bluuebunny/crossref_metadata_2025 huggingface dataset:
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification
Authors: Dabydeen Sarah A. , Desai Arshad , Sahoo Debashis
Published: May 2019

Cell proliferation is essential for the development and maintenance of all organisms and is dysregulated in cancer. Using synchronized cells progressing through the cell cycle, pioneering microarray studies defined cell cycle genes based on cyclic variation in their expression. However, the concordance of the small number of synchronized cell studies has been limited, leading to discrepancies in definition of the transcriptionally regulated set of cell cycle genes within and between species. Here we present an informatics approach based on Boolean logic to identify cell cycle genes. This approach used the vast array of publicly available gene expression data sets to query similarity to CCNB1, which encodes the cyclin subunit of the Cdk1-cyclin B complex that triggers the G2-to-M transition. In addition to highlighting conservation of cell cycle genes across large evolutionary distances, this approach identified contexts where well-studied genes known to act during the cell cycle are expressed and potentially acting in nondivision contexts. An accessible web platform enables a detailed exploration of the cell cycle gene lists generated using the Boolean logic approach. The methods employed are straightforward to extend to processes other than the cell cycle.
Longitudinal Growth Trajectories of Written Syntactic Complexity: The Case of Turkish Learners in an Intensive English Program
Authors: Polat Nihat , Mahalingappa Laura , Mancilla Rae L
Published: May 2019

This longitudinal study examined growth patterns of written syntactic complexity of Turkish learners of English. Using a nonexperimental corpus of 852 writing samples by 284 English as a foreign language (EFL) learners over three semesters, the study addressed the following questions: which indices of syntactic complexity characterize the writing of EFL learners most saliently at elementary, pre-intermediate, and intermediate levels? How do levels of the indices of syntactic complexity change over time as learners progress from elementary to pre-intermediate and intermediate levels? Results suggested that lower proficiency level (levels 1 and 2) writers produced similar patterns of written syntactic complexity (reliance on phrasal coordination), while at proficiency level 3, they demonstrated constructions that were more complex and of greater variety. Findings revealed that over time, learners experienced significant syntactic changes in multiple aspects of complexity; however, these changes were not necessarily straightforward or incremental across the three levels. These findings underscore issues of unpredictability and linearity in second language acquisition, while also cautioning us about the role of intensity of classroom instruction in L2 development.
The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: ‘Symphyta’) may reflect asynchronous switching to angiosperm hosts
Authors: Nyman Tommi , Onstein Renske E , Silvestro Daniele , Wutke Saskia , Taeger Andreas , Wahlberg Niklas , Blank Stephan M , Malm Tobias
Published: May 2019

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.
Functional genetic variants of RUVBL1 predict overall survival of Chinese patients with epithelial ovarian cancer
Authors: Li Haoran , Tong Xiaoxia , Xu Yuan , Wang Mengyun , Dai Hongji , Shi Tingyan , Sun Menghong , Chen Kexin , Cheng Xi , Wei Qingyi
Published: May 2019

To date, the 5-year overall survival of epithelial ovarian cancer (EOC) remains poor. Because studies suggest that RUVBL1 may be a chemotherapeutic target for the treatment of cancer, in this study, therefore, we investigated the role of potentially functional single nucleotide polymorphisms (SNPs) of RUVBL1 in the survival of Chinese patients with EOC, and we subsequently performed functional prediction and validation of the identified significant SNPs. We found that RUVBL1 rs1057156 A>G and RUVBL1 rs149652370 A>G were associated with survival of EOC patients in the multivariate Cox proportional hazards regression analysis. Specifically, the RUVBL1 rs149652370 AG genotype was associated with a shorter progression-free survival ([adjusted hazards ratio (HR)] = 3.32, 95% confidence interval (CI) = 1.76–6.25 and P = 2.01E–04), compared with the AA genotype. The RUVBL1 rs1057156 AG (only nine had GG) genotype was also associated with a poor overall survival (adjusted HR = 1.73, 95% CI = 1.19–2.52, P = 0.004), compared with the AA genotype. Further experiments showed that the RUVBL1 rs1057156 A>G change lowered its binding affinity to microRNA-4294 and led to upregulation of the RUVBL1 expression. We further found that overexpression of RUVBL1 promoted cell proliferation and metastatic potential. Overall, RUVBL1 enhanced EOC cell proliferation, invasion and migration presumably by stimulating the process of glycolysis. Thus, this study provides evidence that functional variants of RUVBL1 may regulate its gene expression, a possible mechanism affecting survival of EOC patients and that RUVBL1 may be a potential chemotherapeutic target for the treatment of EOC patients.
Relapse of membranous nephropathy with cancer immunotherapy
Authors: Kim Youngho
Published: May 2019

Advances in monoclonal antibody technology have enabled the application of engineered antibodies to interfere with specific immune pathways. Checkpoint inhibitors have shown promising results in treating certain cancers by employing patients’ own immune systems to attack cancer cells. Checkpoint inhibitors release the brake on the immune system and can cause immune-related diseases. Theoretically this could be disadvantageous in patients with autoimmune diseases. Here I describe a case of nephrotic syndrome relapse in a patient with a history of membranous nephropathy during programmed death-ligand 1 inhibitor therapy for lung cancer. It is postulated that enhancement of the immune system triggered the relapse of nephrotic syndrome by leading to an escape of immune tolerance and increased susceptibility.
Identification and Localization of the Jammer in Wireless Sensor Networks
Authors: Fan Jianhua , Liang Tao , Wang Tongxiang , Liu Jianwei
Published: May 2019

Wireless sensor network can be easily attacked by jammers for its shared character and open access to the wireless channel. Jamming attack could produce a significant threat to the network by interrupting the normal transmission of nodes. To this end, several anti-jamming countermeasures have been proposed to improve the quality of service of the wireless sensor network. As an important building block for anti-jamming countermeasures, the estimation of jammer’s location could provide us a possible way to eliminate jammers artificially. However, existing localization algorithms mainly pay attention to locate the jammers that are equipped with omnidirectional antennas, which usually fail to cope with directional jammers. In order to bridge this gap, an algorithm of antenna identification and localization of the jammer (AILJ) based on the topology information of jamming scenarios is put forward in this paper. At first, a collection protocol is designed to collect the information of boundary nodes and jammed nodes. Then, an identification method based on the classification of the boundary nodes is proposed to derive the type of jammer’s antenna. At last, a range-free method is put forward to locate the jammer without relying on the propagation parameters. The proposed AILJ only depends on the localization of jammed nodes and boundary nodes and employs their geometry knowledge. For the omnidirectional jammer, the mean center of two circumcircles is considered as the jammer’s position. For the directional jammer, the mean value of the intersections between the straight line that represents jammer’s direction and the circumcircles is considered as the directional jammer’s position. Finally, a series of experiments have been conducted to evaluate the identification and localization performance of AILJ.
Utilization of intra-aortic balloon pump to allow MitraClip procedure in patients with non-coapting mitral valve leaflets: a case series
Authors: Eliaz Ran , Turyan Anna , Beeri Ronen , Shuvy Mony
Published: May 2019

Background

The MitraClip (MC) procedure was designed for high-risk surgical patients with severe mitral regurgitation (MR). Some patients do not meet the required anatomical criteria due to advanced left ventricular remodelling and mitral annular dilatation leading to leaflet tethering and insufficient coaptation surface. Theoretically, ‘temporary remodelling’ of the mitral valve apparatus by pharmacological and/or mechanical support using intra-aortic balloon pump (IABP) could improve leaflets coaptation.

Case summary

We report a case series of four patients with severe MR and non-coapting leaflets who underwent MC implantation. Sufficient coaptation was achieved only after insertion of IABP. The first patient presented with worsening heart failure and severe MR after a non-reperfused posterior wall myocardial infarction (MI), underwent a successful procedure with good results. The second patient presented with worsening heart failure secondary to rheumatic MR, and underwent MC procedure with good results after the insertion of IABP. The third patient developed worsening heart failure and severe MR 2 months after an acute inferior-lateral MI, and underwent a successful procedure. The fourth patient presented with respiratory failure, the patient underwent the procedure, but unfortunately died a few days following the procedure from multiorgan failure. In each case, the insertion of the IABP decreased annular mitral diameter and increased the coaptation surface as assessed by transoesophageal echocardiography.

Discussion

For patients suffering from symptomatic severe MR who are not suitable candidates for MC procedure, IABP system enabled us to overcome mitral leaflet gap and complete the MC procedure successfully.
Optimal vaccine allocation during the mumps outbreak in two SIR centres
Authors: Chernov Alexey A , Kelbert Mark Y , Shemendyuk Aleksandr A
Published: May 2019

The aim of this work is to investigate the optimal vaccine sharing between two susceptible, infected, removed (SIR) centres in the presence of migration fluxes of susceptibles and infected individuals during the mumps outbreak. Optimality of the vaccine allocation means the minimization of the total number of lost working days during the whole period of epidemic outbreak $[0,t_f]$, which can be described by the functional $Q=\int _0^{t_f}I(t)\,{\textrm{d}}t$, where $I(t)$ stands for the number of infectives at time $t$. We explain the behaviour of the optimal allocation, which depends on the model parameters and the amount of vaccine available $V$.
S.A.F.E.R. Near Water: An Intervention Targeting Parent Beliefs About Children’s Water Safety
Authors: Sandomierski Megan C , Morrongiello Barbara A , Colwell Scott R
Published: May 2019

Objective

The current study aimed to develop, implement, and evaluate the S.A.F.E.R. Near Water program, an evidence-based and theory-driven intervention targeting parent beliefs relevant to keeping children safe around water.

Methods

A nonrandomized trial was conducted. Parents with children aged two through five years who were enrolled in lessons either at a public or private swim organization in Ontario, Canada were recruited and nonrandomly assigned to either an Intervention (N = 92) or Control (N = 150) condition. All parents completed the same questionnaire measures two times over the course of their child’s swim lesson session period, once at the beginning (preintervention) and again at the end (postintervention; approximately 9–15 weeks later). Questionnaires assessed parents’ perceptions related to supervision, child drowning risk, water safety, and optimism bias. Parents in the Intervention condition participated in S.A.F.E.R. Near Water, an educational water safety program comprising in-person seminars, informational handouts, and posters.

Results

The S.A.F.E.R. Near Water program was associated with increased knowledge in targeted areas and effectively communicated most of the intended messages. A series of primary regression analyses revealed that parents receiving S.A.F.E.R. Near Water demonstrated improvements in: beliefs about the value of supervision; judgments about children’s swim skills and drowning risk; and perceptions related to swim lessons and children’s supervision needs (sr2 range: 0.22–0.38).

Conclusion

These findings provide support for the feasibility and usefulness of a multifaceted, parent-focused, educational program delivered alongside children’s swim programming to promote closer adult supervision of children around water.
Association of Virologic Failure and Nonnucleoside Reverse Transcriptase Inhibitor Resistance Found in Antiretroviral-Naive Children Infected With Human Immunodeficiency Virus and Given Efavirenz-Based Treatment
Authors: Higa Nikki , Pelz Amy , Birch Donald , Beck Ingrid A , Sils Tatiana , Samson Pearl , Bwakura-Dangarembizi Mutsawashe , Bolton-Moore Carolyn , Capparelli Edmund , Chadwick Ellen , Frenkel Lisa M
Published: May 2019

Among 66 antiretroviral-naive children aged <3 years with human immunodeficiency virus (HIV) or coinfected with HIV and tuberculosis and initiating efavirenz-based antiretroviral therapy (ART), non–nucleoside reverse transcriptase inhibitor (NNRTI) resistance was detected before ART in 5 (7.6%). Virologic failure occurred in 2 of these children; they were last tested at 16 and 24 weeks of ART. Pre-ART NNRTI resistance was not associated with virologic failure.
Chasing Pain
Authors: Casey Kenneth L.
Published: May 2019

By several measures, no human experience is
more important than pain. Chasing Pain discusses the evolution of
scientific and clinical evidence that supports contemporary concepts of how pain
is created by the nervous system. These concepts influence medical practice,
neuroscientific research, and philosophical ideas about pain and other
neurological functions. Historically, pain has been conceived as emerging either
from an undefined pattern of neural activity or from anatomically localized and
physiologically unique structures in the nervous system. Research during the
early and middle 20th century showed that pain normally requires both sensory
detectors of noxious events (nociceptors) and brain mechanisms that generate
emotional experience. Realistic models of pain neurobiology must also consider
that the normally tight link between pain and tissue damage is strongly affected
by several neurological diseases, emotionally compelling circumstances, complex
cognitive processes, and pain itself. As one example of physiological pain
modulation, readers may access the author’s videos of surgery performed with
acupuncture as the sole analgesic method. Chasing Pain reviews the
neuroscientific research and clinical experience that has, over time, greatly
enriched our understanding of pain neurobiology, guided medical practice, and
influenced contemporary concepts of neurological functions. The limitations of
our current conceptual models of pain are exemplified by considering several
common, clinically challenging conditions that remain very poorly
understood.
An Exploratory Analysis of Self-Reported Protective Factors against Self-Harm in an Enrolled Veteran General Mental Health Population
Authors: Williamson Alicia K , Riendeau Rachel P , Stolzmann Kelly , Silverman Allie F , Kim Bo , Miller Christopher J , Connolly Samantha L , Pitcock Jeffery , Bauer Mark S
Published: May 2019

Introduction

The purpose of this study is to characterize self-reported protective factors against suicide or self-harm within free-response comments from a harm-risk screening.

Materials and Methods

Veterans enrolled in Department of Veterans Affairs mental health care were administered a self-harm and suicide screening as part of the baseline assessment in an ongoing implementation trial. Veterans indicated if they had thoughts of harming themselves and if so, what kept them from acting on them. Responses were coded based on established Centers for Disease Control protective factor categories. Descriptive analyses of demographic factors (such as age, gender, and race), clinical factors, and quality of life measures were conducted across groups depending on levels of self-harm risk.

Results

Of 593 Veterans, 57 (10%) screened positive for active thoughts of self-harm or suicide. Those with thoughts of self-harm had lower quality of life scores and higher rates of depression diagnoses. Of those individuals, 41 (72%) reported protective factors including Personal Resources (17%), Community Resources or Relationships (68%), and Other including pets and hobbies (15%). Those with stated protective factors had higher rates of employment and lower rates of PTSD diagnoses.

Conclusion

This is one of the first open-response studies of harm-risk protective factors, allowing for a patient-centered approach that prioritizes the individual’s voice and values. New protective factors emerged through the open-response format, indicating important factors that kept Veterans safe from self-harm or suicide such as pets and hobbies. Increasing focus on strengths and positive aspects of Veterans’ lives that serve as protective factors may ultimately improve mental health treatment and prevention of suicide and self-harm.
Impacts of Smoking Ban Policies on Restaurants in Seoul, South Korea: Analysis of Objective Sales Information
Authors: Noh Jin-Won , Choi Minjae , Kwon Young Dae , Yoo Ki-Bong
Published: May 2019

Background

From July 2013 to January 2015, the smoking ban instituted in restaurants in South Korea gradually expanded to cover all restaurants and bars, moving by size of restaurant (≤99 m2, 100–149 m2, ≥150 m2). This study measured the impacts of the smoking ban for restaurants.

Methods

This study examined credit, check, or debit card sales data for every September and October from 2012 to 2015 in 711 census tracts in Seoul, South Korea. We accounted for total restaurant sales in each census tract. Our model controlled for the sales amounts for each census tract, type of restaurant, monthly business survey index, number of restaurants, daily average temperature, daily precipitation, and day of the week, and a dummy for census tract.

Results

These were some positive associations with increase in total sales. However, the significance of the coefficients was not consistent over this period. Overall, our results showed no significant negative effects of smoking ban policy on restaurants.

Conclusions

Smoking ban policies produced benefits in terms of health outcomes, without causing significant negative impacts on sales.

Implications

Although the owners of restaurants anticipated negative impacts on sales from smoking ban policies, the results of this study suggest that restaurants experienced no negative economic impacts on sales from policies with health benefits, which suggest that it would be reasonable to promote and keep on the smoking ban. Also, it is important to apply smoking ban policy to all targets without exclusion.
Job strain and retirement decisions in UK general practice
Authors: Napier J , Clinch M
Published: May 2019

Background

Falling retention in UK general practice is a well-described problem but there has been little previous research into its underlying causes. Poor psychosocial work conditions may help explain falling workforce morale and early retirement from the profession.

Aims

To explore the impact upon morale and retirement decisions of changes in psychosocial aspects of UK general practice over the course of a career.

Methods

Biographical narrative interviewing method (BNIM) was used to obtain and analyse career narratives of 12 London general practitioners (GPs), aged 55–65, half of whom had retired. Findings were theorized using the Job Demands-Control-Support (JDCS) model.

Results

A spontaneous, consistent theme was evident across all 12 interviews: changes in the psychosocial work environment had contributed to a steady decline in morale. Sequential, multilayered reductions in autonomy were the most commonly cited causes for reduced enthusiasm. Increasing demands in the form of both a rising workload as well as a complaints culture drained energy and morale. The GPs described increasingly fragmented teams and therefore reduced social support for the role. Nonetheless, retirement decisions were not straightforward, provoking complex emotions.

Conclusions

The combination of increasing demands with reduced autonomy puts practitioners under intense strain, diminishing the satisfaction they derive from their work and affecting retirement decisions. The Job Demands-Control-Support (JDCS) model is an empirically tested model that could be used to inform improved work design in general practice.
Seroprevalence of Coxiella burnetii (Q fever) Exposure in Humans on Reunion Island
Authors: Jaubert Julien , Naze Florence , Camuset Guillaume , Larrieu Sophie , Pascalis Hervé , Guernier Vanina , Naty Nadège , Bertolotti Antoine , Manaquin Rodolphe , Mboussou Yoan , Atiana Laura , Picot Sandrine , Filleul Laurent , Tortosa Pablo , Cardinale Eric , Gérardin Patrick
Published: May 2019

After the documentation of sporadic cases of Q fever endocarditis, we conducted a serosurvey to assess Coxiella burnetii exposure on Reunion Island. Two hundred forty-one stored frozen human sera were analyzed using an immunofluorescence assay. The weighted seroprevalence of Q fever was of 6.81% (95% confidence interval, 4.02%–9.59%). Despite the absence of infection in youths <20 years of age, exposure was not driven by age or by gender. There was a spatial disparity in exposure across the island, with higher prevalence being reported in regions where ruminant farms are present. The seroprevalence pattern suggests that Q fever is endemic on Reunion Island.
Long-term Care Facility Variation in the Incidence of Pneumonia and Influenza
Authors: Bosco Elliott , Zullo Andrew R , McConeghy Kevin W , Moyo Patience , van Aalst Robertus , Chit Ayman , Mor Vincent , Gravenstein Stefan
Published: May 2019

Background

Pneumonia and influenza (P&I) increase morbidity and mortality among older adults, especially those residing in long-term care facilities (LTCFs). Facility-level characteristics may affect the risk of P&I beyond resident-level risk factors. However, the relationship between facility characteristics and P&I is poorly understood. To address this, we identified potentially modifiable facility-level characteristics that influence the incidence of P&I across LTCFs.

Methods

We conducted a retrospective cohort study using 2013–2015 Medicare claims linked to Minimum Data Set and LTCF-level data. Short-stay (<100 days) and long-stay (100+ days) LTCF residents were followed for the first occurrence of hospitalization, LTCF discharge, Medicare disenrollment, or death. We calculated LTCF risk-standardized incidence rates (RSIRs) per 100 person-years for P&I hospitalizations by adjusting for over 30 resident-level demographic and clinical covariates using hierarchical logistic regression.

Results

We included 1 767 241 short-stay (13 683 LTCFs) and 922 863 long-stay residents (14 495 LTCFs). LTCFs with lower RSIRs had more licensed independent practitioners (nurse practitioners or physician assistants) among short-stay (44.9% vs 41.6%, P < .001) and long-stay residents (47.4% vs 37.9%, P < .001), higher registered nurse hours/resident/day among short-stay and long-stay residents (mean [SD], 0.5 [0.7] vs 0.4 [0.4], P < .001), and fewer residents for whom antipsychotics were prescribed among short-stay (21.4% [11.6%] vs 23.6% [13.2%], P < .001) and long-stay residents (22.2% [14.3%] vs 25.5% [15.0%], P < .001).

Conclusions

LTCF characteristics may play an important role in preventing P&I hospitalizations. Hiring more registered nurses and licensed independent practitioners, increasing staffing hours, and higher-quality care practices may be modifiable means of reducing P&I in LTCFs.
Evaluation of Surgical Resection Goal and Its Relationship to Extent of Resection and Patient Outcomes in a Multicenter Prospective Study of Patients With Surgically Treated, Nonfunctioning Pituitary Adenomas: A Case Series
Authors: Little Andrew S , Chicoine Michael R , Kelly Daniel F , Sarris Christina E , Mooney Michael A , White William L , Gardner Paul A , Fernandez-Miranda Juan C , Barkhoudarian Garni , Chandler James P , Prevedello Daniel M , Liebelt Brandon D , Sfondouris John , Mayberg Marc R ,   TRANSSPHER Study Group
Published: May 2019

BACKGROUND

The influence of the surgeon's preoperative goal regarding the extent of tumor resection on patient outcomes has not been carefully studied among patients with nonfunctioning pituitary adenomas.

OBJECTIVE

To analyze the relationship between surgical tumor removal goal and patient outcomes in a prospective multicenter study.

METHODS

Centrally adjudicated extent of tumor resection (gross total resection [GTR] and subtotal resection [STR]) data were analyzed using standard univariate and multivariable analyses.

RESULTS

GTR was accomplished in 148 of 171 (86.5%) patients with planned GTR and 32 of 50 (64.0%) patients with planned STR (P = .001). Sensitivity, specificity, positive predictive value, and negative predictive value of GTR goal were 82.2, 43.9, 86.5, and 36.0%, respectively. Knosp grade 0-2, first surgery, and being an experienced surgeon were associated with surgeons choosing GTR as the goal (P < .01). There was no association between surgical goal and presence of pituitary deficiency at 6 mo (P = .31). Tumor Knosp grade (P = .004) and size (P = .001) were stronger predictors of GTR than was surgical goal (P = .014). The most common site of residual tumor was the cavernous sinus (29 of 41 patients; 70.1%).

CONCLUSION

This is the first pituitary surgery study to examine surgical goal regarding extent of tumor resection and associated patient outcomes. Surgical goal is a poor predictor of actual tumor resection. A more aggressive surgical goal does not correlate with pituitary gland dysfunction. A better understanding of the ability of surgeons to meet their expectations and of the factors associated with surgical result should improve prognostication and preoperative counseling.
Medial Temporal Encephalocele and Medically Intractable Epilepsy: A Tailored Inferior Temporal Lobectomy and Case Report
Authors: Mikula Anthony L , ReFaey Karim , Grewal Sanjeet S , Britton Jeffrey W , Van Gompel Jamie J
Published: May 2019

BACKGROUND AND IMPORTANCE

Temporal lobe encephaloceles are increasingly recognized as a potential cause of medically refractory epilepsy and surgical treatment has proven effective. Resection of the encephalocele and associated cortex is often sufficient to provide seizure control. However, it is difficult to determine the extent of adjacent temporal lobe that should be resected. We present a case report and our technique of a tailored inferior temporal pole resection.

CLINICAL PRESENTATION

A 32-yr-old man with an 11-yr history of medically refractory epilepsy. Prolonged electroencephalography (EEG) revealed frequent left and rare right frontotemporal sharp waves. Numerous seizures were captured with EEG, all of which originated from the left temporal region. Statistical parametric mapping (SPM) subtraction ictal–interictal SPECT coregistered with magnetic resonance imaging (MRI) (SISCOM) demonstrated ictal hyperperfusion in the anterior left temporal lobe. MRI showed 2 encephaloceles in the left anterior temporal lobe with the accompanying bony defects in the floor of the middle cranial fossa apparent on the computed tomography scan. The patient underwent left temporal craniotomy with intraoperative electrocorticography, resection of the encephaloceles, and a tailored inferior temporal lobectomy (IFTL) and repair of the middle fossa defects. At 7 mo follow up he reported seizure-freedom since surgery.

CONCLUSION

Resection of temporal encephalocele and adjacent cortex is safe and effective procedure for select patients with medically refractory epilepsy. This video demonstrates our technique which provides a more standardized approach to the resection.
Contrast sensitivity and behavioural evidence for lateral inhibition in octopus
Authors: Nahmad-Rohen Luis , Vorobyev Misha
Published: May 2019

Behavioural contrast sensitivity inOctopus tetricuswas measured in the range of 0.05–12 cycles per degree (cpd) using a fixation reflex. We show that the contrast sensitivity reaches its maximum (between 1 and 4%) at 0.3 cpd, and decreases to approximately half of the maximum value at the lowest spatial frequency. Reduction of sensitivity at low spatial frequency is a signature of lateral inhibition in visual systems. In vertebrates and insects, lateral inhibition helps to overcome the bottleneck of encoding information into spikes. In octopus, photoreceptors generate spikes themselves and are directly connected to the brain through their axons. Therefore, the neural processing occurring in the octopus brain cannot help overcome the bottleneck of encoding information into spikes. We conclude that, in octopus, either the lateral inhibition occurs in the brain after information has been encoded into spikes, or photoreceptors inhibit each other. This is the first time behavioural contrast sensitivity has been measured in a cephalopod.
Repeated evolution of drag reduction at the air–water interface in diving kingfishers
Authors: Crandell K. E. , Howe R. O. , Falkingham P. L.
Published: May 2019

Piscivorous birds have a unique suite of adaptations to forage under the water. One method aerial birds use to catch fish is the plunge dive, wherein birds dive from a height to overcome drag and buoyancy in the water. The kingfishers are a well-known clade that contains both terrestrially foraging and plunge-diving species, allowing us to test for morphological and performance differences between foraging guilds in an evolutionary context. Diving species have narrower bills in the dorsoventral and sagittal plane and longer bills (size-corrected data,n= 71 species,p< 0.01 for all). Although these differences are confounded by phylogeny (phylogenetically corrected ANOVA for dorsoventralp= 0.26 and lengthp= 0.14), beak width in the sagittal plane remains statistically different (p< 0.001). We examined the effects of beak morphology on plunge performance by physically simulating dives with three-dimensional printed models of beaks coupled with an accelerometer, and through computational fluid dynamics (CFD). From physically simulated dives of bill models, diving species have lower peak decelerations, and thus enter the water more quickly, than terrestrial and mixed-foraging species (ANOVAp= 0.002), and this result remains unaffected by phylogeny (phylogenetically corrected ANOVAp= 0.05). CFD analyses confirm these trends in three representative species and indicate that the morphology between the beak and head is a key site for reducing drag in aquatic species.
Weber’s Law-based perception and the stability of animal groups
Authors: Perna Andrea , Facchini Giulio , Deneubourg Jean-Louis
Published: May 2019

Group living animals form aggregations and flocks that remain cohesive in spite of internal movements of individuals. This is possible because individual group members repeatedly adjust their position and motion in response to the position and motion of other group members. Here, we develop a theoretical approach to address the question, what general features—if any—underlie the interaction rules that mediate group stability in animals of all species? We do so by considering how the spatial organization of a group would change in the complete absence of interactions. Without interactions, a group would disperse in a way that can be easily characterized in terms of Fick’s diffusion equations. We can hence address the inverse theoretical problem of finding the individual-level interaction responses that are required to counterbalance diffusion and to preserve group stability. We show that an individual-level response to neighbour densities in the form of Weber’s Law (a ‘universal’ law describing the functioning of the sensory systems of animals of all species) results in an ‘anti-diffusion’ term at the group level. On short timescales, this anti-diffusion restores the initial group configuration in a way that is reminiscent of methods for image deblurring in image processing. We also show that any non-homogeneous, spatial density distribution can be preserved over time if individual movement patterns have the form of a Weber’s Law response. Weber’s Law describes the fundamental functioning of perceptual systems. Our study indicates that it is also a necessary—but not sufficient—feature of collective interactions in stable animal groups.
Osteocyte TSC1 promotes sclerostin secretion to restrain osteogenesis in mice
Authors: Liu Wen , Wang Zhenyu , Yang Jun , Wang Yongkui , Li Kai , Huang Bin , Yan Bo , Wang Ting , Li Mangmang , Zou Zhipeng , Yang Jian , Xiao Guozhi , Cui Zhong-Kai , Liu Anling , Bai Xiaochun
Published: May 2019

Osteocytes secrete the glycoprotein sclerostin to inhibit bone formation by osteoblasts, but how sclerostin production is regulated in osteocytes remains unclear. Here, we show that tuberous sclerosis complex 1 (TSC1) in osteocytes promotes sclerostin secretion through inhibition of mechanistic target of rapamycin complex 1 (mTORC1) and downregulation of Sirt1. We generated mice with
DMP1
-Cre-directed
Tsc1
gene deletion (
Tsc1
CKO) to constitutively activate mTORC1 in osteocytes. Although osteocyte TSC1 disruption increased RANKL expression and osteoclast formation, it markedly reduced sclerostin production in bone, resulting in severe osteosclerosis with enhanced bone formation in mice. Knockdown of TSC1 activated mTORC1 and decreased sclerostin, while rapamycin inhibited mTORC1 and increased sclerostin mRNA and protein expression levels in MLO-Y4 osteocyte-like cells. Furthermore, mechanical loading activated mTORC1 and prevented sclerostin expression in osteocytes. Mechanistically, TSC1 promotes sclerostin production and prevents osteogenesis through inhibition of mTORC1 and downregulation of Sirt1, a repressor of the sclerostin gene
Sost
. Our findings reveal a role of TSC1/mTORC1 signalling in the regulation of osteocyte sclerostin secretion and bone formation in response to mechanical loading
in vitro
. Targeting TSC1 represents a potential strategy to increase osteogenesis and prevent bone loss-related diseases.
Engineering
Saccharomyces cerevisiae
cells for production of fatty acid-derived biofuels and chemicals
Authors: Hu Yating , Zhu Zhiwei , Nielsen Jens , Siewers Verena
Published: May 2019

The yeast
Saccharomyces cerevisiae
is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of
S. cerevisiae
for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.
A Bidirectional Network for Appetite Control in Larval Zebrafish
Authors: Wee Caroline Lei , Song Erin Yue , Johnson Robert Evan , Ailani Deepak , Randlett Owen , Kim Jiyoon , Nikitchenko Maxim , Bahl Armin , Yang Chao-Tsung , Ahrens Misha B. , Kawakami Koichi , Engert Florian , Kunes Samuel
Published: May 2019

Medial and lateral hypothalamic loci are known to suppress and enhance appetite, respectively, but the dynamics and functional significance of their interaction have yet to be explored. Here we report that, in larval zebrafish, primarily serotonergic neurons of the ventromedial caudal hypothalamus (cH) become increasingly active during food deprivation, whereas activity in the lateral hypothalamus (LH) is reduced. Exposure to food sensory and consummatory cues reverses the activity patterns of these two nuclei, consistent with their representation of opposing internal hunger states. Baseline activity is restored as food-deprived animals return to satiety via voracious feeding. The antagonistic relationship and functional importance of cH and LH activity patterns were confirmed by targeted stimulation and ablation of cH neurons. Collectively, the data allow us to propose a model in which these hypothalamic nuclei regulate different phases of hunger and satiety and coordinate energy balance via antagonistic control of distinct behavioral outputs.
4-oxo-2-nonenal Adducts In HDL Are Elevated In Familial Hypercholesterolemia: Identification Of Modified Sites And Functional Consequences
Authors: May-Zhang Linda S. , Yermalitsky Valery , Melchior John T. , Morris Jamie , Tallman Keri A. , Borja Mark S. , Pleasent Tiffany , Venkataraman Amarnath , Yancey Patricia G. , Davidson W. Sean , Linton MacRae F. , Davies Sean S.
Published: May 2019

The lipid aldehyde 4-oxo-2-nonenal (ONE) derived from peroxidation of n-6 polyunsaturated fatty acids and generated in parallel to 4-hydroxynonenal (HNE) is a highly reactive protein crosslinker. Crosslinking of proteins in high-density lipoprotein (HDL) by lipid peroxidation products causes HDL dysfunction and contributes to atherogenesis. While HNE is relatively well studied, the relevance of ONE in atherosclerosis and in modifying HDL has not been examined. In the present study, we found a significant increase in ONE-ketoamide (lysine) adducts in HDL derived from patients with familial hypercholesterolemia (FH) (1620 ± 985.4 pmol/mg) compared to healthy controls (664 ± 219.5 pmol/mg). ONE crosslinked apoA-I on HDL at a concentration of >3 mol ONE per 10 mol apoA-I (0.3 eq), which is 100-fold lower than HNE but comparable to the potent protein crosslinker, isolevuglandin. ONE-modified HDL partially inhibited the ability of HDL to protect against LPS-induced TNFα and IL-1β mRNA expression in murine macrophages. At 3 eq., ONE dramatically decreased the ability of apoA-I to exchange from HDL, from ~46.5% to only ~18.4% (P<0.001). Surprisingly, ONE-modification of HDL or apoA-I did not alter macrophage cholesterol efflux capacity. LC/MS/MS analysis showed modification of Lys12, Lys23, Lys96, and Lys226 of apoA-I by ONE-ketoamide adducts. Compared to other dicarbonyl scavengers, pentylpyridoxamine (PPM) was most efficacious at blocking ONE-induced protein crosslinking in HDL. Our studies show that ONE HDL adducts are elevated in FH who have severe hypercholesterolemia and atherosclerosis and causes HDL dysfunction. We demonstrate the use of PPM in preferentially scavenging ONE in biological systems.
Conserved epigenetic regulatory logic infers genes governing cell identity
Authors: Shim Woo Jun , Sinniah Enakshi , Xu Jun , Vitrinel Burcu , Alexanian Michael , Andreoletti Gaia , Shen Sophie , Sun Yuliangzi , Balderson Brad , Boix Carles , Peng Guangdun , Jing Naihe , Wang Yuliang , Kellis Manolis , Tam Patrick P L , Smith Aaron , Piper Michael , Christiaen Lionel , Nguyen Quan , Bodén Mikael , Palpant Nathan J.
Published: May 2019

Determining genes orchestrating cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive tri-methylation of histone 3 lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, that uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate TRIAGE’s performance for identifying cell-type specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validateRNF220as a regulator ofCionacardiopharyngeal development andSIX3as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper’s Transparent Peer Review process is included in the Supplemental Information.
Effects of two benzenedicarboxylic acids on the construction of CdII coordination polymers incorporating a flexible N-donor ligand
Authors: Li Xiao-Fei , Cheng Di , Meng Xiang-Ru , Yang Huai-Xia
Published: May 2019

Compared with the monomorphic type of ligand, combining mixed ligands in one coordination polymer offers greater tunability of the structural framework. Employment of N-heterocyclic ligands and aromatic polycarboxylates is an effective approach for the construction of metal–organic frameworks (MOFs). Two new coordination polymers incorporating both 2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole (imb) and benzenedicarboxylic acid isomers, namely, catena-poly[[[di-μ-chlorido-bis[(2-carboxybenzoato-κ2
O
1,O
1′)cadmium(II)]]-bis{μ-2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole-κ2
N:N′}] dihydrate], {[Cd(C8H5O4)Cl(C11H10N4)]·H2O}
n
, (I), and poly[[aqua(μ2-benzene-1,3-dicarboxylato-κ3
O
1,O
1′:O
3){μ2-2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole-κ2
N:N′}cadmium(II)] dihydrate], {[Cd(C8H4O4)(C11H10N4)(H2O)]·2H2O}
n
, (II), have been prepared and structurally characterized by single-crystal X-ray diffraction. In polymer (I), imb ligands bridge CdII ions, forming a one-dimensional chain, and 2-carboxybenzoate anions coordinate to the CdII ions in a terminal fashion. Polymer (II) exhibits a two-dimensional network structure in which imb ligands and the benzene-1,3-dicarboxylate anions join CdII ions co-operatively. This indicates that changing of the aromatic dicarboxylic acids can result in polymers with different compositions and architectures. Moreover, their IR spectra, PXRD (powder X-ray diffraction) patterns, thermogravimetric analyses and fluorescence properties were also investigated.
Clustering in the presence of side information: a non-linear approach
Authors: Abin Ahmad Ali
Published: May 2019

Purpose

Constrained clustering is an important recent development in clustering literature. The goal of an algorithm in constrained clustering research is to improve the quality of clustering by making use of background knowledge. The purpose of this paper is to suggest a new perspective for constrained clustering, by finding an effective transformation of data into target space on the reference of background knowledge given in the form of pairwise must- and cannot-link constraints.

Design/methodology/approach

Most of existing methods in constrained clustering are limited to learn a distance metric or kernel matrix from the background knowledge while looking for transformation of data in target space. Unlike previous efforts, the author presents a non-linear method for constraint clustering, whose basic idea is to use different non-linear functions for each dimension in target space.

Findings

The outcome of the paper is a novel non-linear method for constrained clustering which uses different non-linear functions for each dimension in target space. The proposed method for a particular case is formulated and explained for quadratic functions. To reduce the number of optimization parameters, the proposed method is modified to relax the quadratic function and approximate it by a factorized version that is easier to solve. Experimental results on synthetic and real-world data demonstrate the efficacy of the proposed method.

Originality/value

This study proposes a new direction to the problem of constrained clustering by learning a non-linear transformation of data into target space without using kernel functions. This work will assist researchers to start development of new methods based on the proposed framework which will potentially provide them with new research topics.
A hybrid genetic algorithm for multi-objective flexible job shop scheduling problem considering transportation time
Authors: Huang Xiabao , Yang Lixi
Published: May 2019

Purpose

Flexible job-shop scheduling is significant for different manufacturing industries nowadays. Moreover, consideration of transportation time during scheduling makes it more practical and useful. The purpose of this paper is to investigate multi-objective flexible job-shop scheduling problem (MOFJSP) considering transportation time.

Design/methodology/approach

A hybrid genetic algorithm (GA) approach is integrated with simulated annealing to solve the MOFJSP considering transportation time, and an external elitism memory library is employed as a knowledge library to direct GA search into the region of better performance.

Findings

The performance of the proposed algorithm is tested on different MOFJSP taken from literature. Experimental results show that proposed algorithm performs better than the original GA in terms of quality of solution and distribution of the solution, especially when the number of jobs and the flexibility of the machine increase.

Originality/value

Most of existing studies have not considered the transportation time during scheduling of jobs. The transportation time is significantly desired to be included in the FJSP when the time of transportation of jobs has significant impact on the completion time of jobs. Meanwhile, GA is one of primary algorithms extensively used to address MOFJSP in literature. However, to solve the MOFJSP, the original GA has a possibility to get a premature convergence and it has a slow convergence speed. To overcome these problems, a new hybrid GA is developed in this paper.