bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a Novel Functional Electrical Stimulation Gait Training System in 2 Adolescents With Cerebral Palsy: A Case Series Exploring Neurotherapeutic Changes
Authors: Behboodi Ahad , Zahradka Nicole , Alesi James , Wright Henry , Lee Samuel C K 
Published: March 2019

Abstract

Background and Purpose
Cerebral palsy (CP) is characterized by decreased passive joint range-of-motion and impaired walking, resulting in progressive loss of function. Typical gait training interventions for children with CP appear insufficient to mitigate these effects. The purpose of this case report is to describe the use of a new treadmill-based gait training intervention using active correction with functional electrical stimulation (FES) in 2 adolescents with CP.

Case Description
Two participants with CP (13-year-old girls, Gross Motor Function Classification System [GMFCS] level II and III) trained by walking on a treadmill, with FES assistance, for 30 minutes, 3 times per week, for 12 weeks. The intervention used a feedback control system to detect all 7 phases of gait in real time and triggered FES to the appropriate muscle groups (up to 5 bilaterally) based on the detected gait phase. Joint kinematics, step width, stride length, walking endurance, peak oxygen uptake ($\dot{v}^{o}_{2}$), and oxygen (O2) cost of walking were evaluated preintervention and postintervention.

Outcomes
Both participants showed improved knee and ankle angles and step width relative to children who are typically developing, and both exhibited increased stride length. One participant (GMFCS III) improved peak $\dot{v}^{o}_{2}$and walking endurance but not O2 cost of walking at her original self-selected walking speed. The other participant (GMFCS II) improved O2 cost of walking but not peak $\dot{v}^{o}_{2}$ or walking endurance. These differences are partly explained by differences in gait type, functional abilities, and initial fitness levels. Most improvements persisted at follow-up, indicating short-term neurotherapeutic effects.

Discussion
Most improvements persisted at follow-up, suggesting short-term neurotherapeutic effects. This case series demonstrates the promising utility of FES-assisted gait-training interventions, tailored to target individual gait deviations, in improving walking performance.
Predictors of Walking Efficiency in Children With Cerebral Palsy: Lower-Body Joint Angles, Moments, and Power
Authors: Noorkoiv Marika , Lavelle Grace , Theis Nicola , Korff Thomas , Kilbride Cherry , Baltzopoulos Vasilios , Shortland Adam , Levin Wendy , Ryan Jennifer M 
Published: March 2019

Abstract

Background
People with cerebral palsy (CP) experience increased muscle stiffness, muscle weakness, and reduced joint range of motion. This can lead to an abnormal pattern of gait, which can increase the energy cost of walking and contribute to reduced participation in physical activity.

Objective
The aim of the study was to examine associations between lower-body joint angles, moments, power, and walking efficiency in adolescents with CP.

Design
This was a cross-sectional study.

Methods
Sixty-four adolescents aged 10 to 19 years with CP were recruited. Walking efficiency was measured as the net nondimensional oxygen cost (NNcost) during 6 minutes of overground walking at self-selected speed. Lower-body kinematics and kinetics during walking were collected with 3-dimensional motion analysis, synchronized with a treadmill with integrated force plates. The associations between the kinematics, kinetics, and NNcost were examined with multivariable linear regression.

Results
After adjusting for age, sex, and Gross Motor Function Classification System level, maximum knee extension angle (β = −0.006), hip angle at midstance (β = −0.007), and maximum hip extension (β = −0.008) were associated with NNcost. Age was a significant modifier of the association between the NNcost and a number of kinematic variables.

Limitations
This study examined kinetic and kinematic variables in the sagittal plane only. A high interindividual variation in gait pattern could have influenced the results.

Conclusions
Reduced knee and hip joint extension are associated with gait inefficiency in adolescents with CP. Age is a significant factor influencing associations between ankle, knee, and hip joint kinematics and gait efficiency. Therapeutic interventions should investigate ways to increase knee and hip joint extension in adolescents with CP.
The Business Case for Surgical Quality—Using a Multidisciplinary Team to Drive Pediatric Surgery Quality Improvement
Authors: Wolcott Kori , Schriefer Jan , Michels Julie , Meyers Jeffrey , Hilt Suzanne , Gitzelmann Christopher , Pegoli Walter , Caserta Mary , McGuire Anna , Thirukumaran Caroline , Pulhamus Marsha , Foito Theresa , Sanders James 
Published: March 2019

Background
Quality improvement efforts in pediatric surgery can positively impact both outcomes and cost.

Purpose
The use of the American College of Surgeons National Surgical Quality Improvement Program (NSQIP)–Pediatrics was essential in determining where to focus our efforts.

Methods
Utilizing risk-adjusted outcomes data is the key driver behind our successes as a multidisciplinary team. This team, which now includes a parent representative, meets at least monthly to review data, identify trends and problems, propose new change ideas, identify barriers to change, and celebrate success. Detailed agendas and minutes are circulated to all team members to ensure a shared mental model.

Results
Since initiation in 2011, our efforts have resulted in a decrease in multiple morbidities, including surgical site infections, blood transfusions, preoperative Computerized Tomography use for patients undergoing appendectomy, unplanned reintubations, shorter lengths of stay, and fewer readmissions. Our improvement efforts resulted in an estimated cost savings of $1.5 million over a 2-year period (2015–2016).

Conclusions
Our team used NSQIP data to direct and guide quality improvements in patient care.

Implications
The business case for surgical quality comes from getting a return on investment in NSQIP with multidisciplinary teams led by surgeons and nurses.
Time-series genome-centric analysis unveils bacterial response to operational disturbance in activated sludge
Authors: Pérez María Victoria , Guerrero Leandro D. , Orellana Esteban , Figuerola Eva L. , Erijman Leonardo 
Published: March 2019

ABSTRACTUnderstanding ecosystem response to disturbances and identifying the most critical traits for the maintenance of ecosystem functioning are important goals for microbial community ecology. In this study, we used 16S rRNA amplicon sequencing and metagenomics to investigate the assembly of bacterial populations in a full-scale municipal activated sludge wastewater treatment plant over a period of three years, including a period of nine month of disturbance, characterized by short-term plant shutdowns. Following the reconstruction of 173 metagenome-assembled genomes, we assessed the functional potential, the number of rRNA gene operons and thein situgrowth rate of microorganisms present throughout the time series. Operational disturbances caused a significant decrease in bacteria with a single copy of the ribosomal RNA (rrn) operon. Despite only moderate differences in resource availability, replication rates were distributed uniformly throughout time, with no differences between disturbed and stable periods. We suggest that the length of the growth lag phase, rather than the growth rate, as the primary driver of selection under disturbed conditions. Thus, the system could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions.IMPORTANCEIn this work we investigated the response of microbial communities to disturbances in a full-scale activated sludge wastewater treatment plant over a time-scale that included periods of stability and disturbance. We performed a genome-wide analysis, which allowed us the direct estimation of specific cellular traits, including the rRNA operon copy number and the in situ growth rate of bacteria. This work builds upon recent efforts to incorporate growth efficiency for the understanding of the physiological and ecological processes shaping microbial communities in nature. We found evidence that would suggest that activated sludge could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions. This paper provides relevant insights into wastewater treatment process, and may also reveal a key role for growth traits in the adaptive response of bacteria to unsteady environmental conditions.
High prevalence of antibiotic resistance inHelicobacter pyloriisolates from Iran: importance of functional and mutational analysis of resistance genes and virulence genotyping
Authors: Farzi Nastaran , Yadegar Abbas , Aghdaei Hamid Asadzadeh , Sadeghi Amir , Zali Mohammad Reza 
Published: March 2019

AbstractThe high prevalence of antibiotic resistance inHelicobacter pylorihas become a great challenge in Iran. The genetic mutations that contribute to the resistance have yet to be precisely identified. This study aimed to investigate the prevalence of antibiotic resistance and virulence markers in IranianH. pyloriisolates and to analyze if there is any association between resistance and genotype. Antibiotic susceptibility patterns of 33H. pyloriisolates were investigated against metronidazole, clarithromycin, amoxicillin, rifampicin, ciprofloxacin, levofloxacin and tetracycline by the agar dilution method. ThefrxA, rdxA, gyrA, gyrBand 23S rRNA genes of the isolates were sequenced. The virulence genotypes were also determined using PCR. Metronidazole resistance was present in 81.8% of the isolates, followed by clarithromycin (36.4%), ciprofloxacin (36.4%), amoxicillin (30.3%), rifampicin (30.3%), levofloxacin (27.3%) and tetracycline (6.1%). Most of the metronidazole-resistant isolates carried frameshift mutations in bothfrxAandrdxAgenes, and premature termination was occurred in positions Q5Stop and Q50Stop, respectively. Amino acid substitutions M191I, G208E, and V199A were predominantly found ingyrAgene of fluoroquinolone-resistant isolates. A2143G and C2195T mutations of 23S rRNA were found in four isolates. Interestingly, significant associations were demonstrated between intactcagPAI and resistance to rifampicin (P= 0.027), and between susceptibility to amoxicillin andcagPAI intactness (P= 0.016). The prevalence ofH. pyloriantibiotic resistance is high in our region, particularly that of metronidazole, clarithromycin, ciprofloxacin and multidrug resistance. Occurrence of mutations in resistance genes were involved in the development of resistance, especially in less virulent isolates.
Notch signaling and taxis mechanims regulate early stage angiogenesis: A mathematical and computational model
Authors: Vega Rocío , Carretero Manuel , Travasso Rui D.M. , Bonilla Luis L. 
Published: March 2019

AbstractDuring angiogenesis, new blood vessels sprout and grow from existing ones. This process plays a crucial role in organ development and repair, in wound healing and in numerous pathological processes such as cancer progression or diabetes. Here, we present a mathematical model of early stage angiogenesis that permits exploration of the relative importance of mechanical, chemical and cellular cues. Endothelial cells proliferate and move over an extracellular matrix by following external gradients of Vessel Endothelial Growth Factor, adhesion and stiffness, which are incorporated to a Cellular Potts model with a finite element description of elasticity. The dynamics of Notch signaling involving Delta-4 and Jagged-1 ligands determines tip cell selection and vessel branching. Through their production rates, competing Jagged-Notch and Delta-Notch dynamics determine the influence of lateral inhibition and lateral induction on the selection of cellular phenotypes, branching of blood vessels, anastomosis (fusion of blood vessels) and angiogenesis velocity. Anastomosis may be favored or impeded depending on the mechanical configuration of strain vectors in the ECM near tip cells. Numerical simulations demonstrate that increasing Jagged production results in pathological vasculatures with thinner and more abundant vessels, which can be compensated by augmenting the production of Delta ligands.Author SummaryAngiogenesis is the process by which new blood vessels grow from existing ones. This process plays a crucial role in organ development, in wound healing and in numerous pathological processes such as cancer growth or in diabetes. Angiogenesis is a complex, multi-step and well regulated process where biochemistry and physics are intertwined. The process entails signaling in vessel cells being driven by both chemical and mechanical mechanisms that result in vascular cell movement, deformation and proliferation. Mathematical models have the ability to bring together these mechanisms in order to explore their relative relevance in vessel growth. Here, we present a mathematical model of early stage angiogenesis that is able to explore the role of biochemical signaling and tissue mechanics. We use this model to unravel the regulating role of Jagged, Notch and Delta dynamics in vascular cells. These membrane proteins have an important part in determining the leading cell in each neo-vascular sprout. Numerical simulations demonstrate that increasing Jagged production results in pathological vasculatures with thinner and more abundant vessels, which can be compensated by augmenting the production of Delta ligands.
Th2 cytokine profile in appendicular lavage fluid is compatible with allergy as an etiology for acute appendicitis
Authors: Carvalho Nuno , Barros André , Coelho Hélder O. , Moita Catarina F. , Neves-Costa Ana , Pedroso Dora , Borges Filipe C. , Moita Luís F. , Costa Paulo M. 
Published: March 2019

AbstractAcute appendicitis is the most frequent surgical abdominal emergency, but its etiology remains poorly understood. Histological examination of the appendix, following its removal due to acute appendicitis, consistently shows features in common with bronchial asthma, suggesting an allergic reaction as a candidate etiologic factor. Here we propose the concept of appendicular lavage and used it to study the levels of the Th2 cytokines IL-4, IL-5 and IL-9 in patients with a clinical diagnosis of acute appendicitis. The study group included 20 patients with a histological diagnosis of phlegmonous appendicitis, 13 patients with gangrenous appendicitis, and a control group of 8 patients with clinical diagnosis of appendicitis but with normal histology. Cytokines levels were higher in acute appendicitis. The difference was more pronounced when comparing phlegmonous appendicitis with non-pathological appendix (p=0.01) for IL-4 (48,3 vs 21,3 pg/mL), IL-5 (29,2 vs 8,0 pg/mL) and IL-9 (34,1 vs 16,6 pg/mL). This Th2 cytokine profile is compatible with the hypothesis of allergy as an etiologic factor for acute appendicitis and may have important implications for the diagnosis, prevention and treatment of this condition.
MetaMLP: A fast word embedding based classifier to profile target gene databases in metagenomic samples
Authors: Arango-Argoty G. A. , Heath L. S. , Pruden A. , Vikesland P. J. , Zhang L. 
Published: March 2019

AbstractThe functional profile of metagenomic samples allows the understanding of the role of the microbes in their environment. Such analysis consists of assigning short sequencing reads to a particular functional category. Normally, manually curated databases are used for functional assignment where genes are arranged into different classes. Sequence alignment has been widely used to profile metagenomic samples against curated databases. However, this method is time consuming and requires high computing resources. Although several alignment free methods based on k-mer composition have been developed in the recent years, they still require a large amount of memory. In this paper, MetaMLP (Metagenomics Machine Learning Profiler) a machine learning method that represents sequences into numerical vectors (embeddings) and uses a simple one hidden layer neural network to profile functional categories is proposed. Unlike other methods, MetaMLP enables partial matching by using a reduced alphabet to build sequence embeddings from full and partial kmers. MetaMLP is able to identify a slightly larger number of reads compared to Diamond (one of the fastest sequence alignment method) as well as to perform accurate predictions with 0.99 precision and 0.99 recall. MetaMLP can process 100M reads in around 10 minutes in a laptop computer which is 50x faster than Diamond. MetaMLP is free for use, available athttps://bitbucket.org/gaarangoa/metamlp/src/master/.
Genetic mapping of fitness determinants across the malaria parasitePlasmodium falciparumlife cycle
Authors: Li Xue , Kumar Sudhir , McDew-White Marina , Haile Meseret , Cheeseman Ian H. , Emrich Scott , Button-Simons Katie , Nosten François , Kappe Stefan H.I. , Ferdig Michael T. , Anderson Tim J.C. , Vaughan Ashley M. 
Published: March 2019

AbstractMalaria is transmitted through female Anopheline mosquitoes where gamete fusion and meiosis occurs, and humans where parasites proliferate asexually. We describe a powerful approach to identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-cycle stages in human malaria parasitePlasmodium falciparumusing bulk segregant analysis (BSA). We combined experimental genetic crosses using humanized mice, with selective whole genome amplification and BSA at multiple developmental stages in both mosquito and vertebrate host to examine parasite competition and identify genomic regions under selection. We generated crosses between artemisinin resistant (ART-R,kelch13-C580Y) and ART-sensitive (ART-S,kelch13-WT) parasite clones recently isolated from Southeast Asian patients. We then quantified genome-wide changes in allele frequency in the parasite progeny population from infected midgut and salivary glands ofAnopheles stephensimosquitoes, infected livers, emerging merozoites and aliquots ofin vitrocultured progeny parasites at intervals over 30 days. Three striking results emerge: we observed (i) a strong skew (>80%) towards alleles from the ART-R parent in the mosquito stage, that dropped to ∼50% in the blood stage as selfed ART-R parasites were selected against; (ii) highly repeatable skews in allele frequencies across the genome in blood stage parasites; (iii) particularly strong selection (selection coefficient (s) ≤ 0.18/asexual cycle) against alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 containing ARPS10. This approach robustly identifies selected loci and has strong potential for identifying parasite genes that interact with the mosquito vector or compensatory loci involved in drug resistance.
Activity-dependent long-term potentiation of electrical synapses in the mammalian thalamus
Authors: Fricker Brandon , Heckman Emily , Cunningham Patrick C. , Haas Julie S. 
Published: March 2019

AbstractActivity-dependent changes of synapse strength have been extensively characterized at chemical synapses, but the relationship between physiological forms of activity and strength at electrical synapses remains poorly understood. For mammalian electrical synapses composed of hexomers of connexin36, physiological forms of neuronal activity in coupled pairs has thus far have only been linked to long-term depression; activity that results in strengthening of electrical synapses has not yet been identified. The thalamic reticular nucleus (TRN), a central brain area primarily connected by gap junctional (electrical) synapses, regulates cortical attention to the sensory surround. Bidirectional plasticity of electrical synapses may be a key mechanism underlying these processes in both healthy and diseased states. Here we show in electrically coupled TRN pairs that tonic spiking in one neuron results in long-term potentiation of electrical synapses between coupled pairs of TRN neurons. Potentiation is expressed asymmetrically, indicating that regulation of connectivity depends on the direction of use. Further, potentiation depends on calcium flux, and we thus propose a calcium-based activity rule for bidirectional plasticity of electrical synapse strength. Because electrical synapses dominate intra-TRN connectivity, these synapses and their modifications are key regulators of thalamic attention circuitry. More broadly, bidirectional modifications of electrical synapses are likely to be a widespread and powerful principle for ongoing, dynamic reorganization of neuronal circuitry across the brain.SummaryLong-term potentiation results from spiking in one cell of an electrically coupled pair. Asymmetry of synapses increases following unidirectional activity. We suggest a calcium-based rule for electrical synapse plasticity.
CHaRTr: An R toolbox for modeling Choices and Response Times in decision-making tasks
Authors: Chandrasekaran Chandramouli , Hawkins Guy E. 
Published: March 2019

AbstractDecision-making is the process of choosing and performing actions in response to sensory cues so as to achieve behavioral goals. A sophisticated research effort has led to the development of many mathematical models to describe the response time (RT) distributions and choice behavior of observers performing decision-making tasks. However, relatively few researchers use these models because it demands expertise in various numerical, statistical, and software techniques. Although some of these problems have been surmounted in existing software packages, the packages have often focused on the classical decision-making model, the diffusion decision model. Recent theoretical advances in decision-making that posit roles for “urgency”, time-varying decision thresholds, noise in various aspects of the decision-formation process or low pass filtering of sensory evidence, have proven to be challenging to incorporate in a coherent software framework that permits quantitative evaluations among these competing classes of decision-making models. Here, we present a toolbox —Choices and Response Times in R, orCHaRTr— that provides the user the ability to implement and test a wide variety of decision-making models ranging from classic through to modern versions of the diffusion decision model, to models with urgency signals, or collapsing boundaries. Earlier versions ofCHaRTrhave been instrumental in a number of recent studies of humans and monkeys performing perceptual decision-making tasks. We also provide guidance on how to extend the toolbox to incorporate future developments in decision-making models.