bluuebunny/crossref_metadata_2025 huggingface dataset:
Inventory of Personal Factors Influencing Conditioned Pain Modulation in Healthy People: A Systematic Literature Review
Authors: Hermans Linda , Van Oosterwijck Jessica , Goubert Dorien , Goudman Lisa , Crombez Geert , Calders Patrick , Meeus Mira
Published: May 2015

Background

Conditioned pain modulation (CPM) is believed to play an important role in the development and exacerbation of chronic pain, because dysfunction of CPM is associated with a shift in balance between pain facilitation and pain inhibition. In many patients with central sensitization, CPM is less efficacious. Besides that, efficacy of CPM is highly variable in healthy people. Consequently, it seems that several individual variables may influence CPM. A systematic review examining personal factors influencing CPM was conducted.

Methods

This systematic review follows the PRISMA guidelines. “Pubmed” and “Web of Science” were searched using different synonyms of CPM. Full‐text clinical reports addressing the influence of personal factors on CPM in healthy adults were included. Checklists for RCTs and case–control studies provided by the Dutch Institute for Healthcare Improvement (CBO) and the Dutch Cochrane Centre were utilized to assess methodological quality. Levels of evidence and strength of conclusion were assigned using the CBO guidelines.

Results

Forty‐six articles were identified that reported the influence of personal factors on CPM. Quality assessment revealed 10 studies with a methodological quality less than 50% wherefore they were excluded (21.8%), resulting in a general total methodological quality score of 72.5%. Overall younger adult age, male gender, ovulatory phase, positive expectations, attention to the conditioning stimulus, and carrier of the 5‐HTTLPR long allele result in better CPM.

Conclusion

It is advised for future studies to take these factors into account. Further research regarding the influence of oral contraceptives, catastrophizing, information about conditioning stimulation, distraction, physical activity, and genetics on CPM magnitude is required.
Impact of Threat Level, Task Instruction, and Individual Characteristics on Cold Pressor Pain and Fear among Children and Their Parents
Authors: Boerner Katelynn E. , Noel Melanie , Birnie Kathryn A. , Caes Line , Petter Mark , Chambers Christine T.
Published: May 2015

The cold pressor task (CPT) is increasingly used to induce experimental pain in children, but the specific methodology of the CPT is quite variable across pediatric studies. This study examined how subtle variations in CPT methodology (eg. provision of low‐ or high‐threat information regarding the task; provision or omission of maximum immersion time) may influence children's and parents' perceptions of the pain experience. Forty‐eight children (8 to 14 years) and their parents were randomly assigned to receive information about the CPT that varied on 2 dimensions, prior to completing the task: (i) threat level: high‐threat (task described as very painful, high pain expressions depicted) or low‐threat (standard CPT instructions provided, low pain expressions depicted); (ii) ceiling: informed (provided maximum immersion time) or uninformed (information about maximum immersion time omitted). Parents and children in the high‐threat condition expected greater child pain, and these children reported higher perceived threat of pain and state pain catastrophizing. For children in the low‐threat condition, an informed ceiling was associated with less state pain catastrophizing during the CPT. Pain intensity, tolerance, and fear during the CPT did not differ by experimental group, but were predicted by child characteristics. Findings suggest that provision of threatening information may impact anticipatory outcomes, but experienced pain was better explained by individual child variables.
Fentanyl Buccal Tablet: A New Breakthrough Pain Medication in Early Management of Severe Vaso‐Occlusive Crisis in Sickle Cell Disease
Authors: De Franceschi Lucia , Mura Paolo , Schweiger Vittorio , Vencato Elisa , Quaglia Francesca Maria , Delmonte Letizia , Evangelista Maurizio , Polati Enrico , Olivieri Oliviero , Finco Gabriele
Published: May 2015

Background

Sickle cell disease (SCD) is a worldwide distributed hereditary red cell disorder. The principal clinical manifestations of SCD are the chronic hemolytic anemia and the acute vaso‐occlusive crisis (VOCs), which are mainly characterized by ischemic/reperfusion tissue injury. Pain is the main symptom of VOCs, and its management is still a challenge for hematologists, requiring a multidisciplinary approach.

Methods

We carried out a crossover study on adult SCD patients, who received two different types of multimodal analgesia during two separate severe VOCs with time interval between VOCs of at least 6 months. The first VOC episode was treated with ketorolac (0.86 mg/kg/day) and tramadol (7.2 mg/kg/day) (TK treatment). In the second VOC episode, fentanyl buccal tablet (FBT; 100 μg) was introduced in a single dose after three hours from the beginning of TK analgesia (TKF treatment). We focused on the first 24 hours of acute pain management. The primary efficacy measure was the time‐weighted‐sum of pain intensity differences (SPID24). The secondary efficacy measures included the pain intensity difference (PID), the total pain relief (TOTPAR), and the time‐wighted sum of anxiety (SAID24).

Results

SPID24 was significantly higher in TKF than in TK treatment. All the secondary measures were significantly ameliorated in TKF compared to TK treatment, without major opioid side effects. Patients satisfaction was higher with TKF treatment than with TK one.

Conclusions

We propose that VOCs might require breakthrough pain drug strategy as vaso‐occlusive phenomena and enhanced vasoconstriction promoting acute ischemic pain component exacerbate the continuous pain of VOCs. FBT might be a powerful and feasible tool in early management of acute pain during VOCs in emergency departments.
Multiplexed, targeted gene editing in Nicotiana benthamiana for glyco‐engineering and monoclonal antibody production
Authors: Li Jin , Stoddard Thomas J. , Demorest Zachary L. , Lavoie Pierre‐Olivier , Luo Song , Clasen Benjamin M. , Cedrone Frederic , Ray Erin E. , Coffman Andrew P. , Daulhac Aurelie , Yabandith Ann , Retterath Adam J. , Mathis Luc , Voytas Daniel F. , D'Aoust Marc‐André , Zhang Feng
Published: May 2015

Biopharmaceutical glycoproteins produced in plants carry N‐glycans with plant‐specific residues core α(1,3)‐fucose and β(1,2)‐xylose, which can significantly impact the activity, stability and immunogenicity of biopharmaceuticals. In this study, we have employed sequence‐specific transcription activator‐like effector nucleases (TALENs) to knock out two α(1,3)‐fucosyltransferase (FucT) and the two β(1,2)‐xylosyltransferase (XylT) genes within Nicotiana benthamiana to generate plants with improved capacity to produce glycoproteins devoid of plant‐specific residues. Among plants regenerated from N. benthamiana protoplasts transformed with TALENs targeting either the FucT or XylT genes, 50% (80 of 160) and 73% (94 of 129) had mutations in at least one FucT or XylT allele, respectively. Among plants regenerated from protoplasts transformed with both TALEN pairs, 17% (18 of 105) had mutations in all four gene targets, and 3% (3 of 105) plants had mutations in all eight alleles comprising both gene families; these mutations were transmitted to the next generation. Endogenous proteins expressed in the complete knockout line had N‐glycans that lacked β(1,2)‐xylose and had a significant reduction in core α(1,3)‐fucose levels (40% of wild type). A similar phenotype was observed in the N‐glycans of a recombinant rituximab antibody transiently expressed in the homozygous mutant plants. More importantly, the most desirable glycoform, one lacking both core α(1,3)‐fucose and β(1,2)‐xylose residues, increased in the antibody from 2% when produced in the wild‐type line to 55% in the mutant line. These results demonstrate the power of TALENs for multiplexed gene editing. Furthermore, the mutant N. benthamiana lines provide a valuable platform for producing highly potent biopharmaceutical products.
Schizophrenia in 2020: Trends in diagnosis and therapy
Authors: Gaebel Wolfgang , Zielasek Jürgen
Published: May 2015

Schizophrenia research is providing an increasing number of studies and important insights into the condition's etiopathogenesis based on genetic, neuropsychological and cranial neuroimaging studies. However, research progress has not yet led to the incorporation of such findings into the revised classification criteria of mental disorders or everyday clinical practice. By 2020, schizophrenia will most likely still be a clinically defined primary psychotic disorder. While there is some hope that treatment will be improved with new antipsychotic drugs, drugs addressing negative symptoms, more refined psychotherapy approaches and the introduction of new treatment modalities like transcranial magnetic stimulation, an additional hope is to improve early detection and prevention. As the results of new research into the etiopathogenesis of schizophrenia are promising to improve diagnosis, classification and therapy in the future, a picture of complex brain dysfunction is currently emerging requiring sophisticated mathematical methods of analysis. The imminent clinical challenge will be to develop comprehensive diagnostic and treatment modules individually tailored to the time‐variable needs of patients and their families.
Overexpression of GsGSTU13 and SCMRP in Medicago sativa confers increased salt–alkaline tolerance and methionine content
Authors: Jia Bowei , Sun Mingzhe , Sun Xiaoli , Li Rongtian , Wang Zhenyu , Wu Jing , Wei Zhengwei , DuanMu Huizi , Xiao Jialei , Zhu Yanming
Published: May 2015

Tau‐class glutathione S‐transferases (GSTUs) are ubiquitous proteins encoded by a large gene family in plants, which play important roles in combating different environmental stresses. In previous studies, we constructed a Glycine soja transcriptional profile, and identified three GSTUs (GsGSTU13, GsGSTU14 and GsGSTU19) as potential salt–alkaline stress‐responsive genes. Two of them, GsGSTU14 and GsGSTU19, have been shown to positively regulate plant salt–alkaline tolerance. In this study, we further demonstrated the positive function of GsGSTU13 in plant salt–alkaline stress responses by overexpressing it in Medicago sativa. Stress tolerance tests suggested that GsGSTU13 transgenic lines showed better growth and physiological indicators than wild alfalfa (cv. Zhaodong) under alkaline stress. Considering the shortage of methionine in alfalfa, we then co‐transformed GsGSTU13 into two main alfalfa cultivars in Heilongjiang Province (cv. Zhaodong and cv. Nongjing No. 1) together with SCMRP, a synthesized gene that could improve the methionine content. We found that GsGSTU13/SCMRP transgenic alfalfa displayed not only higher methionine content but also higher tolerance to alkaline and salt stresses, respectively. Taken together, our results demonstrate that GsGSTU13 acts as a positive regulator in plant responses to salt and alkaline stresses, and can be used as a good candidate for generation of salt–alkaline tolerant crops.
Changes in the current classification of IIP: A critical review
Authors: Neurohr Claus , Behr Juergen
Published: May 2015

Idiopathic interstitial pneumonias (IIP) are a heterogeneous group characterized by unknown aetiology. Establishment of a correct diagnosis of a distinct IIP requires a multidisciplinary approach integrating clinical presentation, physiological data, radiological appearance and histological findings. The 2013 update of the American Thoracic Society/European Respiratory Society classification summarises progress in the field of IIP and outlines potential areas for future research. The main entities defined by the 2002 statement on IIP are preserved, but major IIP are now distinguished from rare IIP and the new category of unclassifiable IIP is introduced. In addition, the existence of idiopathic non‐specific interstitial pneumonia as a separate chronic fibrosing IIP and idiopathic pleuroparenchymal fibroelastosis as a specific rare entity are acknowledged. Moreover, the major IIP are categorized according to the features chronic fibrosing, smoking‐related and acute/subacute clinical course. Furthermore, a clinical classification of IIP according to disease behaviour with suggestions for treatment goals and monitoring strategies is provided. The goal of this review is to discuss the areas of uncertainty in the updated multidisciplinary classification of IIP and point out potential consequences for clinical management.
Effects of chymostatin, a chymase inhibitor, on blood pressure, plasma and tissue angiotensin II, renal haemodynamics and renal excretion in two models of hypertension in the rat
Authors: Roszkowska‐Chojecka Malwina Monika , Walkowska Agnieszka , Gawryś Olga , Baranowska Iwona , Kalisz Małgorzata , Litwiniuk Anna , Martyńska Lidia , Kompanowska‐Jezierska Elżbieta
Published: May 2015

New Findings

What is the central question of this study?

We examined, in hypertensive rats, whether the angiotensin‐converting enzyme‐independent enzymes generating angiotensin II in the tissues modulate blood pressure, peripheral circulation and renal function.

What is the main finding and its importance?

The results suggest that chymostatin‐sensitive enzymes diminish vascular tone in renal and extrarenal vascular beds. Chymase or similar chymostatin‐sensitive enzymes have a significant role in the synthesis of angiotensin II in different tissues but do not control blood pressure in the short term, similarly in salt‐dependent or Goldblatt‐type rat hypertension. In salt‐dependent hypertension, chymase blockade protected renal outer medullary perfusion, probably by reducing the angiotensin II content in the kidney.

Chymase is presumed to be a crucial enzyme of the non‐angiotensin‐converting enzyme pathway of angiotensin II (Ang II) generation in tissues, a process involved in vascular remodelling and development of hypertension. We examined the role of chymase in hypertension induced by exposure of uninephrectomized rats to high dietary salt intake (UNX HS) and in the Goldblatt renal artery stenosis (two‐kidney, one‐clip) model. In acute experiments with anaesthetized rats of either model, chymostatin at 2 mg kg−1 h−1 or 0.05% DMSO solvent was infused i.v. Mean arterial blood pressure, heart rate, iliac blood flow (a measure of hindlimb perfusion), total renal blood flow and intrarenal regional perfusion (laser‐Doppler technique) were measured continuously, along with the glomerular filtration rate and renal excretion. In both models, chymase blockade distinctly decreased plasma and tissue Ang II without lowering mean blood pressure or consistently altering the other functional parameters measured. Unexpectedly, in Goldblatt hypertensive rats the blockade increased the renal and hindlimb vascular resistances by 51 and 33%, respectively (P < 0.05). In UNX HS hypertensive rats, chymase blockade abolished the solvent‐induced decrease in outer medullary blood flow. We conclude that chymase or similar chymostatin‐sensitive enzyme(s) has a significant role in the synthesis of Ang II in different tissues but does not participate in short‐term control of blood pressure in salt‐dependent or Goldblatt‐type rat hypertension. In the Goldblatt model, chymase appeared to reduce the renal and hindlimb vascular resistances by an unknown mechanism. In salt‐dependent hypertension, chymase blockade protected renal outer medullary perfusion, probably by reducing Ang II content in the kidney.
The Effects of Frontal- and Sagittal-Plane Plyometrics on Change-of-Direction Speed and Power in Adolescent Female Basketball Players
Authors: McCormick Brian T. , Hannon James C. , Newton Maria , Shultz Barry , Detling Nicole , Young Warren B.
Published: May 2015

Plyometrics is a popular training modality for basketball players to improve power and change-of-direction speed. Most plyometric training has used sagittal-plane exercises, but improvements in change-of-direction speed have been greater in multidirection programs.

Purpose:

To determine the benefits of a 6-wk frontal-plane plyometric (FPP) training program compared with a 6-wk sagittal-plane plyometric (SPP) training program with regard to power and change-of-direction speed.

Methods:

Fourteen female varsity high school basketball players participated in the study. Multiple 2 × 2 repeated-measures ANOVAs were used to determine differences for the FPP and SPP groups from preintervention to postintervention on 4 tests of power and 2 tests of change-of-direction speed.

Results:

There was a group main effect for time in all 6 tests. There was a significant group × time interaction effect in 3 of the 6 tests. The SPP improved performance of the countermovement vertical jump more than the FPP, whereas the FPP improved performance of the lateral hop (left) and lateral-shuffle test (left) more than the SPP. The standing long jump, lateral hop (right), and lateral-shuffle test (right) did not show a significant interaction effect.

Conclusions:

These results suggest that basketball players should incorporate plyometric training in all planes to improve power and change-of-direction speed.
Establishing Duration-Specific Running Intensities From Match-Play Analysis in Rugby League
Authors: Delaney Jace A. , Scott Tannath J. , Thornton Heidi R. , Bennett Kyle J.M. , Gay David , Duthie Grant M. , Dascombe Ben J.
Published: May 2015

Rugby league coaches often prescribe training to replicate the demands of competition. The intensities of running drills are often monitored in comparison with absolute match-play measures. Such measures may not be sensitive enough to detect fluctuations in intensity across a match or to differentiate between positions.

Purpose:

To determine the position- and duration-specific running intensities of rugby league competition, using a moving-average method, for the prescription and monitoring of training.

Methods:

Data from a 15-Hz global positioning system (GPS) were collected from 32 professional rugby league players across a season. The velocity–time curve was analyzed using a rolling-average method, where maximum values were calculated for 10 different durations, 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 min, for each player across each match.

Results:

There were large differences between the 1- and 2-min rolling averages and all other rolling-average durations. Smaller differences were observed for rolling averages of greater duration. Fullbacks maintained a greater velocity than outside backs and middle and edge forwards over the 1- and 2-min rolling averages (ES 0.8−1.2, P < .05). For rolling averages 3 min and greater, the running demands of the fullbacks were greater than those of the middle forwards and outside backs (ES 1.1−1.4, P < .05).

Conclusions:

These findings suggest that the running demands of rugby league fluctuate vastly across a match. Fullbacks were the only position to exhibit a greater running intensity than any other position, and therefore training prescription should reflect this.
The Impact of 3 Different-Length Between-Matches Microcycles on Training Loads in Professional Rugby League Players
Authors: Moreira Alexandre , Kempton Tom , Aoki Marcelo Saldanha , Sirotic Anita C. , Coutts Aaron J.
Published: May 2015

Purpose:

To examine the impact of varying between-matches microcycles on training characteristics (ie, intensity, duration, and load) in professional rugby league players and to report on match load related to these between-matches microcycles.

Methods:

Training-load data were collected during a 26-wk competition period of an entire season. Training load was measured using the session rating of perceived exertion (session-RPE) method for every training session and match from 44 professional rugby league players from the same National Rugby League team. Using the category-ratio 10 RPE scale, the training intensity was divided into 3 zones (low <4 AU, moderate ≥4-≤7 AU, and high >7 AU). Three different-length between-matches recovery microcycles were used for analysis: 5−6 d, 7−8 d, and 9−10 d.

Results:

A total of 3848 individual sessions were recorded. During the shorter-length between-matches microcycles (5−6 d), significantly lower training load was observed. No significant differences for subsequent match load or intensity were identified between the various match recovery periods. Overall, 16% of the training sessions were completed at the low-intensity zone, 61% at the moderate-intensity zone, and 23% at the high-intensity zone.

Conclusions:

The findings demonstrate that rugby league players undertake higher training load as the length of between-matches microcycles is increased. The majority of in-season training of professional rugby league players was at moderate intensity, and a polarized approach to training that has been reported in elite endurance athletes does not occur in professional rugby league.
Regenerating CNS neurons
Authors: Ferrarelli Leslie K.
Published: May 2015

Proteomic analysis reveals that restoring the transcription factor c-Myc to injured CNS neurons promotes their regeneration in mice.
Committing the Oldest Sins in the Newest Kind of Ways—Antibodies Targeting the Influenza Virus Type A Hemagglutinin Globular Head
Authors: Krause Jens C. , Crowe, JR. James E.
Published: May 2015

The globular head of the trimeric influenza hemagglutinin (HA) contains the receptor-binding domain (RBD) and is the target of potently neutralizing human monoclonal antibodies (mAbs) with high
in vivo
activity. In general, these mAbs are induced easily by vaccination, but only infrequently display cross-neutralizing activity against antigenic drift variants or even against HA molecules from viruses of heterologous subtypes. Recently, the atomic resolution structures of several such antibodies in complex with HA have been determined by X-ray crystallography. Not surprisingly, cross-reactive globular head antibodies target, at least partially, the conserved RBD. The cross-reactive potential of such mAbs is limited by contacts of hypervariable HA residues outside the conserved RBD. The RBD of H2 HA seems especially immunogenic. Increasing the immunogenicity of the RBD of other HA subtypes may be a step toward a universal influenza vaccine. The germ line-encoded Phe54 residue of the CDR-H2 of the V
H
1-69 germ line sequence appears to be ideally suited not only to reach into a conserved, hydrophobic pocket on the HA stem, but also to reach into the conserved, hydrophobic pocket that is the RBD. We have cloned antibodies from different individuals that are encoded by the V
H
1-69 germ line gene segment that contact the universally conserved Trp153 on the bottom of the RBD. These antibodies serve as further evidence of antibody genetic sequence convergence across individuals.
Antibodies: Computer-Aided Prediction of Structure and Design of Function
Authors: Sevy Alexander M. , Meiler Jens
Published: May 2015

With the advent of high-throughput sequencing, and the increased availability of experimental structures of antibodies and antibody-antigen complexes, comes the improvement of computational approaches to predict the structure and design the function of antibodies and antibody-antigen complexes. While antibodies pose formidable challenges for protein structure prediction and design due to their large size and highly flexible loops in the complementarity-determining regions, they also offer exciting opportunities: the central importance of antibodies for human health results in a wealth of structural and sequence information that—as a knowledge base—can drive the modeling algorithms by limiting the conformational and sequence search space to likely regions of success. Further, efficient experimental platforms exist to test predicted antibody structure or designed antibody function, thereby leading to an iterative feedback loop between computation and experiment. We briefly review the history of computer-aided prediction of structure and design of function in the antibody field before we focus on recent methodological developments and the most exciting application examples.
Biofilm Development
Authors: Tolker-Nielsen Tim
Published: May 2015

During the past decade we have gained much knowledge about the molecular mechanisms that are involved in initiation and termination of biofilm formation. In many bacteria, these processes appear to occur in response to specific environmental cues and result in, respectively, induction or termination of biofilm matrix production via the second messenger molecule c-di-GMP. In between initiation and termination of biofilm formation we have defined specific biofilm stages, but the currently available evidence suggests that these transitions are mainly governed by adaptive responses, and not by specific genetic programs. It appears that biofilm formation can occur through multiple pathways and that the spatial structure of the biofilms is species dependent as well as dependent on environmental conditions. Bacterial subpopulations, e.g., motile and nonmotile subpopulations, can develop and interact during biofilm formation, and these interactions can affect the structure of the biofilm. The available evidence suggests that biofilm formation is programmed in the sense that regulated synthesis of extracellular matrix components is involved. Furthermore, our current knowledge suggests that biofilm formation mainly is governed by adaptive responses of individual bacteria, although group-level activities are also involved.
Mammalian Endogenous Retroviruses
Authors: Mager Dixie L. , Stoye Jonathan P.
Published: May 2015

Over 40% of mammalian genomes comprise the products of reverse transcription. Among such retrotransposed sequences are those characterized by the presence of long terminal repeats (LTRs), including the endogenous retroviruses (ERVs), which are inherited genetic elements closely resembling the proviruses formed following exogenous retrovirus infection. Sequences derived from ERVs make up at least 8 to 10% of the human and mouse genomes and range from ancient sequences that predate mammalian divergence to elements that are currently still active. In this chapter we describe the discovery, classification and origins of ERVs in mammals and consider cellular mechanisms that have evolved to control their expression. We also discuss the negative effects of ERVs as agents of genetic disease and cancer and review examples of ERV protein domestication to serve host functions, as in placental development. Finally, we address growing evidence that the gene regulatory potential of ERV LTRs has been exploited multiple times during evolution to regulate genes and gene networks. Thus, although recently endogenized retroviral elements are often pathogenic, those that survive the forces of negative selection become neutral components of the host genome or can be harnessed to serve beneficial roles.
The Integration and Excision of CTnDOT
Authors: Wood Margaret M. , Gardner Jeffrey F.
Published: May 2015

Bacteroides
species are one of the most prevalent groups of bacteria present in the human colon. Many strains carry large, integrated elements including integrative and conjugative elements (ICEs). One such ICE is CTnDOT, which is 65 kb in size and encodes resistances to tetracycline and erythromycin. CTnDOT has been increasing in prevalence in
Bacteroides
spp., and is now found in greater than 80% of natural isolates. In recent years, CTnDOT has been implicated in the spread of antibiotic resistance among gut microbiota. Interestingly, the excision and transfer of CTnDOT is stimulated in the presence of tetracycline. The tyrosine recombinase IntDOT catalyzes the integration and excision reactions of CTnDOT. Unlike the well-characterized lambda Int, IntDOT tolerates heterology in the overlap region between the sites of cleavage and strand exchange. IntDOT also appears to have a different arrangement of active site catalytic residues. It is missing one of the arginine residues that is conserved in other tyrosine recombinases. The excision reaction of CTnDOT is complex, involving excision proteins Xis2c, Xis2d, and Exc, as well as IntDOT and a
Bacteroides
host factor. Xis2c and Xis2d are small, basic proteins like other recombination directionality factors (RDFs). Exc is a topoisomerase; however, the topoisomerase function is not required for the excision reaction. Exc has been shown to stimulate excision frequencies when there are mismatches in the overlap regions, suggesting that it may play a role in resolving Holliday junctions (HJs) containing heterology. Work is currently under way to elucidate the complex interactions involved with the formation of the CTnDOT excisive intasomes.
Reverse Transcription of Retroviruses and LTR Retrotransposons
Authors: Hughes Stephen H.
Published: May 2015

The enzyme reverse transcriptase (RT) was discovered in retroviruses almost 50 years ago. The demonstration that other types of viruses, and what are now called retrotransposons, also replicated using an enzyme that could copy RNA into DNA came a few years later. The intensity of the research in both the process of reverse transcription and the enzyme RT was greatly stimulated by the recognition, in the mid-1980s, that human immunodeficiency virus (HIV) was a retrovirus and by the fact that the first successful anti-HIV drug, azidothymidine (AZT), is a substrate for RT. Although AZT monotherapy is a thing of the past, the most commonly prescribed, and most successful, combination therapies still involve one or both of the two major classes of anti-RT drugs. Although the basic mechanics of reverse transcription were worked out many years ago, and the first high-resolution structures of HIV RT are now more than 20 years old, we still have much to learn, particularly about the roles played by the host and viral factors that make the process of reverse transcription much more efficient in the cell than in the test tube. Moreover, we are only now beginning to understand how various host factors that are part of the innate immunity system interact with the process of reverse transcription to protect the host-cell genome, the host cell, and the whole host, from retroviral infection, and from unwanted retrotransposition.
Animal Models for the Pathogenesis, Treatment, and Prevention of Infection byBacillus anthracis
Authors: Welkos Susan , Bozue Joel , Twenhafel Nancy , Cote Christopher
Published: May 2015

This article reviews the characteristics of the major animal models utilized for studies onBacillus anthracisand highlights their contributions to understanding the pathogenesis and host responses to anthrax and its treatment and prevention. Advantages and drawbacks associated with each model, to include the major models (murine, guinea pig, rabbit, nonhuman primate, and rat), and other less frequently utilized models, are discussed. Although the three principal forms of anthrax are addressed, the main focus of this review is on models for inhalational anthrax. The selection of an animal model for study is often not straightforward and is dependent on the specific aims of the research or test. No single animal species provides complete equivalence to humans; however, each species, when used appropriately, can contribute to a more complete understanding of anthrax and its etiologic agent.
Acute myocardial infarction or acute myocarditis? Discharge registry-based study of likelihood and associated features in hospitalised patients
Authors: Kytö Ville , Sipilä Jussi , Rautava Päivi
Published: May 2015

Objective

To evaluate the likelihood of and patient features associated with acute myocardial infarction (AMI) versus acute myocarditis in different population segments.

Design

Nationwide, multihospital observational retrospective registry study of 9.6 years in Finland.

Participants

All consecutive patients aged ≥18 years hospitalised with a primary diagnosis of AMI (n=89 399) or acute myocarditis (n=2131) in 22 hospitals with a coronary catheterisation laboratory.

Primary outcome measures

Likelihood of AMI versus acute myocarditis and associated patient features.

Results

Men were over-represented in patients with AMI (59.8%) and in patients with acute myocarditis (76.1%). Age distributions of AMI and acute myocarditis were opposite as a majority of patients with myocarditis were aged 18–29 years, while the number of patients with AMI increased gradually up to 80 years of age. Patients aged 18–29 years were more likely to have acute myocarditis as the cause of hospitalisation (relative risk (RR)=11.4; 95% CI 7.6 to 16.1 for myocarditis, p<0.0001), but after 30 years of age the likelihood of infarction was higher with exponentially increasing RR for AMI. In youngest patients (18–29 years), the likelihood of AMI was higher in women, but men had higher odds for AMI after 40 years of age. Overall, men had OR of 1.97 (95% CI 1.74 to 2.23, p<0.0001) for AMI versus myocarditis when compared with women. Hypercholesterolaemia, chronic coronary artery disease, diabetes and hypertension predicted AMI in multivariate analysis. Odds for myocarditis were significantly higher if the patient had an otolaryngeal infection (OR 18.13; 95% CI 8.96 to 36.67, p<0.0001).

Conclusions

Acute myocarditis is more common than AMI in hospitalised patients aged 18–29 years, but the risk of AMI increases exponentially thereafter. Hypercholesterolaemia, diabetes and hypertension predict AMI regardless of age and gender.
Synthesis and conformational studies of 9-benzyloxy-18-substituted [3.3]metacyclophanes
Authors: Islam M. Monarul , Hirotsugu Tomiyasu , Matsumoto Taisuke , Tanaka Junji , Yamato Takehiko
Published: May 2015

A series of syn-[3.3]metacyclophanes (MCPs) containing internal substituted benzyloxy group have been synthesized by the modified TosMIC coupling reaction followed by acid treatment and Wolff–Kishner reduction. anti-Mono- and di-benzyloxy[3.3]MCPs are synthesized by O-benzylation of the corresponding hydroxy[3.3]MCPs, which are obtained by demethylation of methoxy[3.3]MCPs with BBr3at room temperature. An interesting and intriguing result was obtained when syn-6,15-di-tert-butyl-9-methoxy-18-methyl[3.3]MCP-2,11-dione was treated with TMSI to afford the formation of a dihydrobenzofuran ring by a nucleophilic intramolecular cyclization reaction. The1H NMR and X-ray analysis of 6a confirms that it adopts a syn (chair–chair) conformation in both solution and solid state.
Intracellular distribution of cadmium during the growth of Abortiporus biennis on cadmium-amended media
Authors: Grąz Marcin , Pawlikowska-Pawlęga Bożena , Jarosz-Wilkołazka Anna
Published: May 2015

Heavy metals are difficult to remediate and traditional remedial processes are expensive, so bioremediation technology using bacteria, fungi, or plants is of interest. Many studies have demonstrated that basidiomycetes fungi are able to growth under heavy metals stress. In this study the distribution of cadmium (Cd) in Abortiporus biennis cells was studied. Cd accumulated especially within cytoplasm and its presence caused changes in the cytoplasm appearance, which became denser in comparison to the cytoplasm of control cells. Vacuolization of cytoplasm and periplasmic region in A. biennis cells was also observed. The growth rate of A. biennis was inhibited up to 75% during the growth on medium amended with 1 mmol/L cadmium oxide. The presence of Cd in growing media inhibited oxalic acid secretion by A. biennis, but oxalate concentration increased together with elevated Cd concentration in growing medium. The influence of initial pH of growing media on the accumulation of Cd by A. biennis was also observed. The highest accumulation of Cd in mycelium was detected during A. biennis growth on media with a pH of 6. Studies addressing metals uptake by fungi and metal distribution in fungal cells may allow these organisms to be applied in bioremediation processes more effectively or to be used as bioindicators of contaminated environmental pollutions.
Phenomenological description of the interior of the Schwarzschild black hole
Authors: Kawai Hikaru , Yokokura Yuki
Published: May 2015

We discuss a sufficiently large four-dimensional Schwarzschild black hole which is in equilibrium with a heat bath. In other words, we consider a black hole which has grown up from a small one in the heat bath adiabatically. We express the metric of the interior of the black hole in terms of two functions: One is the intensity of the Hawking radiation, and the other is the ratio between the radiation energy and the pressure in the radial direction. Especially in the case of conformal matters we check that it is a self-consistent solution of the semiclassical Einstein equation, Gμν = 8πG〈Tμν〉. It is shown that the strength of the Hawking radiation is proportional to the c-coefficient, that is, the coefficient of the square of the Weyl tensor in the four-dimensional Weyl anomaly.
Plane number of links
Authors: Matsuzaki Shosaku
Published: May 2015

Let L = L1 ∪ L2 ∪ ⋯ ∪ Ln be a link in ℝ3 such that Li is a trivial link for each i, 1 ≤ i ≤ n. Let P1, P2,…,Pn be mutually distinct flat planes in ℝ3 such that no two of them are parallel. Then there is a link [Formula: see text] in ℝ3 such that L is ambient isotopic to L′ and [Formula: see text] for each i, 1 ≤ i ≤ n.
Chaotic information processing by extremal black holes
Authors: Axenides Minos , Floratos Emmanuel , Nicolis Stam
Published: May 2015

We review an explicit regularization of the AdS2/CFT1 correspondence, that preserves all isometries of bulk and boundary degrees of freedom. This scheme is useful to characterize the space of the unitary evolution operators that describe the dynamics of the microstates of extremal black holes in four spacetime dimensions. Using techniques from algebraic number theory to evaluate the transition amplitudes, we remark that the regularization scheme expresses the fast quantum computation capability of black holes as well as its chaotic nature.
Studying re-scattering effect in heavy-ion collision through K* production
Authors: Singha Subhash , Mohanty Bedangadas , Lin Zi-Wei
Published: May 2015

We have studied the K* production within a multi-phase transport model (AMPT) for Au + Au collisions at [Formula: see text] to understand the hadronic re-scattering effect on the measured yields of the resonance. The hadronic re-scattering of the K* decay daughter particles (π and K) will alter their momentum distribution thereby making it difficult to reconstruct the K* signal through the invariant mass method. An increased hadronic re-scattering effect thus leads to a decrease in the reconstructed yield of K* in the heavy-ion collisions. Through this simulation study, we argue that a decrease in K*/K ratio with the increase in collision centrality necessarily reflects the hadronic re-scattering effect. Since the re-scattering occurs in the hadronic phase and K* has a lifetime of 4 fm/c, we present a toy model-based discussion on using measured K*/K to put a lower limit on the hadronic phase lifetime in high energy nuclear collisions.
Type-amalgamation properties and polygroupoids in stable theories
Authors: Goodrick John , Kim Byunghan , Kolesnikov Alexei
Published: May 2015

We show that in a stable first-order theory, the failure of higher dimensional type amalgamation can always be witnessed by algebraic structures that we call n-ary polygroupoids. This generalizes a result of Hrushovski in [16] that failures of 4-amalgamation are witnessed by definable groupoids (which correspond to 2-ary polygroupoids in our terminology). The n-ary polygroupoids are definable in a mild expansion of the language (adding a predicate for a Morley sequence).
Time functions revisited
Authors: Fathi Albert
Published: May 2015

In this paper we revisit our joint work with Antonio Siconolfi on time functions. We will give a brief introduction to the subject. We will then show how to construct a Lipschitz time function in a simplified setting. We will end with a new result showing that the Aubry set is not an artifact of our proof of existence of time functions for stably causal manifolds.
Torsional Properties of Boron Nitride Nanocones with Different Cone Heights, Disclination Angles and Simulation Temperatures
Authors: Li Yuan , Tian Yanling , Yang Chengjuan , Cai Kunhai , Zhang Dawei
Published: May 2015

The torsional properties of single-walled boron nitride (BN) nanocones at different cone heights, disclination angles and simulation temperatures have been investigated using molecular dynamics (MD) simulation. The simulation results indicate that the torque and average potential energy decrease with the increasing cone height and disclination angle, and the failure torsion angle increases with the increasing cone height and disclination angle. For different simulation temperatures, the torsional behavior of BN nanocones at higher simulation temperature is more serious and earlier to reach a failure point, the maximum torque and average potential energy of the system decrease with the increasing simulation temperature. For different loading rates, the failure torsion angle decreases with the increasing loading rate, so the fracture of BN nanocone occurred earlier with higher loading rate. Therefore, the cone height, disclination angle, simulation temperature and loading rate are considered to be four main influencing factors for the torsional properties of the BN nanocones.
City-Scale Social Event Detection and Evaluation with Taxi Traces
Authors: Zhang Wangsheng , Qi Guande , Pan Gang , Lu Hua , Li Shijian , Wu Zhaohui
Published: May 2015

A social event is an occurrence that involves lots of people and is accompanied by an obvious rise in human flow. Analysis of social events has real-world importance because events bring about impacts on many aspects of city life. Traditionally, detection and impact measurement of social events rely on social investigation, which involves considerable human effort. Recently, by analyzing messages in social networks, researchers can also detect and evaluate country-scale events. Nevertheless, the analysis of city-scale events has not been explored. In this article, we use human flow dynamics, which reflect the social activeness of a region, to detect social events and measure their impacts. We first extract human flow dynamics from taxi traces. Second, we propose a method that can not only discover the happening time and venue of events from abnormal social activeness, but also measure the scale of events through changes in such activeness. Third, we extract traffic congestion information from traces and use its change during social events to measure their impact. The results of experiments validate the effectiveness of both the event detection and impact measurement methods.
A Small-Footprint Accelerator for Large-Scale Neural Networks
Authors: Chen Tianshi , Zhang Shijin , Liu Shaoli , Du Zidong , Luo Tao , Gao Yuan , Liu Junjie , Wang Dongsheng , Wu Chengyong , Sun Ninghui , Chen Yunji , Temam Olivier
Published: May 2015

Machine-learning tasks are becoming pervasive in a broad range of domains, and in a broad range of systems (from embedded systems to data centers). At the same time, a small set of machine-learning algorithms (especially Convolutional and Deep Neural Networks, i.e., CNNs and DNNs) are proving to be state-of-the-art across many applications. As architectures evolve toward heterogeneous multicores composed of a mix of cores and accelerators, a machine-learning accelerator can achieve the rare combination of efficiency (due to the small number of target algorithms) and broad application scope.

Until now, most machine-learning accelerator designs have been focusing on efficiently implementing the computational part of the algorithms. However, recent state-of-the-art CNNs and DNNs are characterized by their large size. In this study, we design an accelerator for large-scale CNNs and DNNs, with a special emphasis on the impact of memory on accelerator design, performance, and energy.

We show that it is possible to design an accelerator with a high throughput, capable of performing 452 GOP/s (key NN operations such as synaptic weight multiplications and neurons outputs additions) in a small footprint of 3.02mm2 and 485mW; compared to a 128-bit 2GHz SIMD processor, the accelerator is 117.87 × faster, and it can reduce the total energy by 21.08 ×. The accelerator characteristics are obtained after layout at 65nm. Such a high throughput in a small footprint can open up the usage of state-of-the-art machine-learning algorithms in a broad set of systems and for a broad set of applications.
Reliable Cron across the planet
Authors: Davidovič Štěpán , Guliani Kavita
Published: May 2015

… or: How I stopped worrying and learned to love time.
Adaptive Hybrid Compression for Wireless Sensor Networks
Authors: Ali Azad , Khelil Abdelmajid , Suri Neeraj , Mahmudimanesh Mohammadreza
Published: May 2015

Wireless Sensor Networks (WSNs) are often deployed to sample the desired environmental attributes and deliver the acquired samples to a central station, termed as the sink, for processing as needed by the application. Many applications stipulate high granularity and data accuracy that results in high data volumes. However, sensor nodes are battery powered, and sending the requested large amounts of data rapidly depletes their energy. Fortunately, environmental attributes (e.g., temperature, pressure) often exhibit spatial and temporal correlations. Moreover, a large class of applications such as scientific analysis and simulations tolerate high latency for sensor data collection. Hence, we exploit the spatiotemporal correlation of sensor readings while benefiting from possible data delivery latency tolerance to minimize the amount of data to be transported to the sink. Accordingly, we develop a fully distributed adaptive hybrid compression scheme that exploits both spatial and temporal data redundancies and fuses both temporal and spatial compression for maximal data compression with accuracy guarantees. We present two main contributions: (i)
an adaptive modeling technique
that allows frugal and maximized
temporal compression
on resource-constraint sensor nodes by exploiting the data collection latency, and (ii)
a novel model-based hierarchical clustering technique
that allows for maximized
spatial compression
resulting into a hybrid compression scheme. Compared to the existing spatiotemporal compression approaches, our approach is fully decentralized and the proposed clustering scheme is based on sensor data models rather than instantaneous sensor data values, which allows merging nearby nodes with similar models into large clusters over a longer period of time rather than specific time instances. The analysis for computation and message overheads, the analysis for theoretical compressibility, and simulations using real-world data demonstrate that our proposed scheme can provide significant communication/energy savings without sacrificing the accuracy of collected data.
Bringing evidence-based education to CS
Authors: Guzdial Mark
Published: May 2015

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.

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

Mark Guzdial says computer science teachers should use more evidence, less intuition.
Forging relationships
Authors: Savage Neil
Published: May 2015

Michael Stonebraker didn't realize at the outset that it would take six years to create INGRES, one of the world's first relational databases.
Turing lectureThe computer science of concurrency
Authors: Lamport Leslie
Published: May 2015

Leslie Lamport is the recipient of the 2013 ACM A.M. Turing Award.
The cyber education project
Authors: Fitzgerald Sue
Published: May 2015

The Cyber Education Project (CEP) is an initiative to develop undergraduate curriculum guidelines and a case for accreditation for undergraduate degrees in "Cyber Science". The project is supported by a diverse group of computing professionals representing academic institutions, a broad spectrum of industries and several professional societies.