bluuebunny/crossref_metadata_2025 huggingface dataset:
Fecal microbiota transplantation for recurrent Clostridium difficile infection in hematopoietic stem cell transplant recipients
Authors: Webb B.J. , Brunner A. , Ford C.D. , Gazdik M.A. , Petersen F.B. , Hoda D.
Published: May 2016

Recurrent Clostridium difficile infection (CDI) is a consequence of intestinal dysbiosis and is particularly common following hematopoietic stem cell transplantation (HSCT). Fecal microbiota transplantation (FMT) is an effective method of treating CDI by correcting intestinal dysbiosis by passive transfer of healthy donor microflora. FMT has not been widely used in immunocompromised patients, including HSCT recipients, owing to concern for donor‐derived infection. Here, we describe initial results of an FMT program for CDI at a US HSCT center. Seven HSCT recipients underwent FMT between February 2015 and February 2016. Mean time post HSCT was 635 days (25–75 interquartile range [IQR] 38–791). Five of the patients (71.4%) were on immunosuppressive therapy at FMT; 4 had required long‐term suppressive oral vancomycin therapy because of immediate recurrence after antibiotic cessation. Stool donors underwent comprehensive health and behavioral screening and laboratory testing of serum and stool for 32 potential pathogens. FMT was administered via the naso‐jejunal route in 6 of the 7 patients. Mean follow‐up was 265 days (IQR 51–288). Minor post‐FMT adverse effects included self‐limited bloating and urgency. One patient was suspected of having post‐FMT small intestinal bacterial overgrowth. No serious adverse events were noted and all‐cause mortality was 0%. Six of 7 (85.7%) patients had no recurrence; 1 patient recurred at day 156 post FMT after taking an oral antibiotic and required repeat FMT, after which no recurrence has occurred. Diarrhea was improved in all patients and 1 patient with gastrointestinal graft‐versus‐host disease was able to taper off systemic immunosuppression after FMT. With careful donor selection and laboratory screening, FMT appears to be a safe and effective therapy for CDI in HSCT patients and may confer additional benefits. Larger studies are necessary to confirm safety and efficacy and explore other possible effects.
Contribution of peripheral and central chemoreceptors to sympatho‐excitation in heart failure
Authors: Toledo Camilo , Andrade David C. , Lucero Claudia , Schultz Harold D. , Marcus Noah , Retamal Mauricio , Madrid Carlos , Del Rio Rodrigo
Published: May 2016

Chronic heart failure (CHF) is a major public health problem. Tonic hyper‐activation of sympathetic neural outflow is commonly observed in patients with CHF. Importantly, sympatho‐excitation in CHF exacerbates its progression and is strongly related to poor prognosis and high mortality risk. Increases in both peripheral and central chemoreflex drive are considered markers of the severity of CHF. The principal peripheral chemoreceptors are the carotid bodies (CBs) and alteration in their function has been described in CHF. Mainly, during CHF the CB chemosensitivity is enhanced leading to increases in ventilation and sympathetic outflow. In addition to peripheral control of breathing, central chemoreceptors (CCs) are considered a dominant mechanism in ventilatory regulation. Potentiation of the ventilatory and sympathetic drive in response to CC activation has been shown in patients with CHF as well as in animal models. Therefore, improving understanding of the contribution of the peripheral and central chemoreflexes to augmented sympathetic discharge in CHF could help in developing new therapeutic approaches intended to attenuate the progression of CHF. Accordingly, the main focus of this review is to discuss recent evidence that peripheral and central chemoreflex function are altered in CHF and that they contribute to autonomic imbalance and progression of CHF.

image
Lymphatic pumping: mechanics, mechanisms and malfunction
Authors: Scallan Joshua P. , Zawieja Scott D. , Castorena‐Gonzalez Jorge A. , Davis Michael J.
Published: May 2016

A combination of extrinsic (passive) and intrinsic (active) forces move lymph against a hydrostatic pressure gradient in most regions of the body. The effectiveness of the lymph pump system impacts not only interstitial fluid balance but other aspects of overall homeostasis. This review focuses on the mechanisms that regulate the intrinsic, active contractions of collecting lymphatic vessels in relation to their ability to actively transport lymph. Lymph propulsion requires not only robust contractions of lymphatic muscle cells, but contraction waves that are synchronized over the length of a lymphangion as well as properly functioning intraluminal valves. Normal lymphatic pump function is determined by the intrinsic properties of lymphatic muscle and the regulation of pumping by lymphatic preload, afterload, spontaneous contraction rate, contractility and neural influences. Lymphatic contractile dysfunction, barrier dysfunction and valve defects are common themes among pathologies that directly involve the lymphatic system, such as inherited and acquired forms of lymphoedema, and pathologies that indirectly involve the lymphatic system, such as inflammation, obesity and metabolic syndrome, and inflammatory bowel disease.

image
Estimation of trabecular bone parameters in children from multisequence MRI using texture‐based regression
Authors: Lekadir Karim , Hoogendoorn Corné , Armitage Paul , Whitby Elspeth , King David , Dimitri Paul , Frangi Alejandro F.
Published: May 2016

Purpose:

This paper presents a statistical approach for the prediction of trabecular bone parameters from low‐resolution multisequence magnetic resonance imaging (MRI) in children, thus addressing the limitations of high‐resolution modalities such as HR‐pQCT, including the significant exposure of young patients to radiation and the limited applicability of such modalities to peripheral bones in vivo.

Methods:

A statistical predictive model is constructed from a database of MRI and HR‐pQCT datasets, to relate the low‐resolution MRI appearance in the cancellous bone to the trabecular parameters extracted from the high‐resolution images. The description of the MRI appearance is achieved between subjects by using a collection of feature descriptors, which describe the texture properties inside the cancellous bone, and which are invariant to the geometry and size of the trabecular areas. The predictive model is built by fitting to the training data a nonlinear partial least square regression between the input MRI features and the output trabecular parameters.

Results:

Detailed validation based on a sample of 96 datasets shows correlations >0.7 between the trabecular parameters predicted from low‐resolution multisequence MRI based on the proposed statistical model and the values extracted from high‐resolution HRp‐QCT.

Conclusions:

The obtained results indicate the promise of the proposed predictive technique for the estimation of trabecular parameters in children from multisequence MRI, thus reducing the need for high‐resolution radiation‐based scans for a fragile population that is under development and growth.
Biochemical Characterization of the Active Anti-Hepatitis C Virus Metabolites of 2,6-Diaminopurine Ribonucleoside Prodrug Compared to Sofosbuvir and BMS-986094
Authors: Ehteshami Maryam , Tao Sijia , Ozturk Tugba , Zhou Longhu , Cho Jong Hyun , Zhang Hongwang , Amiralaei Sheida , Shelton Jadd R. , Lu Xiao , Khalil Ahmed , Domaoal Robert A. , Stanton Richard A. , Suesserman Justin E. , Lin Biing , Lee Sam S. , Amblard Franck , Whitaker Tony , Coats Steven J. , Schinazi Raymond F.
Published: May 2016

Ribonucleoside analog inhibitors (rNAI) target the hepatitis C virus (HCV) RNA-dependent RNA polymerase nonstructural protein 5B (NS5B) and cause RNA chain termination. Here, we expand our studies on β-
d
-2′-
C
-methyl-2,6-diaminopurine-ribonucleotide (DAPN) phosphoramidate prodrug 1 (PD1) as a novel investigational inhibitor of HCV. DAPN-PD1 is metabolized intracellularly into two distinct bioactive nucleoside triphosphate (TP) analogs. The first metabolite, 2′-
C
-methyl-GTP, is a well-characterized inhibitor of NS5B polymerase, whereas the second metabolite, 2′-
C
-methyl-DAPN-TP, behaves as an adenosine base analog.
In vitro
assays suggest that both metabolites are inhibitors of NS5B-mediated RNA polymerization. Additional factors, such as rNAI-TP incorporation efficiencies, intracellular rNAI-TP levels, and competition with natural ribonucleotides, were examined in order to further characterize the potential role of each nucleotide metabolite
in vivo
. Finally, we found that although both 2′-
C
-methyl-GTP and 2′-
C
-methyl-DAPN-TP were weak substrates for human mitochondrial RNA (mtRNA) polymerase (POLRMT)
in vitro
, DAPN-PD1 did not cause off-target inhibition of mtRNA transcription in Huh-7 cells. In contrast, administration of BMS-986094, which also generates 2′-
C
-methyl-GTP and previously has been associated with toxicity in humans, caused detectable inhibition of mtRNA transcription. Metabolism of BMS-986094 in Huh-7 cells leads to 87-fold higher levels of intracellular 2′-
C
-methyl-GTP than DAPN-PD1. Collectively, our data characterize DAPN-PD1 as a novel and potent antiviral agent that combines the delivery of two active metabolites.
Individual or Combined Effects of Meropenem, Imipenem, Sulbactam, Colistin, and Tigecycline on Biofilm-Embedded Acinetobacter baumannii and Biofilm Architecture
Authors: Wang Yung-Chih , Kuo Shu-Chen , Yang Ya-Sung , Lee Yi-Tzu , Chiu Chun-Hsiang , Chuang Ming-Fen , Lin Jung-Chung , Chang Feng-Yee , Chen Te-Li
Published: May 2016

Acinetobacter baumannii
biofilms are difficult to eradicate. We investigated the effects of meropenem (2 mg/liter), imipenem (2 mg/liter), sulbactam (4 mg/liter), colistin (2 mg/liter), and tigecycline (2 mg/liter), alone or in combination, on biofilm-embedded carbapenem-resistant and carbapenem-susceptible
A. baumannii
(CRAb and CSAb, respectively) cells, as well as on the architecture of the biofilms.
A. baumannii
ATCC 15151 (Ab15151) and its OXA-82-overproducing transformant, along with two clinical CSAb and two clinical CRAb isolates of differing clonalities, were used. The minimal bactericidal concentrations for biofilm-embedded cells of the six tested isolates were >50-fold those of their planktonic cells. When used individually, meropenem exhibited a higher killing effect than the other four antimicrobials on biofilm-embedded CSAb cells in the colony biofilm assay. For two clinical CRAb isolates, meropenem plus sulbactam or sulbactam plus tigecycline showed >100-fold the bactericidal effect exhibited by these agents used alone after 48 h of treatment. The effect of antimicrobials on the architecture of Ab15151 biofilm emitting green fluorescence was determined by confocal laser scanning microscopy using COMSTAT software. Significant decreases in the maximum biofilm thickness were observed after exposure to meropenem and imipenem. Meropenem plus sulbactam significantly decreased the biomass and mean thickness and increased the roughness coefficient of biofilms, but sulbactam plus tigecycline only decreased the maximum and mean biofilm thickness compared to any of these agents used alone. Meropenem was active against biofilm-embedded CSAb, whereas meropenem plus sulbactam exhibited synergism against biofilm-embedded CRAb and caused significantly more damage to the biofilm architecture than did any of the agents used alone.
A Transposon Screen Identifies Genetic Determinants of Vibrio cholerae Resistance to High-Molecular-Weight Antibiotics
Authors: Dörr Tobias , Delgado Fernanda , Umans Benjamin D. , Gerding Matthew A. , Davis Brigid M. , Waldor Matthew K.
Published: May 2016

Gram-negative bacteria are notoriously resistant to a variety of high-molecular-weight antibiotics due to the limited permeability of their outer membrane (OM). The basis of OM barrier function and the genetic factors required for its maintenance remain incompletely understood. Here, we employed transposon insertion sequencing to identify genes required for
Vibrio cholerae
resistance to vancomycin and bacitracin, antibiotics that are thought to be too large to efficiently penetrate the OM. The screen yielded several genes whose protein products are predicted to participate in processes important for OM barrier functions and for biofilm formation. In addition, we identified a novel factor, designated
vigA
(for vancomycin inhibits growth), that has not previously been characterized or linked to outer membrane function. The
vigA
open reading frame (ORF) codes for an inner membrane protein, and in its absence, cells became highly sensitive to glycopeptide antibiotics (vancomycin and ramoplanin) and bacitracin but not to other large antibiotics or detergents. In contrast to wild-type (WT) cells, the
vigA
mutant was stained with fluorescent vancomycin. These observations suggest that VigA specifically prevents the periplasmic accumulation of certain large antibiotics without exerting a general role in the maintenance of OM integrity. We also observed marked interspecies variability in the susceptibilities of Gram-negative pathogens to glycopeptides and bacitracin. Collectively, our findings suggest that the OM barrier is not absolute but rather depends on specific OM-antibiotic interactions.
Thioridazine as Chemotherapy for Mycobacterium avium Complex Diseases
Authors: Deshpande Devyani , Srivastava Shashikant , Musuka Sandirai , Gumbo Tawanda
Published: May 2016

Mycobacterium avium-intracellulare
complex (MAC) causes an intractable intracellular infection that presents as chronic pulmonary disease. Currently, therapy consists of ethambutol and macrolides and takes several years to complete. The neuroleptic phenothiazine thioridazine kills mycobacteria by inhibiting the electron transport chain. In several experiments with bacterial populations of up to 10
12
CFU/ml, we failed to isolate any bacteria resistant to 3 times the MIC of thioridazine, suggesting the absence of resistant mutants at bacterial burdens severalfold higher than those encountered in patients. In the hollow-fiber model of intracellular MAC (HFS-MAC), thioridazine achieved an extracellular half-life of 16.8 h and an intracellular half-life of 19.7 h. Thioridazine concentrations were >28,000-fold higher inside infected macrophages than in the HFS-MAC central compartment (equivalent to plasma). Thioridazine maximal kill was 5.20 ± 0.75 log
10
CFU/ml on day 7 (
r
2
= 0.96) and 7.19 ± 0.31 log
10
CFU/ml on day 14 (
r
2
= 0.99), the highest seen with any drug in the system. Dose fractionation studies revealed that thioridazine efficacy and acquired drug resistance were driven by the peak concentation-to-MIC ratio, with a 50% effective concentration (EC
50
) of 2.78 ± 0.44 for microbial killing. Acquired drug resistance was encountered by day 21 with suboptimal doses, demonstrating that fluctuating drug concentrations drive evolution faster than static concentrations in mutation frequency studies. However, the thioridazine EC
50
changed 16.14-fold when the concentration of fetal bovine serum was changed from 0% to 50%, suggesting that intracellular potency could be heavily curtailed by protein binding. Efficacy in patients will depend on the balance between trapping of the drug in the pulmonary system and the massive intracellular concentrations versus very high protein binding of thioridazine.
Eosinophilic cholecystitis with common bile duct stricture: a rare disease
Authors: Mehanna Daniel , Naseem Zainab , Mustaev Muslim
Published: May 2016

Although the most common cause of cholecystitis is gallstones, other conditions may present as acute cholecystitis. We describe a case of eosinophilic cholecystitis with common bile duct stricture. A 36-year-old woman initially had generalised abdominal pain and peripheral eosinophilia. Diagnostic laparoscopy showed eosinophilic ascites and necrotic nodules on the posterior abdominal wall. She was treated with anthelminthics on presumption of toxacara infection based on borderline positivity of serological tests. She later presented with acute cholecystitis and had a cholecystectomy and choledocotomy. Day 9 T-tube cholangiogram showed irregular narrowing of the distal common bile duct. The patient's symptoms were improved with steroids and the T-tube was subsequently removed.
Change in fasting plasma glucose and incident type 2 diabetes mellitus: results from a prospective cohort study
Authors: Mozaffary Amirhossein , Asgari Samaneh , Tohidi Maryam , Kazempour-Ardebili Sara , Azizi Fereidoun , Hadaegh Farzad
Published: May 2016

Objective

To investigate the association between changes in fasting plasma glucose (FPG) values and incident type 2 diabetes (T2D) in a cohort of the Iranian population.

Design

Prospective cohort study.

Setting

This study was conducted within the framework of the Tehran Lipid and Glucose Study (TLGS) to investigate the association between change in FPG between baseline examination (1999–2001) and the second visit (2002–2005) with incident T2D.

Participants

A total of 3981 non-diabetic participants aged ≥20 years.

Outcome measure

T2D was defined if the participant was using antidiabetic drugs or if FPG was ≥7 mmol/L or if the 2 h post-challenge plasma glucose (2-hPCG) was ≥11.1 mmol/L.

Results

During a median follow-up of 6.17 years, after the second examination, 288 new cases of T2D were identified. In a multivariate Cox proportional hazard analysis using age as timescale, we presented a simple model including FPG change (HR 1.19, 95% CI 1.07 to 1.33) and baseline waist circumference (WC) (HR 1.004, 95% CI 1.001 to 1.008) with a discriminative power (C-index) of 72%. Furthermore, we showed that the highest quartile of FPG change enhanced the T2D risk to 1.65 (95% CI 1.2 to 2.27) compared with the lowest quartile (p for trend=0.004).The independent risk of FPG change resisted further adjustment with 2-hPCG change. Adding the 2-hPCG change only slightly increased the discriminative power of the model including FPG change and baseline value of WC (0.73% vs 0.72%). After the study population had been limited to those with normal fasting glucose/normal glucose tolerance, FPG change remained an independent predictor (HR 1.57, 95% CI 1.31 to 1.88).

Conclusions

Two measurements of FPG obtained about 3 years apart can help to identify populations at risk of incident T2D independently of important traditional risk factors and their changes, including 2-hPCG change.
Comparison of the force applied on oral structures during intubation attempts by novice physicians between the Macintosh direct laryngoscope, Airway Scope and C-MAC PM: a high-fidelity simulator-based study
Authors: Nakanishi Taizo , Shiga Takashi , Homma Yosuke , Koyama Yasuaki , Goto Tadahiro
Published: May 2016

Objective

We examined whether the use of Airway Scope (AWS) and C-MAC PM (C-MAC) decreased the force applied on oral structures during intubation attempts as compared with the force applied with the use of Macintosh direct laryngoscope (DL).

Design

Prospective cross-over study.

Participants

A total of 35 novice physicians participated.

Interventions

We used 6 simulation scenarios based on the difficulty of intubation and intubation devices.

Outcome measures

Our primary outcome measures were the maximum force applied on the maxillary incisors and tongue during intubation attempts, measured by a high-fidelity simulator.

Results

The maximum force applied on maxillary incisors was higher with the use of the C-MAC than with the DL and AWS in the normal airway scenario (DL, 26 Newton (N); AWS, 18 N; C-MAC, 52 N; p<0.01) and the difficult airway scenario (DL, 42 N; AWS, 24 N; C-MAC, 68 N; p<0.01). In contrast, the maximum force applied on the tongue was higher with the use of the DL than with the AWS and C-MAC in both airway scenarios (DL, 16 N; AWS, 1 N; C-MAC, 7 N; p<0.01 in the normal airway scenario; DL, 12 N; AWS, 4 N; C-MAC, 7 N; p<0.01 in the difficult airway scenario).

Conclusions

The use of C-MAC, compared with the DL and AWS, was associated with the higher maximum force applied on maxillary incisors during intubation attempts. In contrast, the use of video laryngoscopes was associated with the lower force applied on the tongue in both airway scenarios, compared with the DL. Our study was a simulation-based study, and further research on living patients would be warranted.
TOPS: Trial Of Prevention Strategies for low back pain in patients recently recovered from low back pain—study rationale and protocol
Authors: Stevens Matthew L , Lin Chung-Wei C , Hancock Mark J , Latimer Jane , Buchbinder Rachelle , Grotle Margreth , van Tulder Maurits , New Charles H , Wisby-Roth Trish , Maher Chris G
Published: May 2016

Introduction

Low back pain (LBP) is the health condition that carries the greatest disability burden worldwide; however, there is only modest support for interventions to prevent LBP. The aim of this trial is to establish the effectiveness and cost-effectiveness of group-based exercise and educational classes compared with a minimal intervention control in preventing recurrence of LBP in people who have recently recovered from an episode of LBP.

Methods and analysis

TOPS will be a pragmatic comparative effectiveness randomised clinical trial with a parallel economic evaluation combining three separate cohorts (TOPS Workers, TOPS Primary Care, TOPS Defence) with the same methodology. 1482 participants who have recently recovered from LBP will be randomised to either a comprehensive exercise and education programme or a minimal intervention control. Participants will be followed up for a minimum of 1 year. The primary outcome will be days till recurrence of LBP. Effectiveness will be assessed using survival analysis. Cost-effectiveness will be assessed from the societal perspective.

Ethics and dissemination

This trial has been approved by the University of Sydney Human Research Ethics Committee (HREC) (ref: 2015/728) and prospectively registered with the Australian and New Zealand Clinical Trials Registry (ref: 12615000939594). We will also obtain ethics approval from the Australian Defence Force HREC. The results of this study will be submitted for publication in a prominent journal and widely publicised in the general media.

Trial registration number

Australian and New Zealand Clinical Trial Registry (ANZCTR) 12615000939594.
Reasons for non-participation in a primary care-based physical activity trial: a qualitative study
Authors: Attwood S , Morton K L , Mitchell J , Van Emmenis M , Sutton S
Published: May 2016

Objectives

To explore reasons for non-participation in a primary care-based physical activity trial and understand how these may contribute to recruitment of non-representative research samples. We also aimed to elicit non-participants’ own recommendations for enhancing trial uptake in primary care.

Design

Semistructured telephone interviews with non-participants to a randomised controlled trial of a very brief intervention for promoting physical activity conducted in primary care (the Very Brief Interventions trial), with thematic analysis of interview transcripts.

Setting

5 general practice (GP) surgeries in the East of England, UK.

Participants

Interviews were completed with 10 female and 6 male non-participants of white ethnicity and aged between 40 and 71 years. 13 of the 16 interviewees were either active or moderately active according to the GP Physical Activity Questionnaire (GPPAQ).

Results

Interviewees discussed a range of reasons for non-participation. These included beliefs surrounding the personal relevance of the trial based on preconceptions of intervention content. Many interviewees considered themselves either sufficiently active or too functionally limited to increase activity levels further, so rendering participation pointless in their view. Other identified barriers included a lack of free time, for trial participation and for increasing physical activity, and dissatisfaction with appointment scheduling systems in place at GP surgeries. Interviewees questioned the appropriateness of primary care as a context for delivering interventions to promote physical activity. In general, interviewees were positively disposed towards the idea of trial participation, especially if personal benefits are made salient, but suggested that interventions could be delivered in a different setting such as the internet.

Conclusions

To increase participation in physical activity promotion trials conducted in primary care, the content of invitation materials and procedures for contacting potential participants require reconsideration. Specific recommendations include streamlining intervention materials and enhancing their relevance to the health concerns of invitees.

Trial registration number

ISRCTN72691150; Pre-results.
Standing waves braneworlds
Authors: Gogberashvili Merab , Mantidze Irakli , Sakhelashvili Otari , Shengelia Tsotne
Published: May 2016

The class of nonstationary braneworld models generated by the coupled gravitational and scalar fields is reviewed. The model represents a brane in a spacetime with single time and one large (infinite) and several small (compact) spacelike extra dimensions. In some particular cases the model has the solutions corresponding to the bulk gravi-scalar standing waves bounded by the brane. Pure gravitational localization mechanism of matter particles on the node of standing waves, where the brane is placed, is discussed. Cosmological applications of the model is also considered.
EXPERIMENTAL INVESTIGATION ON FRICTION STIR WELDING OF CRYOROLLED AA2219 ALUMINUM ALLOY JOINTS
Authors: BABU K. KAMAL , PANNEERSELVAM K. , SATHIYA P. , HAQ A. NOORUL , SUNDARRAJAN S. , MASTANAIAH P. , MURTHY C. V. SRINIVASA
Published: May 2016

In this paper, experimental investigation on cryorolled aluminum AA2219-T87 plate by using friction stir welding (FSW) process is carried out. AA2219-T87 plates with a size of 200[Formula: see text]100[Formula: see text]22.4 mm were rolled and reduced to 12.2[Formula: see text]mm thickness (more than 45% of reduction in total thickness of the base material) at cryogenic temperature (operating temperature range [Formula: see text]90–[Formula: see text]30[Formula: see text]C). The cryorolled (CR) plates have reduced grain size, improved hardness and increased corrosion resistance property compared with the uncryorolled AA2219-T87 plates. FSW joints of cryorolled AA2219-T87 plates were prepared using cylindrical threaded FSW tool pin profile. Mechanical and metallurgical behaviors of friction stir welded joints were analyzed and the effects of the FSW process parameters are discussed in this paper. The variation of microhardness in the FSW joint regions were correlated with the microstructure of FSW joints. Cryorolled plate and FSW joints were tested for corrosion resistance using potentiodynamic polarization test. FSW joints shows better result during the corrosion resistance analysis compared to base AA2219-T87. The X-ray diffraction (XRD) test results showed that fine [Formula: see text]-Al grains with eutectic phase (Al2Cu) were present in the weld nugget (WN). The large clusters of strengthening precipitates were reduced in size and merged with the weld nugget portion.
CHARACTERIZATION OF MOTOR UNIT AT DIFFERENT STRENGTHS WITH MULTI-CHANNEL SURFACE ELECTROMYOGRAPHY
Authors: HE JINBAO , YI XINHUA , LUO ZAIFEI
Published: May 2016

In this study, specific changes in electromyographic characteristics of individual motor units (MUs) associated with different muscle contraction forces are investigated using multi-channel surface electromyography (SEMG). The gradient convolution kernel compensation (GCKC) algorithm is employed to separate individual MUs from their surface interferential electromyography (EMG) signals and provide the discharge instants, which is later used in the spike-triggered averaging (STA) techniques to obtain the complete waveform. The method was tested on experimental SEMG signals acquired during constant force contractions of biceps brachii muscles in five subjects. Electromyographic characteristics including the recruitment number, waveform amplitude, discharge pattern and innervation zone (IZ) are studied. Results show that changes in the action potential of single MU with different contraction force levels are consistent with those for all MUs, and that the amplitude of MU action potentials (MUAPs) provides a useful estimate of the muscle contraction forces.
Geological structure of the northern part of the Eastern Black Sea from regional seismic reflection data including the DOBRE-2 CDP profile
Authors: Sydorenko G. , Stephenson R. , Yegorova T. , Starostenko V. , Tolkunov A. , Janik T. , Majdanski M. , Voitsitskiy Z. , Rusakov O. , Omelchenko V.
Published: May 2016

The margin of the northeastern Black Sea is formed by the Crimea and Kerch peninsulas, which separate it from the Azov Sea to the north. The age and architecture of the sedimentary successions in this area are described from exploration reflection seismic profiling acquired in the area, in addition to the regional DOBRE-2 CDP profile acquired in 2007. The sediments range in age from Mesozoic to Quaternary and can be divided into five seismo-stratigraphic complexes linked to the tectono-sedimentological evolution of the area. The present regional basin architecture consists of a series of basement structural highs separating a series of sedimentary depocentres and is mainly a consequence of the compressional tectonic regime affecting the area since the Eocene. This has focused shortening deformation and uplift along the axis of the Crimea–Caucasus Inversion Zone on the Kerch Peninsula and Kerch Shelf of the Black Sea. Two major sedimentary basins that mainly formed during this time – the Sorokin Trough in the Black Sea and the Indolo-Kuban Trough to the north of the Kerch Peninsula in the Azov Sea – formed as marginal troughs to the main inversion zone.
The value of fieldwork in making connections between onshore outcrops and offshore models: an example from India
Authors: Racey Andy , Fisher John , Bailey Haydon , Roy Sandip Kumar
Published: May 2016

Fieldwork provides an efficient and economical way of obtaining genuine geological data that can be used to constrain, test and develop exploration models in frontier areas. This study of the Cretaceous outcrops of NW India has been used to characterize models for petroleum systems postulated to have developed beneath the Deccan volcanic sequence, offshore western India, where well data are not available. To date, exploration of ‘sub-Deccan plays’ has mainly been limited to the NW, where the presence of a working Cretaceous petroleum system has been proven in the offshore Kutch Basin.

A revised chronostratigraphic framework has been defined for the Cretaceous section as a result of new biostratigraphic data collected during this study and a thorough revision of existing palaeontological data. The revised framework, together with lithofacies observations from the field, has provided a basis for regional sequence stratigraphic correlation, which has been used to link data from onshore outcrops to models of offshore petroleum systems.

A Lower Cretaceous clastic package that, in part, corresponds to the Lower Goru and Bhuj Formation reservoirs of the Indus Basin of Pakistan and the Kutch Basin in India has been correlated across the region. Towards the top of this package, a transition from fluvial to shallow-marine sedimentation marks the onset of a marine transgression that reaches its peak in the Turonian. Marly limestones and claystones associated with this regionally mapped event are a potential topseal to the Lower Cretaceous clastic package. Geochemical evaluation of several outcrop locations has identified potential source-prone facies that, if present downdip in the offshore, may provide a mechanism for charging a pre-Deccan play.
Physical key extraction attacks on PCs
Authors: Genkin Daniel , Pachmanov Lev , Pipman Itamar , Shamir Adi , Tromer Eran
Published: May 2016

Computers broadcast their secrets via inadvertent physical emanations that are easily measured and exploited.
Nine things I didn't know I would learn being an engineer manager
Authors: Matsudaira Kate
Published: May 2016

Many of the skills aren't technical at all.
The flame graph
Authors: Gregg Brendan
Published: May 2016

This visualization of software execution is a new necessity for performance profiling and debugging.
The solution to AI, what real researchers do, and expectations for CS classrooms
Authors: Langford John , Meyer Bertrand , Guzdial Mark
Published: May 2016

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

John Langford on AlphaGo, Bertrand Meyer on Research as Research, and Mark Guzdial on correlating CS classes with laboratory results.
Body Size Evolution Across the Geozoic
Authors: Smith Felisa A. , Payne Jonathan L. , Heim Noel A. , Balk Meghan A. , Finnegan Seth , Kowalewski Michał , Lyons S. Kathleen , McClain Craig R. , McShea Daniel W. , Novack-Gottshall Philip M. , Anich Paula Spaeth , Wang Steve C.
Published: May 2016

The Geozoic encompasses the 3.6 Ga interval in Earth history when life has existed. Over this time, life has diversified from exclusively tiny, single-celled organisms to include large, complex multicellular forms. Just how and why this diversification occurred has been a major area of interest for paleontologists and evolutionary biologists for centuries. Here, we compile data on organism size throughout the Geozoic fossil record for the three domains of life. We describe canonical trends in the evolution of body size, synthesize current understanding of the patterns and causal mechanisms at various hierarchical scales, and discuss the biological and geological consequences of variation in organismal size.
Mass Fractionation Laws, Mass-Independent Effects, and Isotopic Anomalies
Authors: Dauphas Nicolas , Schauble Edwin A.
Published: May 2016

Isotopic variations usually follow mass-dependent fractionation, meaning that the relative variations in isotopic ratios scale with the difference in mass of the isotopes involved (e.g., δ17O ≈ 0.5×δ18O). In detail, however, the mass dependence of isotopic variations is not always the same, and different natural processes can define distinct slopes in three-isotope diagrams. These variations are subtle, but improvements in analytical capabilities now allow precise measurement of these effects and make it possible to draw inferences about the natural processes that caused them (e.g., reaction kinetics versus equilibrium isotope exchange). Some elements, in some sample types, do not conform to the regularities of mass-dependent fractionation. Oxygen and sulfur display a rich phenomenology of mass-independent fractionation, documented in the laboratory, in the rock record, and in the modern atmosphere. Oxygen in meteorites shows isotopic variations that follow a slope-one line (δ17O ≈ δ18O) whose origin may be associated with CO photodissociation. Sulfur mass-independent fractionation in ancient sediments provides the tightest constraint on the oxygen partial pressure in the Archean and the timing of Earth's surface oxygenation. Heavier elements also show departures from mass fractionation that can be ascribed to exotic effects associated with chemical reactions such as magnetic effects (e.g., Hg) or the nuclear field shift effect (e.g., U or Tl). Some isotopic variations in meteorites and their constituents cannot be related to the terrestrial composition by any known process, including radiogenic, nucleogenic, and cosmogenic effects. Those variations have a nucleosynthetic origin, reflecting the fact that the products of stellar nucleosynthesis were not fully homogenized when the Solar System formed. Those anomalies are found at all scales, from nanometer-sized presolar grains to bulk terrestrial planets. They can be used to learn about stellar nucleosynthesis, mixing in the solar nebula, and genetic relationships between planetary bodies (e.g., the origin of the Moon). They can also confound interpretations based on dating techniques (e.g., 146Sm-142Nd) when they are misidentified as isotopic variations of radiogenic origin. To summarize, there is a world to explore outside of mass-dependent fractionation whose impact is promised to expand as analytical capabilities to measure ever-subtler isotopic anomalies on ever-smaller samples continue to improve.
Evolution of Oxygenic Photosynthesis
Authors: Fischer Woodward W. , Hemp James , Johnson Jena E.
Published: May 2016

The origin of oxygenic photosynthesis was the most important metabolic innovation in Earth history. It allowed life to generate energy and reducing power directly from sunlight and water, freeing it from the limited resources of geochemically derived reductants. This greatly increased global primary productivity and restructured ecosystems. The release of O2as an end product of water oxidation led to the rise of oxygen, which dramatically altered the redox state of Earth's atmosphere and oceans and permanently changed all major biogeochemical cycles. Furthermore, the biological availability of O2allowed for the evolution of aerobic respiration and novel biosynthetic pathways, facilitating much of the richness we associate with modern biology, including complex multicellularity. Here we critically review and synthesize information from the geological and biological records for the origin and evolution of oxygenic photosynthesis. Data from both of these archives illustrate that this metabolism first appeared in early Paleoproterozoic time and, despite its biogeochemical prominence, is a relatively late invention in the context of our planet's history.
Inflow Turbulence Generation Methods
Authors: Wu Xiaohua
Published: May 2016

Research activities on inflow turbulence generation methods have been vigorous over the past quarter century, accompanying advances in eddy-resolving computations of spatially developing turbulent flows with direct numerical simulation, large-eddy simulation (LES), and hybrid Reynolds-averaged Navier-Stokes–LES. The weak recycling method, rooted in scaling arguments on the canonical incompressible boundary layer, has been applied to supersonic boundary layer, rough surface boundary layer, and microscale urban canopy LES coupled with mesoscale numerical weather forecasting. Synthetic methods, originating from analytical approximation to homogeneous isotropic turbulence, have branched out into several robust methods, including the synthetic random Fourier method, synthetic digital filtering method, synthetic coherent eddy method, and synthetic volume forcing method. This article reviews major progress in inflow turbulence generation methods with an emphasis on fundamental ideas, key milestones, representative applications, and critical issues. Directions for future research in the field are also highlighted.
Characterizing Localized Surface Plasmons Using Electron Energy-Loss Spectroscopy
Authors: Cherqui Charles , Thakkar Niket , Li Guoliang , Camden Jon P. , Masiello David J.
Published: May 2016

Electron energy-loss spectroscopy (EELS) offers a window to view nanoscale properties and processes. When performed in a scanning transmission electron microscope, EELS can simultaneously render images of nanoscale objects with subnanometer spatial resolution and correlate them with spectroscopic information at a spectral resolution of ∼10–100 meV. Consequently, EELS is a near-perfect tool for understanding the optical and electronic properties of individual plasmonic metal nanoparticles and few-nanoparticle assemblies, which are significant in a wide range of fields. This review presents an overview of basic plasmonics and EELS theory and highlights several recent noteworthy experiments involving the interrogation of plasmonic metal nanoparticle systems using electron beams.
Water-Mediated Hydrophobic Interactions
Authors: Ben-Amotz Dor
Published: May 2016

Hydrophobic interactions are driven by the combined influence of the direct attraction between oily solutes and an additional water-mediated interaction whose magnitude (and sign) depends sensitively on both solute size and attraction. The resulting delicate balance can lead to a slightly repulsive water-mediated interaction that drives oily molecules apart rather than pushing them together and thus opposes their direct (van der Waals) attraction for each other. As a consequence, competing solute size-dependent crossovers weaken hydrophobic interactions sufficiently that they are only expected to significantly exceed random thermal energy fluctuations for processes that bury more than ∼1 nm2of water-exposed area.
Root Border Cells and Their Role in Plant Defense
Authors: Hawes Martha , Allen Caitilyn , Turgeon B. Gillian , Curlango-Rivera Gilberto , Minh Tran Tuan , Huskey David A. , Xiong Zhongguo
Published: May 2016

Root border cells separate from plant root tips and disperse into the soil environment. In most species, each root tip can produce thousands of metabolically active cells daily, with specialized patterns of gene expression. Their function has been an enduring mystery. Recent studies suggest that border cells operate in a manner similar to mammalian neutrophils: Both cell types export a complex of extracellular DNA (exDNA) and antimicrobial proteins that neutralize threats by trapping pathogens and thereby preventing invasion of host tissues. Extracellular DNases (exDNases) of pathogens promote virulence and systemic spread of the microbes. In plants, adding DNase I to root tips eliminates border cell extracellular traps and abolishes root tip resistance to infection. Mutation of genes encoding exDNase activity in plant-pathogenic bacteria (Ralstonia solanacearum) and fungi (Cochliobolus heterostrophus) results in reduced virulence. The study of exDNase activities in plant pathogens may yield new targets for disease control.
Socio-Genomic Research Using Genome-Wide Molecular Data
Authors: Conley Dalton
Published: May 2016

Recent advances in molecular genetics have provided social scientists with new tools with which to explore human behavior. By deploying genomic analysis, we can now explore long-term patterns of human migration and mating, explore the biological aspects of important sociological outcomes such as educational attainment, and, most importantly, model gene-by-environment interaction effects. The intuition motivating much socio-genomic research is that to have a more complete understanding of social life, scholars must take into consideration both nature and nurture as well as their interplay. Most promising is gene-by-environment research that deploys polygenic measures of genotype as a prism through which to refract and detect heterogenous treatment effects of plausibly exogenous environmental influences. This article reviews much recent work in this vein and argues for a broader integration of genomic data into social inquiry.
The Socioeconomic, Demographic, and Political Effects of Housing in Comparative Perspective
Authors: Zavisca Jane R. , Gerber Theodore P.
Published: May 2016

Few sociologists treat housing as a key independent variable, despite the emergence of disparate bodies of research analyzing how housing affects outcomes that traditionally interest sociologists. Scholars across the social sciences have proposed and tested mechanisms whereby housing could shape subjective well-being, socioeconomic status, demography, and politics. We review the evidence for causal effects across these domains. Next, we make recommendations for research designs to advance this literature. Most studies only test effects of homeownership, and most are focused on the United States and Western Europe. The evidence for causation is often weak, although studies increasingly employ complex techniques for identifying effects. Throughout, we emphasize studies beyond the United States, and we conclude by discussing distinctive insights yielded by comparative research. We advocate for a comparative perspective and more expansive conceptualization of housing status as a means to build theory and evidence regarding the conditions under which housing exerts effects.
The Vascular Endothelial Growth Factors-Expressing Character of Mesenchymal Stem Cells Plays a Positive Role in Treatment of Acute Lung InjuryIn Vivo
Authors: Yang Yi , Hu Shuling , Xu Xiuping , Li Jinze , Liu Airan , Han Jibin , Liu Songqiao , Liu Ling , Qiu Haibo
Published: May 2016

Recently, mesenchymal stem cells (MSC) have been proved to be beneficial in acute respiratory distress syndrome (ARDS). Vascular endothelial growth factor (VEGF) is an important angiogenesis factor that MSC release. However, the precise role of VEGF-expressing character of MSC in the MSC treatment for ARDS remains obscure. Here, we firstly knocked down the gene VEGF in MSC (MSC-ShVEGF) with lentiviral transduction. Then we injected the MSC-ShVEGF to rats with lipopolysaccharide-induced acute lung injury (ALI) via the tail vein. Data showed that MSC transplantation significantly increased VEGF levels in the lung, reduced lung permeability, protected lung endothelium from apoptosis, facilitated VE-cadherin recovery, controlled inflammation, and attenuated lung injury. However, VEGF gene knockdown in MSC led to relatively insufficient VEGF expression in the injured lung and significantly diminished the therapeutic effects of MSC on ALI, suggesting an important role of VEGF-expressing behavior of MSC in the maintenance of VEGF in the lung and the MSC treatment for ALI. Hence, we conclude that MSC restores the lung permeability and attenuates lung injury in rats with ALI in part by maintaining a “sufficient” VEGF level in the lung and the VEGF-expressing character of MSC plays a positive role in the therapeutic effects of MSC on ARDS.
Mitochondria‐Targeted Antioxidants: Future Perspectives in Kidney Ischemia Reperfusion Injury
Authors: Kezic Aleksandra , Spasojevic Ivan , Lezaic Visnja , Bajcetic Milica
Published: May 2016

Kidney ischemia/reperfusion injury emerges in various clinical settings as a great problem complicating the course and outcome. Ischemia/reperfusion injury is still an unsolved puzzle with a great diversity of investigational approaches, putting the focus on oxidative stress and mitochondria. Mitochondria are both sources and targets of ROS. They participate in initiation and progression of kidney ischemia/reperfusion injury linking oxidative stress, inflammation, and cell death. The dependence of kidney proximal tubule cells on oxidative mitochondrial metabolism makes them particularly prone to harmful effects of mitochondrial damage. The administration of antioxidants has been used as a way to prevent and treat kidney ischemia/reperfusion injury for a long time. Recently a new method based on mitochondria‐targeted antioxidants has become the focus of interest. Here we review the current status of results achieved in numerous studies investigating these novel compounds in ischemia/reperfusion injury which specifically target mitochondria such as MitoQ, Szeto‐Schiller (SS) peptides (Bendavia), SkQ1 and SkQR1, and superoxide dismutase mimics. Based on the favorable results obtained in the studies that have examined myocardial ischemia/reperfusion injury, ongoing clinical trials investigate the efficacy of some novel therapeutics in preventing myocardial infarct. This also implies future strategies in preventing kidney ischemia/reperfusion injury.