bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationships Among 3 Movement Analysis Tests in Preterm Infants
Authors: Azim Rezaei Derya , Acar Gonul , Turkdogan Dilsad , Unver Olcay , Kaya Narter Fatma
Published: June 2019

Purpose:

To investigate the relationships among the Infant Motor Profile (IMP), the Neuro-Sensory Motor Developmental Assessment (NSMDA), and the Alberta Infant Motor Scale (AIMS) in prematurely born infants.

Methods:

Sixty-one preterm infants with a birth weight under 2500 g were assessed by the IMP, the NSMDA, and the AIMS.

Results:

There was a significant correlation between the IMP total score and the AIMS percentile and between the IMP total score and the NSMDA functional levels. There were significant correlations between the AIMS percentile age and the NSMDA functional levels and between the AIMS total scores and the IMP total scores. In the infants with atypical development, the relationship was significant between the AIMS and the IMP; however, there was no relationship between the IMP and the NSMDA.

Conclusions:

The 3 movement analysis tests are related. The IMP was found to be consistent with other movement analysis tests.
Physical Therapy for a Patient With Alternating Hemiplegia of Childhood: A Case Report
Authors: Lardinois Kara L. , Guge Nora
Published: June 2019

Purpose:

Alternating hemiplegia of childhood (AHC) is a rare neurological disorder that can influence posture and movement during critical periods of motor development. There are no descriptions of physical therapy for children with AHC. The purpose of this case report is to present an example of physical therapy evaluation, intervention, and outcomes for a child with AHC.

Summary of Key Points:

Physical therapy services were provided over 9 sequential plans of care between 14 and 52 months of age. The child demonstrated improvements in motor control, walked independently at 16.5 months of age, and her Gross Motor Function Measure-88 score increased from 78% to 95% between 27 and 52 months of age.

Conclusions and Recommendations for Clinical Practice:

The importance in this case lies in the use of a multisystem approach to treatment, careful consideration of frequency of intervention, and discussion of the unique features of AHC.
Vague Posterior Knee Discomfort in a Soccer Player
Authors: Schroeder Allison , Onishi Kentaro
Published: June 2019

A 24-yr-old male soccer player presented with a 7-yr history of left posterior knee “looseness.” Evaluation 7 yrs ago, at the time of initial injury, revealed atraumatic anterior and posterior cruciate ligament sprains. On representation, the patient described the pain as a constant, dull ache, 3/10, but his biggest complaint was this feeling of “instability” and looseness where his knee would “buckle” 3–4 times a week. Physical examination was positive for grade 1 posterior drawer and grade 1 posterior sag signs. Reverse KT-1000 testing showed a 3-mm side-to-side difference. Sonographic evaluation confirmed magnetic resonance imaging findings of posterior cruciate ligament laxity and buckling and a small cystic lesion abutting the posteromedial margin of the distal 1/3 of the posterior cruciate ligament. After a trial of physical therapy, the patient elected to undergo experimental injection of dextrose hyperosmolar solution. This resulted in resolution of the cyst and reverse KT-1000 measurements improved to a side-to-side difference of 1 mm. The patient's subjective feeling of looseness and instability resolved by 7 wks.
A Strategy for the Renovation of a Clinical Pathways Program
Authors: Pugh-Bernard Aimee , Nickels Sarah , Melendez Jessieca , Shawkat Jehan , Rolison Elise , Swanson Angela , Bajaj Lalit , Hyman Daniel , Bakel Leigh Anne
Published: June 2019

Introduction:

Clinical pathways (CPs) translate best available evidence to the local care context and intend to inform clinical decision-making, optimize care, and decrease variation. This article describes a CPs program improvement process at a free-standing academic children’s hospital. Aims: (1) improve the pathway development process; (2) identify and address gaps; (3) strengthen measurement; (4) increase efficiency in cycle time to build a pathway; (5) increase multidisciplinary participation; (6) integrate into the electronic health record ; and (7) and increase pathway utilization.

Methods:

We renovated the CP program using a structured, improvement process. A series of internal stakeholder and external colleague interviews informed the process. To improve the program, we developed and implemented different interventions.

Results:

The streamlined process reduced the overall time for completion from a median of 15 to 5 months (measured from the date of first meeting with the clinical improvement team to approval), a 70% increase in efficiency. Between 1994 and 2015, the hospital had 33 CPs. There was a 78% increase in the total number of pathways after the renovation with 26 additional pathways.

Conclusions:

Renovation of the CP program led to early success through an improved development process, alleviation of programmatic gaps, inclusion of measures within each pathway, increased timely completion, multidisciplinary involvement, integration into the electronic health record, and improved utilization. Initial results are encouraging, and the lessons learned should be helpful to other programs. Further program development is ongoing, focusing on continued improvements in implementation and overall program measures.
Development and Validation of HIV-ASSIST, an Online, Educational, Clinical Decision Support Tool to Guide Patient-Centered ARV Regimen Selection
Authors: Maddali Manoj V. , Mehtani Nicky J. , Converse Caro , Kapoor Sunaina , Pham Paul , Li Jonathan Z. , Shah Maunank
Published: June 2019

Background:

Multiple antiretroviral (ARV) regimens are effective at achieving HIV viral suppression, but differ in pill burden, side effects, barriers to resistance, and impact on comorbidities. Current guidelines advocate for an individualized approach to ARV regimen selection, but synthesizing these modifying factors is complex and time-consuming.

Methods:

We describe the development of HIV-ASSIST (https://www.hivassist.com), a free, online decision support tool for ARV selection and HIV education. HIV-ASSIST ranks potential ARV options for any given patient scenario using a composite objective of achieving viral suppression while maximizing tolerability and adherence. We used a multiple-criteria decision analysis framework to construct mathematical algorithms and synthesize various patient-specific (eg, comorbidities and treatment history) and virus-specific (eg, HIV mutations) attributes. We then conducted a validation study to evaluate HIV-ASSIST with prescribing practices of experienced HIV providers at 4 large academic centers. We report on concordance of provider ARV selections with the 5 top-ranked HIV-ASSIST regimens for 10 diverse hypothetical patient-case scenarios.

Results:

In the validation cohort of 17 experienced HIV providers, we found 99% concordance between HIV-ASSIST recommendations and provider ARV selections for 4 case-scenarios of ARV-naive patients. Among 6 cases of ARV-experienced patients (3 with and 3 without viremia), there was 84% and 88% concordance, respectively. Among 3 cases of ARV-experienced patients with viremia, providers reported 20 different ARV selections, suggesting substantial heterogeneity in ARV preferences in clinical practice.

Conclusions:

HIV-ASSIST is a novel patient-centric educational decision support tool that provides ARV recommendations concordant with experienced HIV providers for a diverse set of patient scenarios.
Asymptomatic Bone Marrow Edema Detected by 67Ga Scintigraphy
Authors: Miwa Shinji , Otsuka Takanobu , Yamada Satoshi , Aiba Hisaki , Tsuchiya Hiroyuki
Published: June 2019

A 46-year-old woman presented with a complaint of fever. CRP was 2.1 mL/L in blood, white blood cell count was 20–29/hpf, and bacterial count was 3418/μL in a urinalysis. 67Ga scan revealed accumulation of 67Ga in the left distal femur, although she had no symptoms around the site. MRI demonstrated diffuse high signal intensity on T2-weighted STIR images. Osteomyelitis was suspected, and biopsy was performed. Bacterial culture of the bone marrow was negative, and histological examination showed no infiltration of inflammatory cells. Two months after the biopsy, disappearance of altered signal intensity of MRI was observed.
Innovative and Contemporary Interventional Therapies for Esophageal Diseases
Authors: Strollo Diane C. , Chan Ernest G. , Jaimes Vanegas Natalia , Ocak Iclal , Joubert Kyla , Villa Sanchez Manuel
Published: June 2019

Esophageal surgery has become quite specialized, and both dedicated diagnostic and refined surgical techniques are required to deliver state-of-the-art care. The field has evolved to include endoscopic mucosal resection and radiofrequency ablation for early-stage esophageal cancer and minimally invasive esophagectomy with the reconstruction of a gastric conduit for carefully selected patients with esophageal cancer or those with “end-stage” esophagus from benign diseases. Reoperative esophageal surgery after esophagectomy deserves special mention given that these patients, with improved survival, are presenting years after esophagectomy with functional and anatomic disorders that sometimes require surgical intervention. Different diagnostic modalities are essential for assessing patients and planning surgical treatment. Recognizing early and late postoperative complications on imaging may expedite and improve patient outcomes. Finally, endoscopic management of achalasia with peroral endoscopic myotomy and the use of the LINX device for gastroesophageal reflux disease are highly effective and minimally invasive treatments that may reduce complications, costs, and length of hospital stay.
Clinical association to FKBP5 rs1360780 in patients with depression
Authors: Dam Henrik , Buch Jens O.D. , Nielsen Annelaura B. , Weikop Pia , Werge Thomas , Jørgensen Martin B.
Published: June 2019

The FKBP5 protein is of importance for the function of the glucocorticoid receptor. The purpose of the present study was to examine the possible association between the different genotypes of rs1360780 in the FKBP5 gene, and clinical symptoms in patients with unipolar depression. Seven hundred eighteen patients and 673 controls from the Danish Psychiatric Biobank were participated. No association was found between any genotype and diagnosis of unipolar depression. It was found that the group of depressed patients with the CC genotype showed significantly earlier start of treatment with medicine, had a significantly greater tendency to be treated with electroconvulsive therapy and showed a significantly higher frequency of family history of depression compared with the combined group of patients with the CT and TT genotypes. The only informations about controls were their sex and that they were recruited from the blood bank. The clinical data were not complete for all patients
Using background noise to improve sound localization following simulated hearing loss
Authors: Ryan-Warden Lindsey , Ng Eva , Keating Peter
Published: June 2019

Many listening abilities become more difficult in noisy environments, particularly following hearing loss. Sound localization can be disrupted even if target sounds are clearly audible and distinct from background noise. Since subjects locate sounds by comparing the input to the two ears, sound localization is also considerably impaired by unilateral hearing loss. Currently, however, it is unclear whether the effects of unilateral hearing loss are worsened by background noise. To address this, we measured sound localization abilities in the presence or absence of broadband background noise. Adult human subjects of either sex were tested with normal hearing or with a simulated hearing loss in one ear (earplug). To isolate the role of binaural processing, we tested subjects with narrowband target sounds. Surprisingly, we found that continuous background noise improved narrowband sound localization following simulated unilateral hearing loss. By contrast, we found the opposite effect under normal hearing conditions, with background noise producing illusory shifts in sound localization. Previous attempts to model these shifts are inconsistent with behavioural and neurophysiological data. However, here we found that a simple hemispheric model of sound localization provides an explanation for our results, and provides key hypotheses for future neurophysiological studies. Overall, our results suggest that continuous background noise may be used to improve sound localization under the right circumstances. This has important implications for real-world hearing, both in normal-hearing subjects and the hearing-impaired.

Significance Statement

In noisy environments, many listening abilities become more difficult, even if target sounds are clearly audible. For example, background noise can produce illusory shifts in the perceived direction of target sounds. Because sound localization relies on the two ears working together, it is also distorted by a hearing loss in one ear. We might therefore expect background noise to worsen the effects of unilateral hearing loss. Surprisingly, we found the opposite, with background noise improving sound localization when we simulated a hearing loss in one ear. A simple hemispheric model of sound localization also helped explain the negative effects of background noise under normal hearing conditions. Overall, our results highlight the potential for using background noise to improve sound localization.
Molecular determinants of the Ska-Ndc80 interaction and their influence on microtubule tracking and force-coupling
Authors: Huis in ’t Veld Pim J. , Volkov Vladimir A. , Stender Isabelle , Musacchio Andrea , Dogterom Marileen
Published: June 2019

Errorless chromosome segregation requires load-bearing attachments of the plus ends of spindle microtubules to chromosome structures named kinetochores. How these end-on kinetochore attachments are established following initial lateral contacts with the microtubule lattice is poorly understood. Two microtubule-binding complexes, the Ndc80 and Ska complexes, are important for efficient end-on coupling and may function as a unit in this process, but precise conditions for their interaction are unknown. Here, we report that the Ska-Ndc80 interaction is phosphorylation-dependent and does not require microtubules, applied force, or several previously identified functional determinants including the Ndc80-loop and the Ndc80-tail. Under force, Ska stabilizes end-on microtubule attachments in parallel with the Ndc80-tail, which we reveal to be essential for end-tracking by Ndc80 multimers. Modulation of force-coupling efficiency demonstrates that the duration of stalled microtubule disassembly predicts whether a microtubule is stabilized and rescued by the kinetochore, likely reflecting a structural transition of the microtubule end.

Abstract Figure
Category-Selective Visual Regions Have Distinctive Signatures of Connectivity in Neonates
Authors: Cabral Laura , Zubiaurre Leire , Wild Conor , Linke Annika , Cusack Rhodri
Published: June 2019

The development of the ventral visual stream is shaped both by an innate proto-organization and by experience. The fusiform face area (FFA), for example, has stronger connectivity to early visual regions representing the fovea and lower spatial frequencies. In adults, category-selective regions in the ventral stream (e.g. the FFA) also have distinct signatures of connectivity to widely distributed brain regions, which are thought to encode rich cross-modal, motoric, and affective associations (e.g., tool regions to the motor cortex). It is unclear whether this long-range connectivity is also innate, or if it develops with experience. We used MRI diffusion-weighted imaging with tractography to characterize the connectivity of face, place, and tool category-selective regions in neonates (N=445), 1-9 month old infants (N=11), and adults (N=14). Using a set of linear-discriminant classifiers, category-selective connectivity was found to be both innate and shaped by experience. Connectivity for faces was the most developed, with no evidence of significant change in the time period studied. Place and tool networks were present at birth but also demonstrated evidence of development with experience, with tool connectivity developing over a more protracted period (9 months). Taken together, the results support an extended proto-organizon to include long-range connectivity that could provide additional constraints on experience dependent development.
Host mucin is subverted by Pseudomonas aeruginosa during infection to provide free glycans required for successful colonization
Authors: Hoffman Casandra L , Aballay Alejandro
Published: June 2019

The mucosal barrier, found lining epithelial cells, serves multiple functions in a range of animals. The major structural components of mucus are mucins, which are heavily glycosylated proteins that are either membrane bound or secreted by the epithelial cells. Mucins are key components of the innate immune system, as they are involved in the clearance of pathogens from the airways and intestines, and their expression is typically upregulated upon epithelial cell exposure to a variety of pathogens. In this study, we identified the mucin MUL-1 as an innate immune factor that appears to be utilized by P. aeruginosa to colonize hosts. We found that while the expression of several mucins, including MUL-1, increased upon P. aeruginosa infection of the nematode Caenorhabditis elegans, silencing of or deletion of mul-1 resulted in enhanced survival and reduced bacterial accumulation. P. aeruginosa required host sialidase CTSA-1.1 to use mucin-derived glycans to colonize the host, while sialidase-encoding bacteria required host MUL-1 but not CTSA-1.1 to cause a lethal infection. This role of mucins and free glycans in host-pathogen interaction appears to be conserved from C. elegans to humans, as P. aeruginosa binding to human lung epithelial cells was also enhanced in the presence of free glycans, and free glycans reversed the binding defect of P. aeruginosa to human lung cells lacking the mucin MUC1.

Author Summary

The gastrointestinal, respiratory, reproductive, and urinary tracts, are large surfaces exposed to the exterior environment and thus, these mucosal epithelial tissues serve as primary routes of infection. One of the first lines of defense present at these barriers is mucus, which is a highly viscous material formed by mucin glycoproteins. Mucins serve various functions, but importantly they aid in the clearance of pathogens and debris from epithelial barriers and serve as innate immune effectors. In this study, we describe the ability of Pseudomonas aeruginosa to utilize mucin-derived glycans to colonize the intestine and ultimately cause death in Caenorhabditis elegans. We also show conserved mechanisms of P. aeruginosa virulence traits, by demonstrating that free glycans alter the ability of the bacteria to bind to human lung alveolar epithelial cells. Over the course of host-pathogen evolution, pathogens seem to have evolved to use mucins for their own advantage, and thus one of the biggest questions is which party benefits from pathogen-mucin binding. By gaining a better understanding of pathogen-mucin interactions, we can better protect against pathogen infection.
Astrocyte subdomains respond independently in vivo
Authors: López-Hidalgo Mónica , Kellner Vered , Schummers James
Published: June 2019

Astrocytes contact thousands of synapses throughout the territory covered by its fine bushy processes. Astrocytes respond to neuronal activity with an increase in calcium concentration that is in turn linked to their capacity to modulate neuronal activity. It remains unclear whether astrocytes behave as a single functional unit that integrates all of these inputs, or if multiple functional subdomains reside within an individual astrocyte. We utilized the topographic organization of ferret visual cortex to test whether local neuronal activity can elicit spatially restricted events within an individual astrocyte. We monitored calcium activity throughout the extent of astrocytes in ferret visual cortex while presenting visual stimuli that elicit coordinated neuronal activity spatially restricted to functional columns. We found visually-driven calcium responses throughout the entire astrocyte that was largely independent in individual subdomains, often responding to different visual stimulus orientations. A model of the spatial interaction of astrocytes and neuronal orientation maps recapitulated these measurements, consistent with the hypothesis that astrocyte subdomains integrate local neuronal activity. Together, these results suggest that astrocyte responses to neural circuit activity are dominated by functional subdomains that respond locally and independently to neuronal activity.
Multiple steps mediate ventricular layer attrition to form the adult mouse spinal cord central canal
Authors: Cañizares Marco A. , Albors Aida Rodrigo , Singer Gail , Suttie Nicolle , Gorkic Metka , Felts Paul , Storey Kate G.
Published: June 2019

The ventricular layer of the spinal cord is remodelled during embryonic development and ultimately forms the adult central canal, which retains neural stem cell potential. This anatomical transformation involves the process of dorsal collapse, however, accompanying changes in tissue organization and cell behaviour as well as the origin of cells contributing to the adult central canal are not well understood. Here we describe sequential localised cell rearrangements which contribute to the gradual attrition of the spinal cord ventricular layer during development. This includes local breakdown of the pseudostratified organisation of the dorsal ventricular layer prefiguring dorsal collapse and evidence for a new phenomenon, ventral dissociation, during which the ventral-most floor plate cells separate from a subset that are retained in the central canal. Using cell proliferation markers and cell-cycle reporter mice, we further show that following dorsal collapse, ventricular layer attrition involves an overall reduction in cell proliferation, characterised by an intriguing increase in the percentage of cells in G1/S. In contrast, programmed cell death does not contribute to ventricular layer remodelling. By analysing transcript and protein expression patterns associated with key signalling pathways, we provide evidence for a gradual decline in ventral sonic hedgehog activity and an accompanying ventral expansion of initial dorsal bone morphogenetic protein signalling, which comes to dominate the forming central canal. This study identifies multiple steps that contribute to spinal cord ventricular layer attrition and adds to increasing evidence for the heterogenous origin of the adult spinal cord central canal, which includes cells from the floor plate and the roof plate as well as ventral progenitor domain.
Evaluating Protein Transfer Learning with TAPE
Authors: Rao Roshan , Bhattacharya Nicholas , Thomas Neil , Duan Yan , Chen Xi , Canny John , Abbeel Pieter , Song Yun S.
Published: June 2019

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We bench-mark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.
Intertrial Variability in Human Corticospinal Activity during Grasp Force Planning
Authors: Rao Nishant , Parikh Pranav J.
Published: June 2019

Neuronal firing rate variability during planning has been found to contribute to trial-to-trial variability in primate behavior. However, in humans, whether planning related mechanisms contribute to trial-to-trial behavioral variability remains unknown. We investigated the time-course of trial-to-trial variability in corticospinal excitability (CSE) using transcranial magnetic stimulation (TMS) while subjects planned to perform a self-paced reach-to-grasp task. We hypothesized that CSE variability will be modulated during task planning and that such a modulation would explain trial-to-trial behavioral variability. Able-bodied individuals were visually cued to plan their grip force before exertion of either 30% or 5% of maximum force on an object. TMS was delivered at different time points following a cue that instructed the force level. We first modeled the relation between CSE magnitude and its variability at rest (n=12) to study the component of CSE variability during task planning that was not related to changes in CSE magnitude (n=12). We found an increase in CSE variability during task planning at 30% but not at 5% of force. This effect was temporally dissociated from the decrease in CSE magnitude. Importantly, the increase in CSE variability during planning explained 64% of inter-individual differences in time to peak force rate trial-to-trial variability. These results were found to be repeatable across studies and robust to different analysis methods. Our findings suggest that the planning-related mechanisms underlying modulation in CSE variability and CSE magnitude are distinct. Notably, the extent of modulation in planning-related variability in corticospinal system within individuals may explain their trial-to-trial behavioral variability.
Comparativein silicoanalysis offtsZgene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination
Authors: Pal Ayon , Saha Barnan Kr , Saha Jayanti
Published: June 2019

The deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene calledftsZwhich codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study offtsZprotein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that theftsZgene of about ninety three percent of the organisms involved in our analyses show relatively biased codon usage profile and significant GC deviation from their genomic GC content. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring theftsZcoding sequence. Our meticulous analysis of theftsZgene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form and structure for optimized performance in spite of the extrinsic variability in coding features.
Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision
Authors: Spoerer Courtney J , Kietzmann Tim C , Mehrer Johannes , Charest Ian , Kriegeskorte Nikolaus
Published: June 2019

Deep feedforward neural network models of vision dominate in both computational neuroscience and engineering. The primate visual system, by contrast, contains abundant recurrent connections. Recurrent signal flow enables recycling of limited computational resources over time, and so might boost the performance of a physically finite brain or model. Here we show: (1) Recurrent convolutional neural network models outperform feedforward convolutional models matched in their number of parameters in large-scale visual recognition tasks on natural images. (2) Setting a confidence threshold, at which recurrent computations terminate and a decision is made, enables flexible trading of speed for accuracy. At a given confidence threshold, the model expends more time and energy on images that are harder to recognise, without requiring additional parameters for deeper computations. (3) The recurrent model’s reaction time for an image predicts the human reaction time for the same image better than several parameter-matched and state-of-the-art feedforward models. (4) Across confidence thresholds, the recurrent model emulates the behaviour of feedforward control models in that it achieves the same accuracy at approximately the same computational cost (mean number of floating-point operations). However, the recurrent model can be run longer (higher confidence threshold) and then outperforms parameter-matched feedforward comparison models. These results suggest that recurrent connectivity, a hallmark of biological visual systems, may be essential for understanding the accuracy, flexibility, and dynamics of human visual recognition.

Author summary

Deep neural networks provide the best current models of biological vision and achieve the highest performance in computer vision. Inspired by the primate brain, these models transform the image signals through a sequence of stages, leading to recognition. Unlike brains in which outputs of a given computation are fed back into the same computation, these models do not process signals recurrently. The ability to recycle limited neural resources by processing information recurrently could explain the accuracy and flexibility of biological visual systems, which computer vision systems cannot yet match. Here we report that recurrent processing can improve recognition performance compared to similarly complex feedforward networks. Recurrent processing also enabled models to behave more flexibly and trade off speed for accuracy. Like humans, the recurrent network models can compute longer when an object is hard to recognise, which boosts their accuracy. The model’s recognition times predicted human recognition times for the same images. The performance and flexibility of recurrent neural network models illustrates that modeling biological vision can help us improve computer vision.
3D-Cell-Annotator: an open-source active surface tool for single cell segmentation in 3D microscopy images
Authors: Tasnadi Ervin A. , Toth Timea , Kovacs Maria , Diosdi Akos , Pampaloni Francesco , Molnar Jozsef , Piccinini Filippo , Horvath Peter
Published: June 2019

Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a fully- and semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids, embryos) show that the precision of the segmentation reaches the level of a human expert.

Availability and implementation

3D-Cell-Annotator is implemented in CUDA/C++ as a patch for the segmentation module of MITK. The 3D-Cell-Annotator enabled MITK distribution can be downloaded at:www.3D-cell-annotator.org. It works under Windows 64-bit systems and recent Linux distributions even on a consumer level laptop with a CUDA-enabled video card using recent NVIDIA drivers.

Contacts

filippo.piccinini@irst.emr.itandhorvath.peter@brc.mta.hu
Motor cortex can directly drive the globus pallidal neurons in a projection neuron type dependent manner in rat
Authors: Karube Fuyuki , Takahashi Susumu , Kobayashi Kenta , Fujiyama Fumino
Published: June 2019

The basal ganglia (BG) are critical for the control of motor behaviors and for reinforcement learning. Here, we demonstrate in rats that primary and secondary motor areas (M1 and M2) make functional synaptic connections in the globus pallidus (GP), not usually thought of as an input site of the BG using optogenetics and morphological analysis. The cortical excitation in the GP was as strong as that in the STN. GP neurons projecting to the striatum were preferentially innervated by the motor cortex. Morphological observation revealed that the density of axonal boutons from motor cortices in the GP was approximately 30% of that in the striatum, but was comparable to that in the STN. M1 and M2 projected differentially to the BG in terms of topography and substructures. These results suggest that cortico-pallidal innervation is an additional excitatory input to the BG, and can affects behaviors via the cortex-basal ganglia-thalamus loop.
Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations
Authors: Papathanou Maria , Björklund Åsa K. , Martis-Thiele Mihaela M. , Wallén-Mackenzie Åsa
Published: June 2019

The subthalamic nucleus is a compartmentalized structure formed during development with each division serving a different function. A few molecular markers such as transcription factors involved in the formation and maintenance of the STN have been identified, and whilst a few more genes have been reported to be expressed in the STN, the complete transcriptomic landscape of the mature STN remains elusive. So far genes associated with the adult STN have been expressed throughout the structure. It therefore remains to establish if the functional division of this structure is attributed to a molecular diversity comprising of subpopulations. In this study a single-nuclei RNA-sequencing of genetically labelled Pitx2-Cre was conducted to identify the molecular heterogeneity of the STN. The findings revealed two subpopulations of the STN marked by the expression of Baiap3/Fxyd6 or Fgf11. Moreover additional Pitx2+ subpopulations with distinct signature markers that characterize neighboring structures of the STN such as the parasubthalamic nucleus, the lateral hypothalamus, the zona incerta and the mammillary nucleus were also identified.
A Comparison of Comorbidities and their Contribution to Medical Resource Utilization for Matched HIV-Infected and Uninfected Individuals: A Cross-Sectional Analysis
Authors: Odlum Michelle , Yoon Sunmoo
Published: June 2019

HIV long-term survivorship is characterized by higher rates of comorbidities compared to uninfected groups. Aging with HIV involves complex interactions of factors (e.g., Individual Characteristics, Infections) that result in a 20% increase in comorbidity risk. With over half of the 1.1 million people living with HIV in the US age 50 and over, the need exists to further understand this interplay and differences in aging-related outcomes. Electronic health record data was analyzed for HIV infected (N=208) and uninfected (N=208) adult inpatients, propensity score matched by age and gender. Diagnostic codes were extracted that comprise the factors of Individual Characteristics, High Risk Behaviors, Chronic Conditions, Mental Health Conditions and Infections. Identified codes were assessed for their contributions to medical resource utilization, based on Charlson Comorbidity scores. Significant contributors to high Charslon scores for HIV infected patients were age (β=0.116; [95% CI 0.077, 0.155]) and admission frequency (β=0.159; [95% CI 0.114, 0.205]) in addition to the comorbidities of acute kidney failure (β=3.27; [95% CI 1.76, 4.78]), hypertension (β= −1.77; [95% CI −2.99, −0.551]). Significant contributors for HIV uninfected patients were age (β=0.110; [95% CI 0.087, 0.133]), length of hospital stay (β=0.006; [95% CI 0.003, 0.009]), acute kidney failure (β=1.556; [95% CI 0.611, 2.50]), heart failure (β= 1.713; [95% CI 0.717, 2.71]), and diabetes mellitus II (β= 1.385; [95% CI 0.634, 2.14]). Our findings enhance the understanding of the contributions to medical resource utilization based on HIV status and can inform intervention efficacy for improved HIV aging outcomes.
DrosophilaAop imposes a delay on E(spl)-mediated repression of Ato during R8 specification
Authors: Majot Adam T. , Jozwick Lucas M. , Bishop Clifton P. , Bidwai Ashok P.
Published: June 2019

Drosophilaretinal patterning requires the expression of Atonal (Ato) through coordinated regulation of 5’ and 3’ enhancer modules.ato-3’directs initial expression of Ato which then directs autoregulation via5’-ato. Notch (N) signaling also regulates5’-ato, first enhancing Ato expression and later repressing Ato by inducing E(spl) bHLHs. N signaling balances these opposing functions by directing its obligate nuclear transcription factor, Suppressor of Hairless (Su(H)), only in repressing5’-ato. In this study, we reveal a novel and more nuanced role for Su(H) in its regulation of5’-ato. During retinal patterning, Su(H) is required for the expression Anterior open (Aop), which, in turn, promotes5’-atoactivity. We demonstrate that Aop is induced early in retinal patterning via N pathway activity, wherein Aop is required cell-autonomously for robust Ato expression during photoreceptor specification. Inaopmutants, expression from bothatoenhancers is perturbed, suggesting that Aop promotes the Ato autoregulation through maintenance ofato-3’activity. Clonal analysis indicates that Aop indirectly opposes E(spl)-mediated repression of Ato. In the absence of both Aop and E(spl), Ato expression is restored and the founding ommatidial photoreceptors, R8s, are specified. These findings suggest that N signaling, through a potentially conserved relationship with Aop, imposes a delay onatorepression, thus permitting autoregulation and retinogenesis.

Author Summary

The eye of the fruit fly has served as a paradigm to understand tissue patterning. Complex intercellular signaling networks cooperate during retinal development to allow cells to become specialized visual-system precursor neurons at a specific time and place. These neurons are precisely spaced within the developing retina and later recruit other cells to form the repeated units that comprise insect eyes. The exact placement of each precursor cell precipitates from the precise regulation of theatonalgene, which is first expressed in a cluster of (10-20) cells before becoming restricted to only one cell from each cluster. The Notch signaling pathway is required for both aspects ofatonalregulation, first permitting up-regulation within each cluster, and then the subsequent down-regulation to a single cell. However, the connection between these two modes of Notch signaling had remained unclear. In this report, we have identified that theanterior opengene is required to impose a delay on the restrictive mode of Notch signaling, permitting the initial up-regulation of atonal to occur freely. In flies mutant foranterior open,atonalbypasses its own up-regulation and proceeds directly to its singled-out pattern but with significantly diminished robustness than occurs normally.
FEL performance achieved at PAL-XFEL using a three-chicane bunch compression scheme
Authors: Kang Heung-Sik , Yang Haeryong , Kim Gyujin , Heo Hoon , Nam Inhyuk , Min Chang-Ki , Kim Changbum , Baek Soung Youl , Choi Hyo-Jin , Mun Geonyeong , Park Byoung Ryul , Suh Young Jin , Shin Dong Cheol , Hu Jinyul , Hong Juho , Jung Seonghoon , Kim Sang-Hee , Kim KwangHoon , Na Donghyun , Park Soung Soo , Park Yong Jung , Han Jang-Hui , Jung Young Gyu , Jeong Seong Hun , Kim Min Jae , Lee Hong Gi , Lee Sangbong , Lee Woul-Woo , Oh Bonggi , Suh Hyung Suck , Park Ki-Hyeon , Lee Heung-Soo , Khan D. Z. , Raubenheimer T. O. , Wu Juhao
Published: June 2019

PAL-XFEL utilizes a three-chicane bunch compression (3-BC) scheme (the very first of its kind in operation) for free-electron laser (FEL) operation. The addition of a third bunch compressor allows for more effective mitigation of coherent synchrotron radiation during bunch compression and an increased flexibility of system configuration. Start-to-end simulations of the effects of radiofrequency jitter on the electron beam performance show that using the 3-BC scheme leads to better performance compared with the two-chicane bunch compression scheme. Together with the high performance of the linac radiofrequency system, it enables reliable operation of PAL-XFEL with unprecedented stability in terms of arrival timing, pointing and intensity; an arrival timing jitter of better than 15 fs, a transverse position jitter of smaller than 10% of the photon beam size, and an FEL intensity jitter of smaller than 5% are consistently achieved.
Redesign of morphing UAV's winglet using DS algorithm based ANFIS model
Authors: Konar Mehmet
Published: June 2019

Purpose

The purpose of this paper is to present a novel approach based on the differential search (DS) algorithm integrated with the adaptive network-based fuzzy inference system (ANFIS) for unmanned aerial vehicle (UAV) winglet design.

Design/methodology/approach

The winglet design of UAV, which was produced at Faculty of Aeronautics and Astronautics in Erciyes University, was redesigned using artificial intelligence techniques. This approach proposed for winglet redesign is based on the integration of ANFIS into the DS algorithm. For this purpose, the cant angle (c), the twist angle (t) and taper ratio (λ) of winglet are selected as input parameters; the maximum value of lift/drag ratio (Emax) is selected as the output parameter for ANFIS. For the selected input and output parameters, the optimum ANFIS parameters are determined by the DS algorithm. Then the objective function based on optimum ANFIS structure is integrated with the DS algorithm. With this integration, the input parameters for the Emax value are obtained by the DS algorithm. That is, the DS algorithm is used to obtain both the optimization of the ANFIS structure and the necessary parameters for the winglet design. Thus, the UAV was reshaped and the maximum value of lift/drag ratio was calculated based on new design.

Findings

Considerable improvements on the max E are obtained through winglet redesign on morphing UAVs with artificial intelligence techniques.

Research limitations/implications

It takes a long time to obtain the optimum Emax value by the computational fluid dynamics method.

Practical implications

Using artificial intelligence techniques saves time and reduces cost in maximizing Emax value. The simulation results showed that satisfactory Emax values were obtained, and an optimum winglet design was achieved. Thus, the presented method based on ANFIS and DS algorithm is faster and simpler.

Social implications

The application of artificial intelligence methods could be used in designing more efficient aircrafts.

Originality/value

The study provides a new and efficient method that saves time and reduces cost in redesigning UAV winglets.
Under the microscope – an examination of the supports for ethnic entrepreneurs in Ireland
Authors: Birdthistle Naomi
Published: June 2019

Purpose

Because entrepreneurs operate in a world of uncertainty, the ability to analyse a situation, extract the important and ignore the superfluous, compare potential outcomes, and extrapolate from other experiences to the current one is vital. Researchers have identified several skills an entrepreneur requires to operate their business and the purpose of this paper is to examine if the training and support necessary for entrepreneurship to occur within ethnic communities exists in Ireland.

Design/methodology/approach

This study was carried out among established ethnic entrepreneurs and representatives from support agencies in Ireland. A quantitative research methods approach was adopted using online surveys. Responses from 36 ethnic entrepreneurs and eight support organisations were received.

Findings

Targeted programmes offered by service providers included programmes in foreign languages; providing literature in foreign languages; and specially designed seminars for ethnic entrepreneurs. Of the established ethnic entrepreneurs, the majority indicated that, although they have deficiencies in their skillset they did not avail of programmes because they were unaware of them.

Originality/value

Irish service providers need to provide additional services to ethnic entrepreneurs to be on par with their EU counterparts. Irish service providers need to provide general and targeted training programmes through minority languages. If Ireland wants to continue being known as the “land of a hundred thousand welcomes” and be able to support the much-anticipated asylum seekers who may choose entrepreneurship as a career option, it needs to consider the adoption of the recommendations of this study and provide better tailored services for the ethnic entrepreneur.
Refining the PoinTER “human firewall” pentesting framework
Authors: Archibald Jacqueline M. , Renaud Karen
Published: June 2019

Purpose

Penetration tests have become a valuable tool in the cyber security defence strategy in terms of detecting vulnerabilities. Although penetration testing has traditionally focussed on technical aspects, the field has started to realise the importance of the human in the organisation, and the need to ensure that humans are resistant to cyberattacks. To achieve this, some organisations “pentest” their employees, testing their resilience and ability to detect and repel human-targeted attacks. In a previous paper, the authors reported on PoinTER (Prepare TEst Remediate), a human pentesting framework, tailored to the needs of SMEs. This paper aims to propose improvements to refine the framework. The improvements are based on a derived set of ethical principles that have been subjected to ethical scrutiny

Design/methodology/approach

The authors conducted a systematic literature review of academic research, a review of actual hacker techniques, industry recommendations and official body advice related to social engineering techniques. To meet the requirements to have an ethical human pentesting framework, the authors compiled a list of ethical principles from the research literature which they used to filter out techniques deemed unethical.

Findings

Drawing on social engineering techniques from academic research, reported by the hacker community, industry recommendations and official body advice and subjecting each technique to ethical inspection, using a comprehensive list of ethical principles, the authors propose the refined GDPR-compliant and privacy respecting PoinTER framework. The list of ethical principles, as suggested, could also inform ethical technical pentests.

Originality/value

Previous work has considered penetration testing humans, but few have produced a comprehensive framework such as PoinTER. PoinTER has been rigorously derived from multiple sources and ethically scrutinised through inspection, using a comprehensive list of ethical principles derived from the research literature.