bluuebunny/crossref_metadata_2025 huggingface dataset:
Parasite Proximity Drives the Expansion of Regulatory T Cells in Peyer's Patches following Intestinal Helminth Infection
Authors: Mosconi Ilaria , Dubey Lalit Kumar , Volpe Beatrice , Esser-von Bieren Julia , Zaiss Mario M. , Lebon Luc , Massacand Joanna C. , Harris Nicola L.
Published: July 2015

Helminth infections are typically chronic in nature; however, the exact molecular mechanisms by which these parasites promote or thwart host immunity remain unclear. Worm expulsion requires the differentiation of CD4
+
T cells into Th2 cells, while regulatory T cells (Tregs) act to dampen the extent of the Th2 response. Priming of T cells requires drainage or capture of antigens within lymphoid tissues, and in the case of intestinal helminths, such sites include the mucosa-associated Peyer's patches (PPs) and the draining mesenteric lymph nodes (MLN). To gain insight into when and where the activation of the adaptive T cell response takes place following intestinal helminth infection, we analyzed Th2 and Treg responses in the PPs and MLN following infection with the murine intestinal helminth
Heligmosomoides polygyrus
bakeri
. Protective Th2 responses were observed to be largely restricted to the MLN, while a greater expansion of Tregs occurred within the PPs. Interestingly, those PPs that formed a contact with the parasite showed the greatest degree of Treg expansion and no evidence of type 2 cytokine production, indicating that the parasite may secrete products that act in a local manner to selectively promote Treg expansion. This view was supported by the finding that
H. polygyrus
bakeri
larvae could promote Treg proliferation
in vitro
. Taken together, these data indicate that different degrees of Treg expansion and type 2 cytokine production occur within the PPs and MLN following infection with the intestinal helminth
H. polygyrus
bakeri
and indicate that these organs exhibit differential responses following infection with intestinal helminths.
Evaluation of the Role of the
opgGH
Operon in Yersinia pseudotuberculosis and Its Deletion during the Emergence of Yersinia pestis
Authors: Quintard Kévin , Dewitte Amélie , Reboul Angéline , Madec Edwige , Bontemps-Gallo Sébastien , Dondeyne Jacqueline , Marceau Michaël , Simonet Michel , Lacroix Jean-Marie , Sebbane Florent
Published: July 2015

The
opgGH
operon encodes glucosyltransferases that synthesize osmoregulated periplasmic glucans (OPGs) from UDP-glucose, using acyl carrier protein (ACP) as a cofactor. OPGs are required for motility, biofilm formation, and virulence in various bacteria. OpgH also sequesters FtsZ in order to regulate cell size according to nutrient availability.
Yersinia pestis
(the agent of flea-borne plague) lost the
opgGH
operon during its emergence from the enteropathogen
Yersinia pseudotuberculosis
. When expressed in OPG-negative strains of
Escherichia coli
and
Dickeya dadantii
,
opgGH
from
Y. pseudotuberculosis
restored OPGs synthesis, motility, and virulence. However,
Y. pseudotuberculosis
did not produce OPGs (i) under various growth conditions or (ii) when overexpressing its
opgGH
operon, its
galUF
operon (governing UDP-glucose), or the
opgGH
operon or Acp from
E. coli
. A Δ
opgGH
Y. pseudotuberculosis
strain showed normal motility, biofilm formation, resistance to polymyxin and macrophages, and virulence but was smaller. Consistently,
Y. pestis
was smaller than
Y. pseudotuberculosis
when cultured at ≥37°C, except when the plague bacillus expressed
opgGH
.
Y. pestis
expressing
opgGH
grew normally in serum and within macrophages and was fully virulent in mice, suggesting that small cell size was not advantageous in the mammalian host. Lastly,
Y. pestis
expressing
opgGH
was able to infect
Xenopsylla cheopis
fleas normally. Our results suggest an evolutionary scenario whereby an ancestral
Yersinia
strain lost a factor required for OPG biosynthesis but kept
opgGH
(to regulate cell size). The
opgGH
operon was presumably then lost because OpgH-dependent cell size control became unnecessary.
Borrelia burgdorferi RevA Significantly Affects Pathogenicity and Host Response in the Mouse Model of Lyme Disease
Authors: Byram Rebecca , Gaultney Robert A. , Floden Angela M. , Hellekson Christopher , Stone Brandee L. , Bowman Amy , Stevenson Brian , Johnson Barbara J. B. , Brissette Catherine A.
Published: July 2015

The Lyme disease spirochete,
Borrelia burgdorferi
, expresses RevA and numerous outer surface lipoproteins during mammalian infection. As an adhesin that promotes bacterial interaction with fibronectin, RevA is poised to interact with the extracellular matrix of the host. To further define the role(s) of RevA during mammalian infection, we created a mutant that is unable to produce RevA. The mutant was still infectious to mice, although it was significantly less well able to infect cardiac tissues. Complementation of the mutant with a wild-type
revA
gene restored heart infectivity to wild-type levels. Additionally,
revA
mutants led to increased evidence of arthritis, with increased fibrotic collagen deposition in tibiotarsal joints. The mutants also induced increased levels of the chemokine CCL2, a monocyte chemoattractant, in serum, and this increase was abolished in the complemented strain. Therefore, while
revA
is not absolutely essential for infection, deletion of
revA
had distinct effects on dissemination, arthritis severity, and host response.
Ferric Uptake Regulator Fur Control of Putative Iron Acquisition Systems in Clostridium difficile
Authors: Ho Theresa D. , Ellermeier Craig D.
Published: July 2015

Clostridium difficile
is an anaerobic, Gram-positive, spore-forming opportunistic pathogen and is the most common cause of hospital-acquired infectious diarrhea. Although iron acquisition in the host is a key to survival of bacterial pathogens, high levels of intracellular iron can increase oxidative damage. Therefore, expression of iron acquisition mechanisms is tightly controlled by transcriptional regulators. We identified a
C. difficile
homologue of the master bacterial iron regulator Fur. Using targetron mutagenesis, we generated a
fur
insertion mutant of
C. difficile
. To identify the genes regulated by Fur in
C. difficile
, we used microarray analysis to compare transcriptional differences between the
fur
mutant and the wild type when grown in high-iron medium. The
fur
mutant had increased expression of greater than 70 transcriptional units. Using quantitative reverse transcriptase PCR (qRT-PCR), we analyzed several of the Fur-regulated genes identified by the microarray and verified that they are both iron and Fur regulated in
C. difficile
. Among those Fur- and iron-repressed genes were
C. difficile
genes encoding 7 putative cation transport systems of different classes. We found that Fur was able to bind the DNA upstream of three Fur-repressed genes in electrophoretic mobility shift assays. We also demonstrate that expression of Fur-regulated putative iron acquisition systems was increased during
C. difficile
infection using the hamster model. Our data suggest that
C. difficile
expresses multiple iron transport mechanisms in response iron depletion
in vitro
and
in vivo
.

IMPORTANCE
Clostridium difficile
is the most common cause of hospital-acquired infectious diarrhea and has been recently classified as an “urgent” antibiotic resistance threat by the CDC. To survive and cause disease, most bacterial pathogens must acquire the essential enzymatic cofactor iron. While import of adequate iron is essential for most bacterial growth, excess intracellular iron can lead to extensive oxidative damage. Thus, bacteria must regulate iron import to maintain iron homeostasis. We demonstrate here that
C. difficile
regulates expression of several putative iron acquisition systems using the transcriptional regulator Fur. These import mechanisms are induced under iron-limiting conditions
in vitro
and during
C. difficile
infection of the host. This suggests that during a
C. difficile
infection, iron availability is limited
in vivo
.
DNA-Binding Protein HU Coordinates Pathogenicity in Vibrio parahaemolyticus
Authors: Phan Ngoc Quang , Uebanso Takashi , Shimohata Takaaki , Nakahashi Mutsumi , Mawatari Kazuaki , Takahashi Akira
Published: July 2015

HU is one of the most abundant nucleoid-associated proteins in bacterial cells and regulates the expression of many genes involved in growth, motility, metabolism, and virulence. It is known that
Vibrio parahaemolyticus
pathogenicity is related to its characteristic rapid growth and that type III secretion system 1 (T3SS1) contributes to its cytotoxicity. However, it is not known if HU plays a role in the pathogenicity of
V. parahaemolyticus
. In the present study, we investigated the effect of HU proteins HU-2 (HUα) (
V. parahaemolyticus
2911 [vp2911]) and HUβ (vp0920) on the pathogenicity of
V. parahaemolyticus
. We found that a deletion of both HU subunits (yielding the ΔHUs [Δ
vp0920
Δ
vp2911
] strain), but not single deletions, led to a reduction of the growth rate. In addition, expression levels of T3SS1-related genes, including
exsA
(positive regulator),
exsD
(negative regulator),
vp1680
(cytotoxic effector), and
vp1671
(T3SS1 apparatus), were reduced in the ΔHUs strain compared to the wild type (WT). As a result, cytotoxicity to HeLa cells was decreased in the ΔHUs strain. The additional deletion of
exsD
in the ΔHUs strain restored T3SS1-related gene expression levels and cytotoxicity but not the growth rate. These results suggest that the HU protein regulates the levels of T3SS1 gene expression and cytotoxicity in a growth rate-independent manner.

IMPORTANCE
Nucleoid-binding protein HU regulates cellular behaviors, including nucleoid structuring, general recombination, transposition, growth, replication, motility, metabolism, and virulence. It is thought that both the number of bacteria and the number of virulence factors may affect the pathogenicity of bacteria. In the present study, we investigated which factor(s) has a dominant role during infection in one of the most rapidly growing bacterial species,
Vibrio parahaemolyticus
. We found that
V. parahaemolyticus
cytotoxicity is regulated, in a growth rate-independent manner, by the HU proteins through regulation of a number of virulence factors, including T3SS1 gene expression.
Energy Conservation Associated with Ethanol Formation from H
2
and CO
2
in Clostridium autoethanogenum Involving Electron Bifurcation
Authors: Mock Johanna , Zheng Yanning , Mueller Alexander P. , Ly San , Tran Loan , Segovia Simon , Nagaraju Shilpa , Köpke Michael , Dürre Peter , Thauer Rudolf K.
Published: July 2015

Most acetogens can reduce CO
2
with H
2
to acetic acid via the Wood-Ljungdahl pathway, in which the ATP required for formate activation is regenerated in the acetate kinase reaction. However, a few acetogens, such as
Clostridium autoethanogenum
,
Clostridium ljungdahlii
, and
Clostridium ragsdalei
, also form large amounts of ethanol from CO
2
and H
2
. How these anaerobes with a growth pH optimum near 5 conserve energy has remained elusive. We investigated this question by determining the specific activities and cofactor specificities of all relevant oxidoreductases in cell extracts of H
2
/CO
2
-grown
C. autoethanogenum
. The activity studies were backed up by transcriptional and mutational analyses. Most notably, despite the presence of six hydrogenase systems of various types encoded in the genome, the cells appear to contain only one active hydrogenase. The active [FeFe]-hydrogenase is electron bifurcating, with ferredoxin and NADP as the two electron acceptors. Consistently, most of the other active oxidoreductases rely on either reduced ferredoxin and/or NADPH as the electron donor. An exception is ethanol dehydrogenase, which was found to be NAD specific. Methylenetetrahydrofolate reductase activity could only be demonstrated with artificial electron donors. Key to the understanding of this energy metabolism is the presence of membrane-associated reduced ferredoxin:NAD
+
oxidoreductase (Rnf), of electron-bifurcating and ferredoxin-dependent transhydrogenase (Nfn), and of acetaldehyde:ferredoxin oxidoreductase, which is present with very high specific activities in H
2
/CO
2
-grown cells. Based on these findings and on thermodynamic considerations, we propose metabolic schemes that allow, depending on the H
2
partial pressure, the chemiosmotic synthesis of 0.14 to 1.5 mol ATP per mol ethanol synthesized from CO
2
and H
2
.

IMPORTANCE
Ethanol formation from syngas (H
2
, CO, and CO
2
) and from H
2
and CO
2
that is catalyzed by bacteria is presently a much-discussed process for sustainable production of biofuels. Although the process is already in use, its biochemistry is only incompletely understood. The most pertinent question is how the bacteria conserve energy for growth during ethanol formation from H
2
and CO
2
, considering that acetyl coenzyme A (acetyl-CoA), is an intermediate. Can reduction of the activated acetic acid to ethanol with H
2
be coupled with the phosphorylation of ADP? Evidence is presented that this is indeed possible, via both substrate-level phosphorylation and electron transport phosphorylation. In the case of substrate-level phosphorylation, acetyl-CoA reduction to ethanol proceeds via free acetic acid involving acetaldehyde:ferredoxin oxidoreductase (carboxylate reductase).
Late and multifocal presentations of malignant peripheral nerve sheath tumours following radiotherapy
Authors: Jones Lara , Bradley Lloyd
Published: July 2015

Peripheral nerve sheath tumours are a well-recognised complication of radiotherapy. Single tumours presenting up to 10 years after initial treatment have been previously described. We report an individual with two anatomically separate nerve sheath tumours developing at different time intervals following initial treatment, after 38 and 42 years, respectively. This case illustrates the importance of maintaining vigilance for the development of complications even at an advanced stage following index radiotherapy treatment.
Immunosuppression and a serious opportunistic infection: an unfortunate price to pay
Authors: Narula Nupoor , Bourne Michael , Bhagra Anjali
Published: July 2015

A 57-year-old woman with diabetes mellitus type 1, status postcadaveric pancreas transplant alone 11 years ago, on chronic immunosuppression, and dialysis-dependent end-stage renal disease, presented with 2 months of progressive generalised weakness, lumbar back pain with right lower extremity radiculopathy and episodic symptomatic hypotension. Preliminary infectious disease work up was unremarkable. She was discharged following symptomatic improvement. She represented 3 days later with continued functional decline and leucocytosis. Chest X-ray demonstrated diffuse pulmonary nodules, confirmed on chest CT scan. CT-guided biopsy of a right upper lobe nodule was performed; studies confirmedNocardia farcinica. Further imaging revealed bilateral white matter intracranial lesions, and extensiveNocardia-positive fluid collections in the right gluteal and vastus musculature, requiring periodic surgical debridement. She was treated with multiple antimicrobials, including trimethoprim-sulfamethoxazole, amoxicillin/clavulanate and moxifloxacin. She was discharged after a 6-month hospitalisation.
Novel use of 4D-CTA in imaging of intranidal aneurysms in an acutely ruptured arteriovenous malformation: is this the way forward?
Authors: Chandran Arun , Radon Mark , Biswas Shubhabrata , Das Kumar , Puthuran Mani , Nahser Hans
Published: July 2015

Ruptured arteriovenous malformation (AVM) is a frequent cause of intracranial hemorrhage. The presence of associated aneurysms, especially intranidal aneurysms, is considered to increase the risk of re-hemorrhage. We present two cases where an intranidal aneurysm was demonstrated on four-dimensional CT angiography (time-resolved CT angiography) (4D-CTA). These features were confirmed by digital subtraction angiography (catheter arterial angiogram). This is the first report of an intranidal aneurysm demonstrated by 4D-CTA. 4D-CTA can offer a comprehensive evaluation of the angioarchitecture and flow dynamics of an AVM for appropriate classification and management.
Perinatal management of fetal supraventricular tachycardia complicated by maternal pertussis
Authors: Dejong Stephanie , Salmanian Bahram , Shamshirsaz Alireza A , Ruano Rodrigo
Published: July 2015

Prenatal pertussis has become a concern once again with the reappearance of the disease in the USA. A 30-year-old mother whose pregnancy was complicated with fetal arrhythmia was referred for further evaluation in the third trimester. After initial treatment with antiarrhythmic medications due to continued irregular rhythm, she was revisited for persistent hacking cough at 38 weeks gestational age. PCR examination confirmed pertussis diagnosis. Owing to increased risk of digoxin toxicity with concurrent antibiotic administration, antiarrhythmic medication was discontinued. Delivery was induced 2 days after the initiation of azithromycin therapy to prevent the transmission of the disease to the neonate. A well-planned delivery in a patient with prenatal diagnosis prevents neonatal infection while considering the obstetrical dilemma for concurrent management of the intrauterine arrhythmia and antibiotic administration.
Prostatic adenocarcinoma presenting as isolated inguinal lymphadenopathy
Authors: Doreswamy Kanakaiah , Karthikeyan Vilvapathy Senguttuvan , Nagabhushana Mahadevappa , Shankaranand Bharatnur
Published: July 2015

Prostatic adenocarcinoma (CaP) is the most common cancer in males and approximately 50% of patients have metastases at presentation, most commonly spreading to the bones and regional lymph nodes. CaP metastasising to inguinal lymph nodes in the absence of pelvic lymphadenopathy or other metastases is very uncommon. A 66-year-old man presented with isolated left inguinal lymphadenopathy of 3 months duration and a history of lower urinary tract symptoms for 1 year. He had prostatic cancer extending into the bladder base and seminal vesicles on contrast-enhanced CT of the pelvis, and asymptomatic vertebral secondaries on skeletal scintigraphy. Transrectal ultrasound biopsy revealed adenocarcinoma (Gleason score 3+4=7), and inguinal lymph node biopsy showed metastatic adenocarcinoma positive for prostate-specific antigen (PSA). As inguinal lymphadenopathy may also be due to other causes, biopsy is useful and meticulous clinical examination is a must in these patients.
Isolated hepatosplenic tuberculosis: a rare presentation
Authors: Hasan Roumina , Kumar Sandeep , Mathew Mary , Kadavigere Rajagopal
Published: July 2015

Tuberculosis caused byMycobacterium tuberculosispresents a major health challenge in endemic countries and spares no organ in the human body. This infection is a mimicker of various disease processes such as metastasis, lymphoproliferative diseases, and other granulomatous conditions such as sarcoidosis and fungal infections. The most challenging and important differential is metastasis, especially in the disseminated form of tuberculosis. We present a histopathologically proven case of isolated hepatosplenic tuberculosis that was provisionally diagnosed as lymphoma due to its unusual, restricted involvement of the liver and spleen.
A systematic review of the predictors of health service utilisation by adults with mental disorders in the UK
Authors: Twomey Conal D , Baldwin David S , Hopfe Maren , Cieza Alarcos
Published: July 2015

Objectives

To identify variables that predict health service utilisation (HSU) by adults with mental disorders in the UK, and to determine the evidence level for these predictors.

Design

A narrative synthesis of peer-reviewed studies published after the year 2000. The search was conducted using four databases (ie,PsycINFO, CINAHL Plus with full text, MEDLINEandEMBASE) and completed on 25 March 2014.

Setting

The majority of included studies were set in health services across primary, secondary, specialist and inpatient care. Some studies used data from household and postal surveys.

Participants

Included were UK-based studies that predicted HSU by adults with mental disorders. Participants had a range of mental disorders including psychotic disorders, personality disorders, depression, anxiety disorders, eating disorders and dementia.

Primary outcome

A wide range of HSU outcomes were examined, including general practitioner (GP) contacts, medication usage, psychiatrist contacts, psychotherapy attendances, inpatient days, accident and emergency admissions and ‘total HSU’.

Results

Taking into account study quality, 28 studies identified a range of variables with good preliminary evidence supporting their ability to predict HSU. Of these variables, comorbidity, personality disorder, age (heterogeneous age ranges), neurotic symptoms, female gender, a marital status of divorced, separated or widowed, non-white ethnicity, high previous HSU and activities of daily living, were associated with increased HSU. Moreover, good preliminary evidence was found for associations of accessing a primary care psychological treatment service and medication use with decreased HSU.

Conclusions

The findings can inform decisions about which variables might be used to derive mental health clusters in ‘payment by results’ systems in the UK. The findings also support the need to investigate whether combining broad diagnoses with care pathways is an effective method for mental health clustering, and the need for research to further examine the association between mental health clusters and HSU.
How family carers engage with technical health procedures in the home: a grounded theory study
Authors: McDonald Janet , McKinlay Eileen , Keeling Sally , Levack William
Published: July 2015

Objectives

To explore the experiences of family carers who manage technical health procedures at home and describe their learning process.

Design

A qualitative study using grounded theory.

Participants

New Zealand family carers (21 women, 5 men) who managed technical health procedures such as enteral feeding, peritoneal dialysis, tracheostomy care, a central venous line or urinary catheter. In addition, 15 health professionals involved in teaching carers were interviewed.

Methods

Semistructured interviews were coded soon after completion and preliminary analysis influenced subsequent interviews. Additional data were compared with existing material and as analysis proceeded, initial codes were grouped into higher order concepts until a core concept was described. Interviewing continued until no new ideas emerged and concepts were well defined.

Results

The response of carers to the role of managing technical health procedures in the home is presented in terms of five dispositions: (1) Embracing care, (2) Resisting, (3) Reluctant acceptance, (4) Relinquishing and (5) Being overwhelmed. These dispositions were not static and carers commonly changed between them. Embracing care included cognitive understanding of the purpose and benefits of a procedure; accepting a ‘technical’ solution; practical management; and an emotional response. Accepting embrace is primarily motivated by perceived benefits for the recipient. It may also be driven by a lack of alternatives. Resisting or reluctant acceptance results from a lack of understanding about the procedure or willingness to manage it. Carers need adequate support to avoid becoming overwhelmed, and there are times when it is appropriate to encourage them to relinquish care for the sake of their own needs.

Conclusions

The concept of embracing care encourages health professionals to extend their attention beyond simply the practical aspects of technical procedures to assessing and addressing carers’ emotional and behavioural responses to health technology during the training process.
Women's interpretation of and responses to potential gynaecological cancer symptoms: a qualitative interview study
Authors: Low E L , Whitaker K L , Simon A E , Sekhon M , Waller J
Published: July 2015

Objective

To explore women's experiences of symptoms potentially indicative of gynaecological cancer in a community-based sample without imposing a cancer perspective.

Design

A qualitative interview study with thematic analysis of transcripts.

Participants

26 women aged ≥30 years, who had experienced a symptom that might indicate gynaecological cancer in the past 3 months, were recruited using a screening questionnaire distributed online and in community settings.

Setting

London, UK.

Results

Women attributed gynaecological symptoms to existing illnesses/conditions or considered themselves to be predisposed to them, either through their ‘genes’ or previous personal experience. Normalising symptoms by attributing them to demographic characteristics (eg, age, sex) was common, as was considering them a side effect of hormonal contraception. When women raised cancer as a possible cause, they often dismissed it as unlikely. Responses to symptoms included self-management (eg, self-medicating, making lifestyle changes), adopting a ‘lay system of care’, or consulting a healthcare professional. Triggers to help-seeking included persistent, painful or debilitating symptoms, concern about symptom seriousness, and feeling that help-seeking was legitimised. Barriers to help-seeking included lack of concern, vague symptoms, unusual symptom location, competing time demands, previous negative experiences with the healthcare system, and not wanting to be perceived as a time-waster.

Conclusions

Attributions of symptoms potentially indicative of a gynaecological cancer were varied, but most often involved women fitting symptoms into their expectations of what was ‘normal’. Normalising acted as a barrier to seeking help from a healthcare professional, alongside competing time demands and negative attitudes towards help-seeking. These barriers may lead to later diagnosis and poorer cancer survival. Our findings could be used to inform the development of interventions to encourage appropriate help-seeking.
The development and evaluation of an evidence-based guideline programme to improve care in a paediatric emergency department
Authors: Akenroye Ayobami T , Stack Anne M
Published: July 2015

Introduction

Care guidelines can improve the quality of care by making current evidence available in a concise format. Emergency departments (EDs) are an ideal site for guidelines given the wide variety of presenting conditions and treating providers, and the need for timely decision making. We designed a programme for guideline development and implementation and evaluated its impact in an ED.

Methods

The setting was an urban paediatric ED with an annual volume of 60 000. Common and/or high-risk conditions were identified for guideline development. Following implementation of the guidelines, their impact on effectiveness of care, patient outcomes, efficiency and equitability of care was assessed using a web-based provider survey and performance on identified metrics. Variation in clinical care between providers was assessed using funnel plots.

Results

Eleven (11) guidelines were developed and implemented. 3 years after the initiation of the programme, self-reported adherence to recommendations was high (95% for physicians and 89% for nurses). 97% of physicians and 92% of nurses stated that the programme improved the quality of care in the ED. For some guidelines, provider-to-provider care practice variation was reduced significantly. We found reduced disparity in imaging when assessing one guideline. There were also reductions in utilisation of diagnostic tests or therapies. As a balancing measure, the percentage of patients with any of the guideline conditions who returned to the ED within 72 h of discharge did not change from before to after guideline initiation. Overall, 80% of physician and 56% of nurse respondents rated the guideline programme at the highest value.

Conclusions

A programme for guideline development and implementation helped to improve efficiency, and standardise and eliminate disparities in emergency care without jeopardising patient outcomes.
Connecting the dots: chromatin and alternative splicing in EMT
Authors: Warns Jessica A. , Davie James R. , Dhasarathy Archana
Published: July 2015

Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.
Improvements to the calculation of actual evaporation from bare soil surfaces
Authors: Tran Dat T.Q. , Fredlund Delwyn G. , Chan Dave H.
Published: July 2015

Evaporation of water from a saturated soil surface with ample free water is known as potential evaporation, PE, and the associated physical processes are quite well understood. However, evaporation of water from an unsaturated soil surface is known as actual evaporation, AE, and the associated physical processes are more complex and less understood. The calculation of actual evaporation is important for many geotechnical engineering applications. Soil suction and the corresponding water content at which the AE rate begins to depart from the PE rate during a drying process are re-assessed using a series of laboratory tests (i.e., thin soil section drying tests and soil column drying tests). Laboratory results show that the suction at which the actual rate of evaporation begins to depart from the PE rate for soil columns (or thick soil layers) may be different than for thin soil layers. Suction at the “evaporation-rate reduction point” (ERRP) appears to be approximately 3000 kPa for thin soil layers, but is between the air-entry value and residual soil suction for thick soil layers or soil columns. The analyses presented in this paper have resulted in the development of a methodology for the estimation of suction corresponding to the ERRP in soil columns. Equations are also proposed to calculate the coefficient of surface moisture availability, vapour pressure, and “surface resistance” at the ground surface. The paper also presents an equation (i.e., new soil–atmosphere moisture flux equation) for predicting evaporation rate from a soil surface using “surface resistance” to vapour water diffusion from the soil to the atmosphere. The proposed soil–atmosphere model is verified using evaporation rate data collected from various drying tests on thin soil layers and soil columns. Reasonably good agreement was found between the computed and measured rates of evaporation. The findings and recommendations in this paper contribute to an improved understanding of the prediction of AE from unsaturated soil surfaces.
Hydrogen elimination from the dissociation of methyl-substituted silanes on tungsten and tantalum surfaces
Authors: Toukabri R. , Shi Y.J.
Published: July 2015

The elimination of H2 from the dissociation of four methyl-substituted silane molecules, including monomethylsilane (MMS), dimethylsilane (DMS), trimethylsilane (TriMS), and tetramethylsilane (TMS), on a heated tungsten or tantalum filament surface has been studied using laser ionization mass spectrometry. Two complementary ionization methods, i.e., single photon ionization (SPI) using a vacuum ultraviolet wavelength at 118 nm (10.5 eV) and a dual ionization source incorporating both 10.5 eV SPI and laser-induced electron ionization, were employed to detect the production of H2. Examination of the intensity of the H2+ peak from the four molecules has shown that it increases with temperature until reaching a plateau at around 2000−2100 °C on both tungsten and tantalum filaments. These methyl-substituted silanes are dissociatively adsorbed on tungsten and tantalum surfaces by Si−H bond cleavage, and as the temperature is raised, by C−H bond rupture. Experiments with the isotopomers of MMS, DMS, and TriMS have shown that the formation of H2 follows the Langmuir−Hinshelwood mechanism where two adsorbed hydrogen atoms on metal surfaces recombine to produce H2. The determined activation energy (Ea) for H2 formation from MMS, DMS, and TriMS, in the range of 58.2−93.4 kJ mol−1, has been found to increase with the number of methyl substitutions in the precursor molecule. Comparison of these Ea values with the reported values of 51.1−78.8 kJ mol−1 for the methyl radical formation from the same three precursor molecules has led to the conclusion that the initial Si−H bond cleavage in the dissociative adsorption of MMS, DMS, and TriMS is the rate-limiting step for the formation of both H2 molecules and ·CH3 radicals.
Dimensionless numbers for the sustainable harvesting of a monospecific uneven-aged forest
Authors: López Torres Ignacio , Fullana Belda Carmen
Published: July 2015

This study proposes a simple and direct method based on dimensionless numbers to provide reliable approximations of the population growth rate, the “sustainable/stable” harvest rate, the proportion of trees that has to remain unharvested to retain the stable diameter distribution, and the stable diameter distribution of a forest stand. Those numbers, obtained under conditions of stable equilibrium from a matrix model, could also serve to estimate boundaries between sustainable and unsustainable harvesting. To exemplify and test the results, the model uses data from uneven-aged managed Pinus nigra Arnold stands, considering three levels of tree diameter growth, six levels of basal area, and 33 levels of recruitment, creating a total of 594 planning scenarios. The best approximation of all the variables observed occurred in any case for the scenarios with the lowest level of diameter growth, the lowest level of basal area, and the highest recruitment level. Furthermore, the study reveals the existence of a strong positive linear correlation between those variables and their respective approximations, as well as a small distance between the stable diameter distribution of the stand and its approximation. Finally, we incorporate natural disturbances into the dimensionless numbers and criteria.
Novel Randomized Feature Selection Algorithms
Authors: Saha Subrata , Rajasekaran Sanguthevar , Ramprasad Rampi
Published: July 2015

Feature selection is the problem of identifying a subset of the most relevant features in the context of model construction. This problem has been well studied and plays a vital role in machine learning. In this paper we present three randomized algorithms for feature selection. They are generic in nature and can be applied for any learning algorithm. Proposed algorithms can be thought of as a random walk in the space of all possible subsets of the features. We demonstrate the generality of our approaches using three different applications. The simulation results show that our feature selection algorithms outperforms some of the best known algorithms existing in the current literature.
A Note on the Minimum H-Subgraph Edge Deletion
Authors: Grigoriev Alexander , Marchal Bert , Usotskaya Natalya
Published: July 2015

In this note we consider the following problem: Given a graph [Formula: see text] and a subgraph [Formula: see text], what is the smallest subset [Formula: see text] of edges in [Formula: see text] that needs to be deleted from the graph to make it [Formula: see text]-free? Several algorithmic results are presented. First, using the general framework of Courcelle [9], we show that, for a fixed subgraph [Formula: see text], the problem can be solved in linear time on graphs of bounded treewidth. It is known that the constant hidden in the big-O notation of Courcelle algorithm is big which makes the approach impractical. Thus, we present two explicit linear time dynamic programming algorithms on graphs of bounded treewidth for restricted settings of the problem with reasonable constants. Third, using the linear time algorithm for graphs of bounded treewidth, we design a Baker's type polynomial time approximation scheme for the problem on planar graphs.
PROVINCIAL DISPARITIES, CONVERGENCE AND EFFECTS ON POVERTY IN THAILAND
Authors: LIMPANONDA SUPHANNADA
Published: July 2015

Thailand's rapid economic development brought about remarkable wealth and poverty reduction over the past three decades. However, the problem of inequality continues to challenge Thailand's development process. The country has long been known for its concentration of growth in and around Bangkok. Despite that, studies on inequality focusing on geographical dimension have been limited. This paper therefore explores disparities as well as convergence in Gross Provincial Product (GPP)-per-capita over the past two decades. It also investigates growth determinants at provincial level. Finally, the disparities in poverty and the extent to which provincial growth and inequality affect poverty are analyzed.
Variational principle of Bogoliubov and generalized mean fields in many-particle interacting systems
Authors: Kuzemsky A. L.
Published: July 2015

The approach to the theory of many-particle interacting systems from a unified standpoint, based on the variational principle for free energy is reviewed. A systematic discussion is given of the approximate free energies of complex statistical systems. The analysis is centered around the variational principle of Bogoliubov for free energy in the context of its applications to various problems of statistical mechanics. The review presents a terse discussion of selected works carried out over the past few decades on the theory of many-particle interacting systems in terms of the variational inequalities. It is the purpose of this paper to discuss some of the general principles which form the mathematical background to this approach and to establish a connection of the variational technique with other methods, such as the method of the mean (or self-consistent) field in the many-body problem. The method is illustrated by applying it to various systems of many-particle interacting systems, such as Ising, Heisenberg and Hubbard models, superconducting (SC) and superfluid systems, etc. This work proposes a new, general and pedagogical presentation, intended both for those who are interested in basic aspects and for those who are interested in concrete applications.
Salient Object Detection via Nonlocal Diffusion Tensor
Authors: Zhang Xiujun , Xu Chen , Sun Xiaoli , Baciu George
Published: July 2015

In this paper, visual attention spreading is formulated as a nonlocal diffusion equation. Different from other diffusion-based methods, a nonlocal diffusion tensor is introduced to consider both the diffusion strength and the diffusion direction. With the help of diffusion tensor, along with the principle direction, the diffusion has been suppressed to preserve the dissimilarity between the foreground and background, while in other directions, the diffusion has been boosted to combine the similar regions and highlight the salient object as a whole. Through a two-stages diffusion, the final saliency maps are obtained. Extensive quantitative or visual comparisons are performed on three widely used benchmark datasets, i.e. MSRA-ASD, MSRA-B and PASCAL-1500 datasets. Experimental results demonstrate the superior performance of our method.
Dedekind sums s(a, b) and inversions modulo b
Authors: Chen Yiwang , Dunn Nicholas , Hewett Campbell , Silas Shashwat
Published: July 2015

We introduce the inversion polynomial for Dedekind sums fb(x) = ∑ x inv (a, b) to study the number of s(a, b) which have the same value for a given b. We prove several properties of this polynomial and present some conjectures. We also introduce connections between Kloosterman sums and the inversion polynomial evaluated at particular roots of unity. Finally, we improve on previously known bounds for the second highest value of the Dedekind sum and provide a conjecture for a possible generalization. Lastly, we include a new sufficient condition for the inequality of two Dedekind sums based on the reciprocity formula.
Stability and Hopf bifurcation for a logistic SIR model with a stage — Structure
Authors: Yang Hong
Published: July 2015

A SIR model of epidemiological dynamics with stage-structure and a type of nonlinear incidence rate is considered under the assumption that the susceptible individual satisfy the logistic equation. The global attractivity of the model is studied using Lyapunov functions and LaSalle's invariance principle. By the uniform persistence theories, the permanence of the system and the existence of the positive equilibrium are obtained. Moreover, by the normal form theory and the center manifold presented by Hassard, a stability and Hopf bifurcation analysis of the system around positive equilibrium from a local perspective are performed. Numerical simulation is carried out to illustrate our results.
Pleistocene submerged landscapes and Palaeolithic archaeology in the tectonically active Aegean region
Authors: Sakellariou D. , Galanidou N.
Published: July 2015

In this paper we review the main, long- and short-term geological and geotectonic processes that have controlled the development of Pleistocene landscapes in the Aegean region above and below the fluctuating sea level. We discuss the potential for further research on reconstruction of submerged landscapes of the continental shelf and beyond with the aim of addressing questions concerning Palaeolithic settlement. The geological, tectonic, morphological and hydrogeological background provides information for the assessment of the natural resources available to hominins. Along with the palaeogeographical evolution of the shallow coastal and shelf areas, they are examined in parallel with the terrestrial archaeological record in order to open windows to future work in a region that has remained marginal to human origins research. On the basis of the multi-variable tectonic evolution and geomorphological configuration of the coastal and shelf areas, we propose to divide the Aegean region into nine geographical units, each with its own geotectonic and morphological history and traits. These units can be further grouped to provide larger neighbouring and culturally meaningful regions, suitable for archaeological analysis, or subdivided to provide smaller target areas in which to work.
Human Activity Recognition Based on the Hierarchical Feature Selection and Classification Framework
Authors: Zheng Yuhuang
Published: July 2015

Human activity recognition via triaxial accelerometers can provide valuable information for evaluating functional abilities. In this paper, we present an accelerometer sensor-based approach for human activity recognition. Our proposed recognition method used a hierarchical scheme, where the recognition of ten activity classes was divided into five distinct classification problems. Every classifier used the Least Squares Support Vector Machine (LS-SVM) and Naive Bayes (NB) algorithm to distinguish different activity classes. The activity class was recognized based on the mean, variance, entropy of magnitude, and angle of triaxial accelerometer signal features. Our proposed activity recognition method recognized ten activities with an average accuracy of 95.6% using only a single triaxial accelerometer.
Two Novel DV-Hop Localization Algorithms for Randomly Deployed Wireless Sensor Networks
Authors: Song Guozhi , Tam Dayuan
Published: July 2015

Aiming at solving the problem of low accuracy in traditional distance vector-hop (DV-hop) algorithm used for wireless sensor networks node location, two refined localization algorithms, that is, hyperbolic-DV-hop localization algorithm and improved weighted centroid DV-hop localization algorithm (IWC-DV-hop), are proposed in this paper. Instead of taking the average HopSize of BeaconNode nearest to the UnknownNode, hyperbolic-DV-hop algorithm chooses the average of average HopSizes of all BeaconNodes, as the average HopSize of the UnknownNode. The ML localization algorithm is also replaced by hyperbolic location algorithm. IWC-DV-hop algorithm improves the accuracy by selecting appropriate BeaconNodes and replacing ML localization with centroid localization. And a weighted scheme is used in IWC-DV-hop so that the influence of different anchors is taken into consideration. Simulations have been conducted to prove that the accuracy is improved by both of the two algorithms and IWC-DV-hop is the best choice.
Immunotherapy of Ovarian Cancer: The Role of Checkpoint Inhibitors
Authors: De Felice Francesca , Marchetti Claudia , Palaia Innocenza , Musio Daniela , Muzii Ludovico , Tombolini Vincenzo , Panici Pierluigi Benedetti
Published: July 2015

Ovarian cancer is the most important cause of gynecological cancer-related mortality, with the majority of women presenting with advanced disease. Although surgery and chemotherapy can improve survival rates, it is necessary to integrate alternative strategies to improve the outcomes. Advances in understanding the role of immune system in the pathogenesis of cancer have led to the rapid evolvement of immunotherapy, which might establish a sustained immune system response against recurring cancer cells. Recently, it has emerged that powerful immunologic effector cells may be blocked by inhibitory regulatory pathways controlled by specific molecules often called “immune checkpoints,” which turn off the immune system. Similarly, cancer cells are able to use these checkpoints to avoid immune control and rejection. Inhibition of these inhibitory pathways represents a potent strategy in the fight against cancer and is currently under investigation with encouraging results in some cancers, such as melanoma. In ovarian cancer researches are still in an early phase, but with promising results. In this review we will explore the rationale of immunotherapy in ovarian cancer with a special focus on these emerging molecules.
Left Atrial Appendage: Physiology, Pathology, and Role as a Therapeutic Target
Authors: Regazzoli Damiano , Ancona Francesco , Trevisi Nicola , Guarracini Fabrizio , Radinovic Andrea , Oppizzi Michele , Agricola Eustachio , Marzi Alessandra , Sora Nicoleta Carmen , Della Bella Paolo , Mazzone Patrizio
Published: July 2015

Atrial fibrillation (AF) is the most common clinically relevant cardiac arrhythmia. AF poses patients at increased risk of thromboembolism, in particular ischemic stroke. The CHADS2 and CHA2DS2-VASc scores are useful in the assessment of thromboembolic risk in nonvalvular AF and are utilized in decision-making about treatment with oral anticoagulation (OAC). However, OAC is underutilized due to poor patient compliance and contraindications, especially major bleedings. The Virchow triad synthesizes the pathogenesis of thrombogenesis in AF: endocardial dysfunction, abnormal blood stasis, and altered hemostasis. This is especially prominent in the left atrial appendage (LAA), where the low flow reaches its minimum. The LAA is the remnant of the embryonic left atrium, with a complex and variable morphology predisposing to stasis, especially during AF. In patients with nonvalvular AF, 90% of thrombi are located in the LAA. So, left atrial appendage occlusion could be an interesting and effective procedure in thromboembolism prevention in AF. After exclusion of LAA as an embolic source, the remaining risk of thromboembolism does not longer justify the use of oral anticoagulants. Various surgical and catheter-based methods have been developed to exclude the LAA. This paper reviews the physiological and pathophysiological role of the LAA and catheter-based methods of LAA exclusion.