the State Trait Anxiety Inventory anxiety score was lower in the experimental group (P=0.026). Patients who viewed the program required less midazolam (3.66 vs. 4.46 mg, P=0.0035) and total procedure time was shorter (24.8 vs. 29 min, P=0.024).

Conclusions:

A web-based multimedia patient engagement program watched before colonoscopy decreased patient anxiety, medication requirements, and procedure time while increasing knowledge. This intervention could help patients understand and feel more comfortable about colonoscopy leading to increased screening rates while increasing efficiency and decreasing recovery time.
Prevalence and Consequences of Axillary Lymph Node Dissection in the Era of Sentinel Lymph Node Biopsy for Breast Cancer
Authors: Yen Tina W.F. , Laud Purushottam W. , Pezzin Liliana E. , McGinley Emily L. , Wozniak Erica , Sparapani Rodney , Nattinger Ann B.
Published: October 2017

Background:

Despite clear guidelines for its use and wide adoption, no population-based study has examined the extent to which patients with early stage breast cancer are benefiting from sentinel lymph node biopsy (SLNB) by being spared a potentially avoidable axillary lymph node dissection (ALND) and its associated morbidity.

Objective:

Examine variation in type of axillary surgery performed by surgeon volume; investigate the extent and consequences of potentially avoidable ALND.

Research Design/Subjects:

Observational study of older women with pathologically node-negative stage I–II invasive breast cancer who underwent surgery in a SEER state in 2008–2009.

Measures:

Surgeon annual volume of breast cancer cases and type of axillary surgery were determined by Medicare claims. An estimated probability of excess lymphedema due to ALND was calculated.

Results:

Among 7686 pathologically node-negative women, 49% underwent ALND (either initially or after SLNB) and 25% were operated on by low-volume surgeons. Even after adjusting for demographic and tumor characteristics, women treated by higher volume surgeons were less likely to undergo ALND [medium volume: odds ratio, 0.69 (95% confidence interval, 0.51–0.82); high volume: odds ratio, 0.59 (95% confidence interval, 0.45–0.76)]. Potentially avoidable ALND cases were estimated to represent 21% of all expected lymphedema cases.

Conclusions:

In this pathologically node-negative population-based breast cancer cohort, only half underwent solely SLNB. Patients treated by low-volume surgeons were more likely to undergo ALND. Resources and guidelines on the appropriate training and competency of surgeons to assure the optimal performance of SLNB should be considered to decrease rates of potentially avoidable ALND and lymphedema.
Young Child Formula
Authors:   ESPGHAN Committee on Nutrition, Hojsak Iva , Bronsky Jiri , Campoy Cristina , Domellöf Magnus , Embleton Nicholas , Fidler Mis Nataša , Hulst Jessie , Indrio Flavia , Lapillonne Alexandre , Mølgaard Christian , Vora Rakesh , Fewtrell Mary
Published: October 2017

Young child formulae (YCF) are milk‐based drinks or plant protein–based formulae intended to partially satisfy the nutritional requirements of young children ages 1 to 3 years. Although widely available on the market, their composition is, however, not strictly regulated and health effects have not been systematically studied. Therefore, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) Committee on Nutrition (CoN) performed a systematic review of the literature to review the composition of YCF and consider their role in the diet of young children. The review revealed limited data but identified that YCF have a highly variable composition, which is in some cases inappropriate with very high protein and carbohydrate content and even high amounts of added sugars. Based on the evidence, ESPGHAN CoN suggests that the nutrient composition of YCF should be similar to that of follow‐on formulae with regards to energy and nutrients that may be deficient in the diets of European young children such as iron, vitamin D, and polyunsaturated fatty acids (n‐3 PUFAs), whereas the protein content should aim toward the lower end of the permitted range of follow‐on formulae if animal protein is used. There are data to show that YCF increase intakes of vitamin D, iron, and n‐3 PUFAs. However, these nutrients can also be provided via regular and/or fortified foods or supplements. Therefore, ESPGHAN CoN suggests that based on available evidence there is no necessity for the routine use of YCF in children from 1 to 3 years of life, but they can be used as part of a strategy to increase the intake of iron, vitamin D, and n‐3 PUFA and decrease the intake of protein compared with unfortified cow's milk. Follow‐on formulae can be used for the same purpose. Other strategies for optimizing nutritional intake include promotion of a healthy varied diet, use of fortified foods, and use of supplements.
A First Report of Secondary Hemophagocytic Lymphohistiocytosis Associated With Papillary Thyroid Carcinoma
Authors: Wakefield Connor , Mehta Parinda A. , Corathers Sarah , Geller James , Gelfand Michael , Olowokure Olugbenga , Marsh Rebecca A.
Published: October 2017

Secondary hemophagocytic lymphohistiocytosis (HLH) is a rare and potentially fatal immune-deficiency disorder that develops in response to diseases that produce strong immunologic activation, such as infection and malignancy. Although secondary HLH is reported to occur in association with various malignancies, there is no report of its association with thyroid cancer. We evaluated a 19-year-old man who presented with HLH. During investigation for an underlying cause of his HLH computed tomographic scan of the neck discovered thyroid nodules that were confirmed with biopsy to be papillary thyroid carcinoma. He was treated with surgery followed by radioactive iodine therapy and remains without any recurrence of malignancy or his secondary HLH. This report documents the first observation of HLH associated with thyroid cancer, and illustrates the need to include imaging of the neck while evaluating patients with secondary HLH for an underlying malignancy.
Burden of Seizure Clusters on Patients With Epilepsy and Caregivers
Authors: Penovich Patricia E. , Buelow Janice , Steinberg Kathy , Sirven Joseph , Wheless James
Published: October 2017

Objectives:

To characterize the burden of seizure clusters (SC) on patients and caregivers, a large internet-based survey was conducted.

Methods:

The Seizure Cluster Burden of Illness US Survey was conducted online by Harris Poll on behalf of The Epilepsy Foundation in September 2014. Respondents included adult patients 18 years and above with epilepsy or a seizure disorder who had experienced SC in the past year (defined as ≥2 seizures within 24 h outside the patient’s typical seizure pattern), caregivers providing current care for a patient with SC (adult or child), and clinicians (neurologists, epileptologists) who treat adult or pediatric patients. Responses to a wide range of topics, including emotional well-being, daily function, productivity, and approach to clinical practice, were collected.

Results:

There were 861 respondents (259 adult SC patients, 263 caregivers, and 339 clinicians). A majority of all respondent groups felt SC have a moderate/major negative impact on patient and caregiver quality of life, including emotional, financial, and social components. Responses indicated possible overutilization of emergency room services and underutilization of rescue treatment. Only 30% of patients reported having a seizure emergency plan. Some responses showed discrepancies between clinicians and patients/caregivers in the perceived degree of negative impact of SC and management practices for SC.

Conclusions:

These results suggest the need for increased education on managing SC. Clinicians need to develop seizure emergency plans and discuss rescue therapies, whereas patients and caregivers need to ask for and utilize these management strategies.
Cerebral Venous Sinus Thrombosis Due to Low–molecular-weight Heparin-induced Thrombocytopenia
Authors: Gleichgerrcht Ezequiel , Lim Ming Y. , Turan Tanya N.
Published: October 2017

Introduction:

Heparin-induced thrombocytopenia (HIT) is an immune-mediated complication of heparin exposure. A limited number of studies have reported cerebral venous sinus thrombosis (CVST) as the presenting thrombotic event induced by HIT, only one of which occurred with exposure to low–molecular-weight heparin (LMWH), with death as outcome. Here, we present a unique case of LMWH-induced HIT leading to CVST but resulting in good clinical outcome.

Case Report:

A 52-year-old woman received subcutaneous LMWH for deep vein thrombosis prophylaxis while in rehabilitation following kyphoplasty for spinal fracture related to recent trauma. On postoperative day 15, she developed acute onset altered mental status with significant agitation and nonsensical speech and was found to have brain imaging findings suggestive of CVST. Work-up revealed a drop in platelets associated with HIT, which did not improve off heparin products and with steroids, requiring intravenous immunoglobulin therapy, likely due to an overlapping immune thrombocytopenic purpura. Patient was managed on an argatroban drip until platelet count normalized and was able to transition to warfarin. Her clinical outcome was very favorable with near-normal neurological exam except for subtle cognitive changes.

Conclusions:

This unique case of LMWH-induced HIT leading to CVST but resulting in good clinical outcome highlights the importance of linking CVST with HIT and of establishing the need for early alternative antithrombotic therapeutic strategies.
Perioperative Stroke and Mortality After Surgical Aortic Valve Replacement
Authors: Thiagarajan Karthy , Jeevanantham Vinodh , Van Ham Raymond , Gleason Thomas G. , Badhwar Vinay , Chang YueFang , Thirumala Parthasarathy D.
Published: October 2017

Objective:

Perioperative stroke rate after surgical aortic valve replacement (SAVR) varies between 1.3% and 6.2%, whereas the operative mortality ranges between 1% and 16.4%. The aim of this study was to determine whether perioperative stroke is a risk factor for operative mortality after SAVR by performing a meta-analysis of relevant studies.

Materials and Methods:

PubMed, EMBASE, and Web of Science databases were searched to retrieve relevant literature. Screening of the articles was done independently on the basis of predetermined criteria. Data from the relevant studies were extracted and a random effects model was used to calculate the odds of mortality among patients with perioperative strokes after aortic valve replacement compared with those without such strokes. Subgroup analyses of patients (1) aged above and below 70 years and (2) undergoing isolated valve replacement procedure were performed. Metaregression to check for association of effect estimate and (1) sex, (2) mechanical valve replacement, (3) New York Heart Association class III/IV, (4) left ventricle ejection fraction <30%, and (5) preoperative atrial fibrillation was performed.

Results:

Statistical analyses using a random effects model showed that patients with perioperative strokes had 4.74 times greater odds for operative mortality after SAVR, independent of the following covariates: (1) sex, (2) mechanical valve replacement, (3) New York Heart Association class III/IV, (4) left ventricle ejection fraction <30%, and (5) preoperative atrial fibrillation.

Conclusions:

Patients with perioperative strokes after SAVR have nearly 5 times greater odds of experiencing operative mortality compared with those without. Thus, perioperative strokes are associated with increased risk of early mortality and require further examination of preventive strategies.
Perfluorocarbons: Knowledge Gained From Clinical Trials
Authors: Hill Steven E.
Published: October 2017

Research into potential use of perfluorocarbons for liquid ventilation and as oxygen delivery agents in humans has been underway since the 1960s. While partial liquid ventilation with perfluorocarbons showed promise in animal models and early human investigation, randomized controlled human trials failed to show benefit and an elevated rate of adverse events. Initial approval of Fluosol-DA (Green Cross Corporation, Osaka, Japan) by the United States Food and Drug Administration as an oxygen delivery agent for use in high-risk coronary angioplasty represents the only approved application of these compounds to supplement tissue oxygenation, but the compound was rendered obsolete and removed from the market with the development of advanced angioplasty catheters in the 1990s. Second-generation perfluorocarbons were developed with a higher capacity to increase the amount of oxygen dissolved in the fluid phase of blood. Early clinical trials of perflubron emulsion in non-cardiac and cardiac surgery were promising, but dose restriction and the requirement for high inspired oxygen concentration to maximize oxygen delivery for prolonged periods of time limited the clinical utility as a replacement for the oxygen carrying capacity of red blood cells. Identification of excess serious adverse events in treated patients resulted in discontinuation of pivotal clinical trials. Continued research investigating different formulations of perfluorocarbons has shown promise in animal studies, but continued research is necessary to prove safety and efficacy in humans.
Obtaining highly excited eigenstates of the localized XX chain via DMRG-X
Authors: Devakul Trithep , Khemani Vedika , Pollmann Frank , Huse David A. , Sondhi S. L.
Published: October 2017

We benchmark a variant of the recently introduced density matrix renormalization group (DMRG)-X algorithm against exact results for the localized random field XX chain. We find that the eigenstates obtained via DMRG-X exhibit a highly accurate l-bit description for system sizes much bigger than the direct, many-body, exact diagonalization in the spin variables is able to access. We take advantage of the underlying free fermion description of the XX model to accurately test the strengths and limitations of this algorithm for large system sizes. We discuss the theoretical constraints on the performance of the algorithm from the entanglement properties of the eigenstates, and its actual performance at different values of disorder. A small but significant improvement to the algorithm is also presented, which helps significantly with convergence. We find that, at high entanglement, DMRG-X shows a bias towards eigenstates with low entanglement, but can be improved with increased bond dimension. This result suggests that one must be careful when applying the algorithm for interacting many-body localized spin models near a transition.

This article is part of the themed issue ‘Breakdown of ergodicity in quantum systems: from solids to synthetic matter’.
Non-thermalization in trapped atomic ion spin chains
Authors: Hess P. W. , Becker P. , Kaplan H. B. , Kyprianidis A. , Lee A. C. , Neyenhuis B. , Pagano G. , Richerme P. , Senko C. , Smith J. , Tan W. L. , Zhang J. , Monroe C.
Published: October 2017

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state.

This article is part of the themed issue ‘Breakdown of ergodicity in quantum systems: from solids to synthetic matter’.
Functional segregation of the human basal forebrain using resting state neuroimaging
Authors: Markello Ross D. , Spreng R. Nathan , Luh Wen-Ming , Anderson Adam K. , De Rosa Eve
Published: October 2017

The basal forebrain (BF) is poised to play an important neuromodulatory role in brain re-gions important to cognition due to its broad projections and complex neurochemistry. While significant in vivo work has been done to elaborate BF function in nonhuman rodents and primates, comparatively limited work has examined the in vivo function of the human BF. In the current study we used multi-echo resting state functional magnetic resonance imaging (rs-fMRI) from 100 young adults (18-34 years) to assess the potential segregation of human BF nuclei as well as their associated projections. Bottom-up clustering of voxel-wise functional connectivity maps yielded adjacent functional clusters within the BF that closely aligned with the distinct, hypothesized nuclei important to cognition: the nucleus basalis of Meynert (NBM) and the me-dial septum/diagonal band of Broca (MS/DB). Examining their separate functional connections, the NBM and MS/DB revealed distinct projection patterns, suggesting a conservation of nuclei-specific functional connectivity with homologous regions known to be anatomically innervated by the BF. Specifically, the NBM demonstrated coupling with a widespread cortical network as well as the amygdala, whereas the MS/DB revealed coupling with a more circumscribed net-work, including the orbitofrontal cortex and hippocampal complex. Collectively, these in vivo rs-fMRI data demonstrate that the human BF nuclei support functional networks distinct as-pects of resting-state functional networks, suggesting the human BF may be a neuromodulatory hub important for orchestrating network dynamics.

Highlights

The basal forebrain NBM and the MS/DB support two distinct functional networks

Functional networks closely overlap with known anatomical basal forebrain

Basal forebrain networks are distinct from known resting-state functional networks
Evidence for convergent evolution of host parasitic manipulation in response to environmental conditions
Authors: Loreto Raquel G. , Araújo João P.M. , Kepler Ryan M. , Fleming Kimberly R. , Moreau Corrie S. , Hughes David P.
Published: October 2017

Environmental conditions exert strong selection on animal behavior. We tested the hypothesis that the altered behavior of hosts due to parasitic manipulation is also subject to selection imposed by changes in environmental conditions over time. Our model system is ants manipulated by parasitic fungi to bite onto vegetation. We analyzed the correlation between forest type (tropical vs. temperate) and biting substrate (leaf vs. twigs), the time required for the fungi to reach reproductive maturity, and the phylogenetic relationship among specimens from tropical and temperate forests in different parts of the globe. We show that the fungal development in temperate forest is longer than the period of time leaves are present and the ants are manipulated to bite twigs. When biting twigs, 90% of the we examined dead ants had their legs wrapped around twigs, which appears to provide better attachment to the plant. Ancestral state character reconstruction suggests that the leaf biting is the ancestral trait and that twig biting is a convergent trait in temperate regions of the globe. These three lines of evidence suggest that changes in environmental conditions have shaped the manipulative behavior of the host by its parasite.
A High-Resolution Probabilistic In Vivo Atlas of Human Subcortical Brain Nuclei
Authors: Pauli Wolfgang M. , Nili Amanda N. , Tyszka J. Michael
Published: October 2017

Recent advances in magnetic resonance imaging (MRI) methods, including data acquisition, pre-processing and analysis, have enabled research on the contributions of subcortical brain nuclei to human cognition and behavior. At the same time, these developments have led to an increasing need for a high-resolution probabilistic in-vivo anatomical atlas of subcortical nuclei. In order to fill this gap, we constructed high spatial resolution, three-dimensional templates, using joint high accuracy diffeomorphic registration of T1- and T2- weighted structural images from 168 typical adults between 22 and 35 years old. In these templates, many tissue boundaries are clearly visible, which would otherwise be impossible to delineate in data from individual studies. The resulting delineation provides a more accurate parcellation of subcortical nuclei than current histology-based atlases. We further created a companion library of software tools for atlas development, to offer an open and evolving resource for the creation of a crowd-sourced in-vivo probabilistic anatomical atlas of the human brain.
Oncogenic addiction to high 26S proteasome levels
Authors: Tsvetkov Peter , Adler Julia , Myers Nadav , Biran Assaf , Reuven Nina , Shaul Yosef
Published: October 2017

Proteasomes are large intracellular complexes responsible for the degradation of cellular proteins. The altered protein homeostasis of cancer cells results in increased dependency on proteasome function. There are several different proteasome complexes that may be assembled in cells, with the 20S catalytic core common to them all. 20S proteasomes can function in isolation, or as part of larger complexes (26S) with regulatory particles (RP) such as the 19S that is needed for the targeting and processing of ubiquitinated substrates. Proteasome inhibitors target the catalytic barrel (20S) and thus this inhibition does not allow the deconvolution of the distinct roles of 20S vs. 26S proteasomes in cancer progression. We examined the degree of dependency of cancer cells specifically to the level of the 26S proteasome complex. We found that oncogenic transformation of human and mouse immortalized cells with mutant Ras induced a strong increase in the translation of the 26S proteasome subunits, giving rise to high 26S complex levels. We show that depletion of a single subunit of the 19S RP was sufficient to significantly reduce the 26S proteasome level and lower the cellular 26S/20S ratio. We further demonstrate that the accumulated 26S proteasome was essential for the viability of the transformed cells. Moreover, the viability of 20 different cancer cell lines, but not normal human fibroblasts, was severely compromised upon specific 26S proteasome suppression regardless of their p53 status. Suppression of 26S activated the UPR and Caspase-3, which at least partially explains the cell-killing effect. Morphologically, suppression of the 26S proteasome resulted in cytoplasm shrinkage and nuclear deformation. Thus, the tumor cell-specific addiction to high 26S proteasome levels sets the stage for future strategies in cancer therapy.
The Bio::Phylo libraries for phylogenetic data analysis, version 2.0
Authors: Vos Rutger A. , Hettling Hannes
Published: October 2017

Motivation

Phylogenetic analysis is a broad and expanding field that requires versatile programming toolkits to manage the various data types, file formats, and needs for scalability, simulation, visualization, and data exploration.

Results

We present version 2.0 of the Bio::Phylo libraries for phylogenetic data analysis. This new release represents a rewrite of the architecture, allowing for extensions that improve speed and persistence, as well as increased functionality in terms of analysis, data reading and writing, and visualization.

Availability

The package is released as open source software under the same terms as Perl itself and available from the comprehensive Perl archive network as well as directly from the source code repository.

Contact

rutger.vos@naturalis.nl

Supplementary information

Supplementary data are available asdoi:10.5281/zenodo.1039210
Blue light is a universal tactic signal forEscherichia coli
Authors: Perlova Tatyana , Gruebele Martin , Chemla Yann R.
Published: October 2017

Blue light has been shown to elicit a tumbling response inE. coli, a non-phototrophic bacterium. The exact mechanism of this phototactic response is still unknown, and its biological significance remains unclear. Here, we quantify phototaxis inE. coliby analyzing single-cell trajectories in populations of free-swimming bacteria before and after light exposure. Bacterial strains expressing only one type of chemoreceptor reveal that all fiveE. colireceptors - Aer, Tar, Tsr, Tap and Trg - are capable of mediating a response to light. In particular, light exposure elicits a running response in Tap-only strain, the opposite of the tumbling response observed for all other strains. Light therefore emerges as a universal stimulus for allE. colichemoreceptors. We also show that blue light exposure causes a reversible decrease in swimming velocity, a proxy for proton motive force. We hypothesize that rather than sensing light directly, chemoreceptors sense light-induced perturbations in proton motive force.

Importance

Our findings provide new insights on the mechanism ofE. coliphototaxis, showing that all five chemoreceptor types respond to light and that their interactions play an important role in cell behavior. Our results also open up new avenues for examining and manipulatingE. colitaxis. Since light is a universal stimulus, it may provide a way to quantify interactions between different types of receptors. Since light is easier to control spatially and temporally than chemicals, it may be used to study swimming behavior in complex environments. Since phototaxis can cause migration ofE. colibacteria in light gradients, light may be used to control bacterial density for studying density-dependent processes in bacteria.
Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging
Authors: Mendoza M. Lisandra Zepeda , Graves Gary R. , Roggenbuck Michael , Vargas Karla Manzano , Hansen Lars Hestbjerg , Brunak Søren , Gilbert M. Thomas P. , Sicheritz-Pontén Thomas
Published: October 2017

Background

Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial and gut microbiomes from the black and turkey vultures. We characterizedi) the functional potential and taxonomic diversity of their microbiomes,ii) the potential pathogenic challenges they face, and iii) elements in the microbiome that could play a protective role to the vulture’s face and gut.

Results

We found elements involved in diseases, such as periodontitis and pneumonia (more abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing health beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based on the identified phages, we suggest that phages aid in the control, and possibly elimination as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also identifiedAdineta vagain the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role though biofilm formation played byFusobacteriaandClostridiain the gut.

Conclusions

Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.
Interplay between folding and binding modulates protein sequences, structures, functions and regulation
Authors: Mészáros Bálint , Dobson László , Fichó Erzsébet , Tusnády Gábor E. , Dosztányi Zsuzsanna , Simon István
Published: October 2017

Intrinsically Disordered Proteins (IDPs) fulfill critical biological roles without having the potential to fold on their own. While lacking inherent structure, the majority of IDPs do reach a folded state via interaction with a protein partner, presenting a deep entanglement of the folding and binding process. Protein disorder has been recognized as a major determinant in several properties of proteins; yet the way the binding process is reflected in these features in general lacks this detail of description. Recent advances in database development enabled us to identify three basic scenarios of the interplay between folding and binding in unprecedented detail. These scenarios have fundamentally different properties in terms of protein sequence, structure, function and regulation, depending on the structural properties of the interacting partners. Strikingly, the existence of a binding partner and its structural properties influence all analyzed properties of proteins to the same extent as the divide between inherent order or disorder. The appreciation of this interplay between folding and binding is the basis for the successful charting of unknown territories in the protein interactome, the understanding of how different binding modes assemble regulatory networks, and the development of future pharmaceutical applications.
Pharaoh ant colonies dynamically regulate colony demography by culling young queen and male-destined larvae
Authors: Warner Michael R. , Lipponen Jessica , Linksvayer Timothy A.
Published: October 2017

The success of social insect colonies is dependent upon efficient and dynamic allocation of resources to alternate queen and worker castes. The developmental and molecular mechanisms regulating the caste fate of individual larvae in response to environmental cues have been the focus of intense study. However, the mechanisms regulating colony-level resource allocation into alternate castes (i.e. caste allocation ratios) are less well studied. Here, we systematically manipulate colony demography to elucidate the social regulatory mechanisms of caste allocation in the antMonomorium pharaonis. We find that differences in caste allocation result from differences in timing and efficiency of culling of very young reproductive-destined larvae, which are always present in colonies. Based on our results, we develop a conceptual model depicting how colonies integrate numerous individual-level caste determination decisions to regulate colony-level caste allocation. We propose that adult workers make decisions about culling larvae based on the ratio of the number of workers to the number of eggs contained in colonies, likely signalled by pheromone present on eggs. This strategy is a bet-hedging strategy which enables the dynamic alteration of colony demography in response to internal and external conditions. The strategy is likely key to the ability ofM. pharaonisand similar ants to thrive in disturbed habitats and to become widespread invasive species.

Significance Statement

The defining feature of social insect societies is the presence of alternate queen (reproductive) and worker (non-reproductive) castes of individuals. The fitness of social insect colonies is dependent upon efficient allocation of resources to alternate castes, particularly in the case of highly polygynous (multi-queen) societies. However, the mechanisms by which such societies regulate caste allocation are largely unknown. In this study, we show that colonies manipulate their production of queens (and also males) versus workers according to the present density of eggs in the colony, which serves as a reliable indicator of queens’ fertility. Provided egg density is high, colonies kill queen-and male-destined larvae; when egg density falls, colonies begin to rear queens and males. This flexible resource allocation strategy is key to the ability of highly polygynous species to thrive in marginal (often human-associated) habitats.
A longitudinal model of human neuronal differentiation for functional investigation of schizophrenia polygenic risk
Authors: Ori Anil P.S. , Bot Merel H.M. , Molenhuis Remco T. , Olde Loohuis Loes M. , Ophoff Roel A.
Published: October 2017

There is a pressing need for in vitro experimental systems that allow for interrogation of polygenic psychiatric disease risk to study the underlying biological mechanisms. We developed an analytical framework that integrates genome-wide disease risk from GWAS with longitudinal in vitro gene expression profiles of human neuronal differentiation. We demonstrate that the cumulative impact of risk loci of specific psychiatric disorders is significantly associated with genes that are differentially expressed across neuronal differentiation. We find significant evidence for schizophrenia, which is driven by a longitudinal synaptic gene cluster that is upregulated during differentiation. Our findings reveal that in vitro neuronal differentiation can be used to translate the polygenic architecture of schizophrenia to biologically relevant pathways that can be modeled in an experimental system. Overall, this work emphasizes the use of longitudinal in vitro transcriptomic signatures as a cellular readout and the application to the genetics of complex traits.