bluuebunny/crossref_metadata_2025_split huggingface dataset:
NF kappaB expression increases and CFTR and MUC1 expression decreases in the endometrium of infertile patients with hydrosalpinx: a comparative study
Authors: Song Yong , Wang Qiushi , Huang Wei , Xiao Li , Shen Licong , Xu Wenming 
Published: October 2012

Abstract

Background
Hydrosalpinx are associated with infertility, due to reduced rates of implantation and increased abortion rates. The aims of this study were to investigate the expression of cystic fibrosis transmembrane conductance regulator (CFTR), nuclear factor kappa B (NF KappaB) and mucin-1 (MUC-1), and analyze the correlation between the expression of CFTR and NF KappaB or MUC1, in the endometrium of infertile women with and without hydrosalpinx.

Methods
Thirty-one infertile women with laparoscopy-confirmed unilateral or bilateral hydrosalpinx and 20 infertile women without hydrosalpinx or pelvic inflammatory disease (control group) were recruited. Endometrial biopsy samples were collected and the expression of CFTR, NF KappaB and MUC1 were analyzed using immunohistochemistry and quantitative real-time PCR.

Results
CFTR, NF KappaB and MUC1 mRNA and protein expression tended to increase in the secretory phase compared to the proliferative phase in both groups; however, these differences were not significantly different. The endometrium of infertile patients with hydrosalpinx had significantly higher NF KappaB mRNA and protein expression, and significantly lower CFTR and MUC1 mRNA and protein expression, compared to control infertile patients. A positive correlation was observed between CFTR and MUC1 mRNA expression (r = 0.65, P < 0.05); a negative correlation was observed between CFTR mRNA and NF KappaB mRNA expression (r = −0.59, P < 0.05).

Conclusions
Increased NF KappaB expression and decreased CFTR and MUC1 expression in the endometrium of infertile patients with hydrosalpinx reinforce the involvement of a molecular mechanism in the regulation of endometrial receptivity.
Impact of antenna correlation on the performance of partial relay selection
Authors: Ferdinand Nuwan S , Jayasinghe Upul , Rajatheva Nandana , Latva-aho Matti 
Published: October 2012

Abstract
Antenna correlation is generally viewed as an obstacle to realize the desired performance of a wireless system. In this article, we investigate the performance of partial relay selection in the presence of antenna correlation. We consider both channel state information (csi)-assisted and fixed gain amplify-and-forward (AF) relay schemes. The source and the destination are equipped with multiple antennas communicating via the best first hop signal-to-noise ratio (SNR) relay. We derived the closed form expression for outage probability, average symbol error rate (SER) for both schemes. Further, an exact expression is derived for the ergodic capacity in the csi-assisted relay case and an approximated expression is considered for the fixed gain case. Moreover, we provide simple asymptotic results and show that the diversity order of the system remains unchanged with the effect of antenna correlation for both types of relay schemes.
Iterative common solutions for monotone inclusion problems, fixed point problems and equilibrium problems
Authors: Takahashi Wataru , Wong Ngai-Ching , Yao Jen-Chih 
Published: October 2012

Abstract
Let H be a real Hilbert space, and let C be a nonempty closed convex subset of H. Let

α
>
0

, and let A be an α-inverse strongly-monotone mapping of C into H. Let T be a generalized hybrid mapping of C into H. Let B and W be maximal monotone operators on H such that the domains of B and W are included in C. Let

0
<
k
<
1

, and let g be a k-contraction of H into itself. Let V be a

γ
¯

-strongly monotone and L-Lipschitzian continuous operator with

γ
¯

>
0

and

L
>
0

. Take

μ
,
γ
∈
R

as follows:

0
<
μ
<

2

γ
¯

L
2

,

0
<
γ
<

γ
¯

−

L
2

μ

2

k

.

Suppose that

F
(
T
)
∩

(
A
+
B
)

−
1

0
∩

W

−
1

0
≠
∅

, where

F
(
T
)

and

(
A
+
B
)

−
1

0

,

W

−
1

0

are the set of fixed points of T and the sets of zero points of

A
+
B

and W, respectively. In this paper, we prove a strong convergence theorem for finding a point

z
0

of

F
(
T
)
∩

(
A
+
B
)

−
1

0
∩

W

−
1

0

, where

z
0

is a unique fixed point of

P

F
(
T
)
∩

(
A
+
B
)

−
1

0
∩

W

−
1

0

(
I
−
V
+
γ
g
)

. This point

z
0

∈
F
(
T
)
∩

(
A
+
B
)

−
1

0
∩

W

−
1

0

is also a unique solution of the variational inequality

〈
(
V
−
γ
g
)

z
0

,
q
−

z
0

〉

≥
0
,

∀
q
∈
F
(
T
)
∩

(
A
+
B
)

−
1

0
∩

W

−
1

0
.

Using this result, we obtain new and well-known strong convergence theorems in a Hilbert space. In particular, we solve a problem posed by Kurokawa and Takahashi (Nonlinear Anal. 73:1562-1568, 2010).

MSC:47H05, 47H10, 58E35.
FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei
Authors: Borges Filipe , Gardner Rui , Lopes Telma , Calarco Joseph P , Boavida Leonor C , Slotkin R Keith , Martienssen Robert A , Becker Jörg D 
Published: October 2012

AbstractBackgroundThe male germline in flowering plants differentiates by asymmetric division of haploid uninucleated microspores, giving rise to a vegetative cell enclosing a smaller generative cell, which eventually undergoes a second mitosis to originate two sperm cells. The vegetative cell and the sperm cells activate distinct genetic and epigenetic mechanisms to control pollen tube growth and germ cell specification, respectively. Therefore, a comprehensive characterization of these processes relies on efficient methods to isolate each of the different cell types throughout male gametogenesis.ResultsWe developed stable transgenicArabidopsislines and reliable purification tools based on Fluorescence-Activated Cell Sorting (FACS) in order to isolate highly pure and viable fractions of each cell/nuclei type before and after pollen mitosis. In the case of mature pollen, this was accomplished by expressing GFP and RFP in the sperm and vegetative nuclei, respectively, resulting in 99% pure sorted populations. Microspores were also purified by FACS taking advantage of their characteristic small size and autofluorescent properties, and were confirmed to be 98% pure.ConclusionsWe provide simple and efficient FACS-based purification protocols forArabidopsismicrospores, vegetative nuclei and sperm cells. This paves the way for subsequent molecular analysis such as transcriptomics, DNA methylation analysis and chromatin immunoprecipitation, in the developmental context of microgametogenesis inArabidopsis.
Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease
Authors: Crespo Isaac , Roomp Kirsten , Jurkowski Wiktor , Kitano Hiroaki , del Sol Antonio 
Published: October 2012

Abstract

Background
The activation of immune cells in the brain is believed to be one of the earliest events in prion disease development, where misfolded PrionSc protein deposits are thought to act as irritants leading to a series of events that culminate in neuronal cell dysfunction and death. The role of these events in prion disease though is still a matter of debate. To elucidate the mechanisms leading from abnormal protein deposition to neuronal injury, we have performed a detailed network analysis of genes differentially expressed in several mouse prion models.

Results
We found a master regulatory core of genes related to immune response controlling other genes involved in prion protein replication and accumulation, and neuronal cell death. This regulatory core determines the existence of two stable states that are consistent with the transcriptome analysis comparing prion infected versus uninfected mouse brain. An in silico perturbation analysis demonstrates that core genes are individually capable of triggering the transition and that the network remains locked once the diseased state is reached.

Conclusions
We hypothesize that this locking may be the cause of the sustained immune response observed in prion disease. Our analysis supports the hypothesis that sustained brain inflammation is the main pathogenic process leading to neuronal dysfunction and loss, which, in turn, leads to clinical symptoms in prion disease.
Functional phosphoproteomic mass spectrometry‐based approaches
Authors: López Elena , Wang Xiangdong , Madero Luis , López‐Pascual Juan , Latterich Martin 
Published: October 2012

AbstractMass Spectrometry (MS)‐based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease.The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un‐phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future.Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies.
Common genetic variants, acting additively, are a major source of risk for autism
Authors: Klei Lambertus , Sanders Stephan J , Murtha Michael T , Hus Vanessa , Lowe Jennifer K , Willsey A Jeremy , Moreno-De-Luca Daniel , Yu Timothy W , Fombonne Eric , Geschwind Daniel , Grice Dorothy E , Ledbetter David H , Lord Catherine , Mane Shrikant M , Martin Christa Lese , Martin Donna M , Morrow Eric M , Walsh Christopher A , Melhem Nadine M , Chaste Pauline , Sutcliffe James S , State Matthew W , Cook Edwin H , Roeder Kathryn , Devlin Bernie 
Published: October 2012

AbstractBackgroundAutism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals.MethodsBy using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status.ResultsBy analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating.ConclusionsOur results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.
An activity theory analysis of boundary objects in cross-border information systems development for disaster management
Authors: Bharosa Nitesh , Lee JinKyu , Janssen Marijn , Rao H Raghav 
Published: October 2012

Abstract
One of the main challenges in cross-border disaster management is the development and use of information systems that cater the needs of heterogeneous relief agencies, policies, activities and cultures. Drawing upon activity theory, this paper examines cross-border information systems development for disaster management. We infuse the concept of boundary objects into activity theory by the characterization of the artifacts. This allows articulating how the socio-technical objects are meshed with the process of cross-border collaboration for systems development. Our longitudinal ethnographic field study on a cross-border flood management project, VIKING, revealed how the project was empowered and developed by four key boundary objects, i.e. the governance structure of the program, two information systems (a disaster management information system and an online collaboration portal), and recurring cross-border exercises as an evaluation and feedback mechanism. The selective institutionalizations of these key boundary objects helped the participants overcome various contradictions existed in the systems development. The study results also show that both goal-oriented actions and boundary objects can affect the outcomes of long-term large-scale disaster management systems development.
Cannabinoid receptor type 2 (CB2)-selective N-aryl-oxadiazolyl-propionamides: synthesis, radiolabelling, molecular modelling and biological evaluation
Authors: Rühl Thomas , Deuther-Conrad Winnie , Fischer Steffen , Günther Robert , Hennig Lothar , Krautscheid Harald , Brust Peter 
Published: October 2012

Abstract

Background
The endocannabinoid system is involved in many physiological and pathological processes. Two receptors (cannabinoid receptor type 1 (CB1) and type 2 (CB2)) are known so far. Many unwanted psychotic side effects of inhibitors of this system can be addressed to the interaction with CB1. While CB1 is one of the most abundant neuroreceptors, CB2 is expressed in the brain only at very low levels. Thus, highly potent and selective compounds for CB2 are desired. N-aryl-((hetero)aromatic)-oxadiazolyl-propionamides represent a promising class of such selective ligands for the human CB2. Here, a library of various derivatives is studied for suitable routes for labelling with 18F. Such 18F-labelled compounds can then be employed as CB2-selective radiotracers for molecular imaging studies employing positron emission tomography (PET).

Results
By varying the N-arylamide substructure, we explored the binding pocket of the human CB2 receptor and identified 9-ethyl-9H-carbazole amide as the group with optimal size. Radioligand replacement experiments revealed that the modification of the (hetero)aromatic moiety in 3-position of the 1,2,4-oxadiazoles shows only moderate impact on affinity to CB2 but high impact on selectivity towards CB2 with respect to CB1. Further, we could show by autoradiography studies that the most promising compounds bind selectively on CB2 receptors in mouse spleen tissue. Molecular docking studies based on a novel three-dimensional structural model of the human CB2 receptor in its activated form indicate that the compounds bind with the N-arylamide substructure in the binding pocket. 18F labelling at the (hetero)aromatic moiety at the opposite site of the compounds via radiochemistry was carried out.

Conclusions
The synthesized CB2-selective compounds have high affinity towards CB2 and good selectivity against CB1. The introduction of labelling groups at the (hetero)aromatic moiety shows only moderate impact on CB2 affinity, indicating the introduction of potential labelling groups at this position as a promising approach to develop CB2-selective ligands suitable for molecular imaging with PET. The high affinity for human CB2 and selectivity against human CB1 of the herein presented compounds renders them as suitable candidates for molecular imaging studies.
Mannose binding lectin: a biomarker of systemic lupus erythematosus disease activity
Authors: Panda Aditya K , Parida Jyoti R , Tripathy Rina , Pattanaik Sarit S , Ravindran Balachandran , Das Bidyut K 
Published: October 2012

Abstract
Introduction
A role for mannose binding lectin (MBL) in autoimmune diseases has been demonstrated earlier and elevated level of MBL has been shown in systemic lupus erythematosus (SLE) patients. In the current study, we investigated MBL as a potential biomarker for disease activity in SLE.

Methods
In a case control study SLE patients (93 females) and 67 age, sex, ethnicity matched healthy controls were enrolled. Plasma MBL levels were quantified by enzyme linked immunosorbent assay (ELISA). Clinical, serological and other markers of disease activity (C3, C4 and anti-dsDNA) were measured by standard laboratory procedures.

Results
Plasma MBL levels were significantly high in SLE patients compared to healthy controls (P < 0.0001). MBL levels were variable in different clinical categories of SLE. Lower levels were associated with musculoskeletal and cutaneous manifestations (P = 0.002), while higher and intermediate MBL levels were significantly associated with nephritis in combination with other systemic manifestations (P = 0.01 and P = 0.04 respectively). Plasma MBL correlated with systemic lupus erythematosus disease activity index (SLEDAI) (P = 0.0003, r = 0.36), anti-dsDNA (P < 0.0001, r = 0.54), proteinuria (P < 0.0001, r = 0.42) and negatively correlated with C3 (P = 0.007, r = -0.27) and C4 (P = 0.01, r = -0.29).

Conclusions
Plasma MBL is a promising marker in the assessment of SLE disease activity.
Periodontitis in established rheumatoid arthritis patients: a cross-sectional clinical, microbiological and serological study
Authors: Smit Menke de , Westra Johanna , Vissink Arjan , Doornbos-van der Meer Berber , Brouwer Elisabeth , van Winkelhoff Arie Jan 
Published: October 2012

Abstract
Introduction
The association between rheumatoid arthritis (RA) and periodontitis is suggested to be linked to the periodontal pathogen Porphyromonas gingivalis. Colonization of P. gingivalis in the oral cavity of RA patients has been scarcely considered. To further explore whether the association between periodontitis and RA is dependent on P. gingivalis, we compared host immune responses in RA patients with and without periodontitis in relation to presence of cultivable P. gingivalis in subgingival plaque.

Methods
In 95 RA patients, the periodontal condition was examined using the Dutch Periodontal Screening Index for treatment needs. Subgingival plaque samples were tested for presence of P. gingivalis by anaerobic culture technique. IgA, IgG and IgM antibody titers to P. gingivalis were measured by ELISA. Serum and subgingival plaque measures were compared to a matched control group of non-RA subjects.

Results
A higher prevalence of severe periodontitis was observed in RA patients in comparison to matched non-RA controls (27% versus 12%, p < 0.001). RA patients with severe periodontitis had higher DAS28 scores than RA patients with no or moderate periodontitis (p < 0.001), while no differences were seen in IgM-RF or ACPA reactivity. Furthermore, RA patients with severe periodontitis had higher IgG- and IgM-anti P. gingivalis titers than non-RA controls with severe periodontitis (p < 0.01 resp. p < 0.05), although subgingival occurrence of P. gingivalis was not different.

Conclusions
Severity of periodontitis is related to severity of RA. RA patients with severe periodontitis have a more robust antibody response against P. gingivalis than non-RA controls, but not all RA patients have cultivable P. gingivalis.
Investigating risk factors for psychological morbidity three months after intensive care: a prospective cohort study
Authors: Wade Dorothy M , Howell David C , Weinman John A , Hardy Rebecca J , Mythen Michael G , Brewin Chris R , Borja-Boluda Susana , Matejowsky Claire F , Raine Rosalind A 
Published: October 2012

Abstract
Introduction
There is growing evidence of poor mental health and quality of life among survivors of intensive care. However, it is not yet clear to what extent the trauma of life-threatening illness, associated drugs and treatments, or patients' psychological reactions during intensive care contribute to poor psychosocial outcomes. Our aim was to investigate the relative contributions of a broader set of risk factors and outcomes than had previously been considered in a single study.

Methods
A prospective cohort study of 157 mixed-diagnosis highest acuity patients was conducted in a large general intensive care unit (ICU). Data on four groups of risk factors (clinical, acute psychological, socio-demographic and chronic health) were collected during ICU admissions. Post-traumatic stress disorder (PTSD), depression, anxiety and quality of life were assessed using validated questionnaires at three months (n =100). Multivariable analysis was used.

Results
At follow-up, 55% of patients had psychological morbidity: 27.1% (95% CI: 18.3%, 35.9%) had probable PTSD; 46.3% (95% CI: 36.5%, 56.1%) probable depression, and 44.4% (95% CI: 34.6%, 54.2%) anxiety. The strongest clinical risk factor for PTSD was longer duration of sedation (regression coefficient = 0.69 points (95% CI: 0.12, 1.27) per day, scale = 0 to 51). There was a strong association between depression at three months and receiving benzodiazepines in the ICU (mean difference between groups = 6.73 points (95% CI: 1.42, 12.06), scale = 0 to 60). Use of inotropes or vasopressors was correlated with anxiety, and corticosteroids with better physical quality of life.
The effects of these clinical risk factors on outcomes were mediated (partially explained) by acute psychological reactions in the ICU. In fully adjusted models, the strongest independent risk factors for PTSD were mood in ICU, intrusive memories in ICU and psychological history. ICU mood, psychological history and socio-economic position were the strongest risk factors for depression.

Conclusions
Strikingly high rates of psychological morbidity were found in this cohort of intensive care survivors. The study's key finding was that acute psychological reactions in the ICU were the strongest modifiable risk factors for developing mental illness in the future. The observation that use of different ICU drugs correlated with different psychological outcomes merits further investigation. These findings suggest that psychological interventions, along with pharmacological modifications, could help reduce poor outcomes, including PTSD, after intensive care.
CHANCE: comprehensive software for quality control and validation of ChIP-seq data
Authors: Diaz Aaron , Nellore Abhinav , Song Jun S 
Published: October 2012

AbstractChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance.