bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice
Authors: Wu Shaogen , Marie Lutz Brianna , Miao Xuerong , Liang Lingli , Mo Kai , Chang Yun-Juan , Du Peicheng , Soteropoulos Patricia , Tian Bin , Kaufman Andrew G. , Bekker Alex , Hu Yali , Tao Yuan-Xiang 
Published: March 2016

Background Peripheral nerve injury leads to changes in gene expression in primary sensory neurons of the injured dorsal root ganglia. These changes are believed to be involved in neuropathic pain genesis. Previously, these changes have been identified using gene microarrays or next generation RNA sequencing with poly-A tail selection, but these approaches cannot provide a more thorough analysis of gene expression alterations after nerve injury. Methods The present study chose to eliminate mRNA poly-A tail selection and perform strand-specific next generation RNA sequencing to analyze whole transcriptomes in the injured dorsal root ganglia following spinal nerve ligation. Quantitative real-time reverse transcriptase polymerase chain reaction assay was carried out to verify the changes of some differentially expressed RNAs in the injured dorsal root ganglia after spinal nerve ligation. Results Our results showed that more than 50 million (M) paired mapped sequences with strand information were yielded in each group (51.87 M–56.12 M in sham vs. 51.08 M–57.99 M in spinal nerve ligation). Six days after spinal nerve ligation, expression levels of 11,163 out of a total of 27,463 identified genes in the injured dorsal root ganglia significantly changed, of which 52.14% were upregulated and 47.86% downregulated. The largest transcriptional changes were observed in protein-coding genes (91.5%) followed by noncoding RNAs. Within 944 differentially expressed noncoding RNAs, the most significant changes were seen in long interspersed noncoding RNAs followed by antisense RNAs, processed transcripts, and pseudogenes. We observed a notable proportion of reads aligning to intronic regions in both groups (44.0% in sham vs. 49.6% in spinal nerve ligation). Using quantitative real-time polymerase chain reaction, we confirmed consistent differential expression of selected genes including Kcna2, Oprm1 as well as lncRNAs Gm21781 and 4732491K20Rik following spinal nerve ligation. Conclusion Our findings suggest that next generation RNA sequencing can be used as a promising approach to analyze the changes of whole transcriptomes in dorsal root ganglia following nerve injury and to possibly identify new targets for prevention and treatment of neuropathic pain.
Increased expression of αv integrin as a regulator of fibrosis in Dupuytren’s nodules
Authors: Matsui Y. , Kon S. , Funakoshi T. , Miyashita T. , Matsuda T. , Iwasaki N. 
Published: March 2016

Although Dupuytren’s contracture is characterized by increased transforming growth factor-β1 (TGF-β1) and fibrosis in the palmar fascia, the relationship between TGF-β1 and integrins, which are considered to be related to fibrosis, remains unclear. We investigated the involvement of TGF-β1 and integrins in the pathological palmar fascia of Dupuytren’s contracture. Seven patients underwent partial fasciectomy for treatment of this disease. The nodule and cord were isolated from the fascial tissues of the patients. Control fasciae were obtained from seven patients with carpal tunnel syndrome. Immunohistochemical analysis was performed to detect the fibrosis marker α-smooth muscle actin and integrins in the fascial tissues. The expression of TGF-β1 and integrins was assessed by real-time polymerase chain reaction. The results suggest that nodules may be areas involved in activation of fibrosis in the fascia, associated with increased expression of TGF-β1 and αv integrin. Thus, αv integrin may contribute to fibrosis in Dupuytren’s contracture by activating TGF-β1. Level of Evidence: IV
Phase II study of gemcitabine plus S-1 chemotherapy in recurrent and metastatic nasopharyngeal carcinoma patients after failure of platinum-based chemotherapy
Authors: Peng PeiJian , Ou XueQing , Liao Hai , Liu YuMeng , Wang SiYang , Cheng ZhiBin , Lin Zhong 
Published: March 2016

Purpose: No standard salvage regimen has been established for patients with recurrent and metastatic nasopharyngeal carcinoma (NPC) and disease progression after prior platinum-based chemotherapy. This phase II study was designed to evaluate the efficacy and safety of gemcitabine plus S-1 (GS) chemotherapy as a remedial regimen in this setting. Methods: In this multicenter phase II study, 49 patients with recurrent and metastatic NPC who failed previous platinum-based chemotherapy received gemcitabine (1.0 g/m2 on days 1 and 8) plus oral S-1 chemotherapy (twice daily from day 1 to 14). Each cycle was repeated every 3 weeks for two cycles at least. The dose of S-1 was determined according to the body surface area (BSA): 40 mg twice a day for BSA <1.25 m2; 50 mg twice a day for 1.25 m2 ⩽ BSA <1.5 m2; and 60 mg twice a day for BSA ⩾1.5 m2. Results: Treatment was generally well-tolerated. A total of seven patients (14.3%) had grade 3 toxicities and the main toxicity was myelosuppression, whereas the nonhematology adverse events were minimal. There were 3 complete responses (6.4%), 17 partial responses (36.2%), and the overall response rate was 42.6% (95% confidence interval: 27.3–61.2). Median time to progression was 5.8 months and median survival was 14.8 months. The 1- and 2-year survival rates were 64% and 30%, respectively. Conclusions: Gemcitabine plus S-1 offers a satisfactory clinical activity and an acceptable safety profile for recurrent and metastatic NPC patients after failure of platinum-based chemotherapy.
Is Psychological Stress a Factor for Incorporation Into Future Closed-Loop Systems?
Authors: Gonder-Frederick Linda A. , Grabman Jesse H. , Kovatchev Boris , Brown Sue A. , Patek Stephen , Basu Ananda , Pinsker Jordan E. , Kudva Yogish C. , Wakeman Christian A. , Dassau Eyal , Cobelli Claudio , Zisser Howard C. , Doyle Francis J. 
Published: March 2016

Background: The relationship between daily psychological stress and BG fluctuations in type 1 diabetes (T1DM) is unclear. More research is needed to determine if stress-related BG changes should be considered in glucose control algorithms. This study in the usual free-living environment examined relationships among routine daily stressors and BG profile measures generated from CGM readings. Methods: A total of 33 participants with T1DM on insulin pumps wore a CGM device for 1 week and recorded daily ratings of psychological stress, carbohydrates, and insulin boluses. Results: Within-subjects ANCOVAs found a significant relationship between daily stress and indices of BG variability/instability ( r = .172 to .185, P = .011 to .018, r2 = 2.97% to 3.43%), increased % time in hypoglycemia ( r = .153, P = .036, r2 = 2.33%) and decreased carbohydrate consumption ( r = –.157, P = .031, r2 = 2.47%). Models accounted for more variance for individuals reporting the highest daily stress. There was no relationship between stress and mean daily glucose or low/high glucose risk indices. Conclusions: These preliminary findings suggest that naturally occurring daily stressors can be associated with increased glucose instability and hypoglycemia, as well as decreased food consumption. In addition, findings support the hypothesis that some individuals are more metabolically reactive to stress. More rigorous studies using CGM technology are needed to understand whether the impact of daily stress on BG is clinically meaningful and if it is a behavioral factor that should be considered in glucose control systems for some individuals.
The role of 4D CT angiography for preoperative screening in patients with intracranial tumors
Authors: Suzuki Kazufumi , Abe Kayoko , Maruyama Takashi , Nitta Masayuki , Amano Kosaku , Yamaguchi Koji , Kawamata Takakazu , Sakai Shuji 
Published: March 2016

Introduction Four-dimensional computed tomography angiography (4D CTA) is now becoming an often used diagnostic imaging modality for the assessment of patients with intracranial tumors. The purpose of this study was to demonstrate the utility of 4D CTA for preoperative screening in patients with intracranial tumors as well as to examine the correlation between perfusion data and grading of gliomas. Methods We performed preoperative screening using 320-row detector CT scanner in 186 patients with intracranial tumors, and 115 patients were finally included in the study. Time-resolved subtracted maximum intensity projection images and volume-rendered images were reconstructed to evaluate vascular structures, tumor staining and incidental lesions. We also evaluated the perfusion functional map for gliomas to find correlations between their vascularity and tumor grading. Results We evaluated gliomas in 70 patients, meningiomas in 29, and other tumors in 16. Patients with gliomas of a pathologically higher grade showed high cerebral blood volume ( p < 0.05). Tumor staining was observed on MIP images for 12 meningiomas, 4 gliomas, and 3 other tumors. Fifty patients showed a mass effect on vascular structures, seven had cerebral venous sinus obstruction, and two had aneurysms. No iatrogenic accidents with the CT procedure were reported. Conclusions The 4D CTA technique is effective and safe for depicting vascular structures such as arteries, veins, tumor-related vessels, and direct and indirect anatomical complications such as vascular obstruction or vascular compression. This information is useful for preoperative screening. Although 4D CTA also provides perfusion data correlating with the tumor vascularity and grading of gliomas, its clinical value remains limited.
Cross-sectional comparison of first-generation antipsychotic long-acting injections vs risperidone long-acting injection: patient-rated attitudes, satisfaction and tolerability
Authors: Singh Sourabh Moti , Haddad Peter M. , Husain Nusrat , Heaney Eamonn , Tomenson Barbara , Chaudhry Imran B. 
Published: March 2016

Objectives: The objective of this study was to compare patients’ attitudes and satisfaction with medication and patient-rated tolerability between those prescribed a first-generation antipsychotic long-acting injection (FGA-LAI) and those prescribed risperidone long-acting injection (RLAI). Method: A cross-sectional study of a representative sample of outpatients prescribed an FGA-LAI or RLAI for a minimum of 6 months and attending a depot clinic. Attitudes to medication were assessed by the Drug Attitude Inventory (DAI-30), tolerability was measured by the Liverpool University Neuroleptic Side Effect Rating Scale (LUNSERS) and satisfaction with antipsychotic medication was assessed by the Satisfaction with Antipsychotic Medication (SWAM) scale. Results: The RLAI ( n = 28) and FGA-LAI ( n = 39) groups did not differ in terms of mean age, sex, diagnosis and ethnicity. All individual LAIs were prescribed within British National Formulary limits. The most commonly prescribed FGA-LAI was flupentixol decanoate ( n = 22). There was no significant difference between the RLAI and FGA-LAI groups in terms of mean total scores on the DAI-30, LUNSERS and SWAM or the tolerability subscales of the LUNSERS or the two subscales (treatment acceptability and medication insight) of the SWAM. In both LAI groups there was a low level of side effects (LUNSERS) and a generally positive attitude (DAI-30) and reasonable satisfaction (SWAM) with medication. Conclusions: Patients treated with FGA-LAI and RLAI for at least 6 months did not differ in terms of patient-rated tolerability, attitudes and satisfaction with medication. The current design cannot determine whether differences would have been evident earlier on during treatment. These results should be regarded as preliminary and are subject to prescribing bias. Randomized studies avoid prescribing bias and are a superior way to compare specific LAIs. Ideally randomized studies should include patient-rated outcome measures including medication tolerability; assessment of side effects, efficacy and quality of life made by blinded raters; and additional objective side-effect data including changes in weight and key blood parameters.
What is the effect of nicotinic acetylcholine receptor stimulation on osteoarthritis in a rodent animal model?
Authors: Bock Kilian , Plaass Christian , Coger Vincent , Peck Claas-Tido , Reimers Kerstin , Stukenborg-Colsman Christina , Claassen Leif 
Published: March 2016

Objectives: Despite the rising number of patients with osteoarthritis, no sufficient chondroprotective and prophylactic therapy for osteoarthritis has been established yet. The purpose of this study was to verify whether stimulation of the nicotinic acetylcholine receptor via nicotine has a beneficial effect on cartilage degeneration in the development of osteoarthritis and is capable of reducing the expression of proinflammatory cytokines and cartilage degrading enzymes in synovial membranes after osteoarthritis induction. Methods: Experimental osteoarthritis was induced in Lewis rats using a standardized osteoarthritis model with monoiodoacetate. A total of 16 Lewis rats were randomized into four groups: control, sham + nicotine application, osteoarthritis, and osteoarthritis + nicotine application. Nicotine (0.625 mg/kg twice daily) was administered intraperitoneally for 42 days. We analyzed histological sections, radiological images and the expression of the proinflammatory cytokines, such as interleukin-1β, tumor necrosis factor-α and interleukin-6, and of matrix metalloproteases 3, 9 and 13 and tissue inhibitors of metalloprotease-1 in synovial membranes via quantitative polymerase chain reaction. Results: Histological and x-ray examination revealed cartilage degeneration in the osteoarthritis group compared to control or sham + nicotine groups (histological control vs osteoarthritis: p = 0.002 and x-ray control vs osteoarthritis: p = 0.004). Nicotine treatment reduced the cartilage degeneration without significant differences. Osteoarthritis induction led to a higher expression of proinflammatory cytokines and matrix metalloproteases as compared to control groups. This effect was attenuated after nicotine administration. The differences of proinflammatory cytokines and matrix metalloproteases did not reach statistical significance. Conclusion: With the present small-scale study, we could not prove a positive effect of nicotinic acetylcholine receptor stimulation on osteoarthritis due to a conservative statistical analysis and the consecutive lack of significant differences. Nevertheless, we found promising tendencies of relevant parameters that might prompt further experiments designed to evaluate the potency of stimulation of this receptor system as an additional treatment approach for osteoarthritis.
A one stop consultant led urology clinic is effective and does not lead to missed diagnoses
Authors: Exarchou Klaire , Tin Su , Hamm Rebecca 
Published: March 2016

Objective: The objective of this study was to review the effectiveness and safety of a one stop urology clinic led by a consultant diagnostic urologist. Methods: Data were collected prospectively on all patients seen by a single consultant diagnostic urologist from February 2007 to February 2008. In 2013, patient records were reviewed and cross-referenced to identify if any patients had been re-referred to the urology service and why. Results: From 889 referrals, 799 patients attended, of these 689 (86%) were discharged after a single visit with 110 (14%) booked follow-up appointments. Ninety patients were re-referred, only two of these had a significant diagnosis. Thirty-four (38%) had a new referral reason. Conclusion: The one stop method of consultation is effective and efficient across a range of presenting complaints in urology. It is safe for patients and leads to a high discharge rate with a low re-referral rate without missing clinically significant diagnoses.
Development and validation of a rapid, aldehyde dehydrogenase bright–based cord blood potency assay
Authors: Shoulars Kevin , Noldner Pamela , Troy Jesse D. , Cheatham Lynn , Parrish Amanda , Page Kristin , Gentry Tracy , Balber Andrew E. , Kurtzberg Joanne 
Published: March 2016

Key PointsCord blood content of ALDHbr cells correlates well with CFUs and may act as a surrogate potency assay for cord blood units. ALDHbr cells in segments are assayed rapidly, allowing potency results to be used for release of the unit from a public cord blood bank.
From the desktop to the grid: scalable bioinformatics via workflow conversion
Authors: de la Garza Luis , Veit Johannes , Szolek Andras , Röttig Marc , Aiche Stephan , Gesing Sandra , Reinert Knut , Kohlbacher Oliver 
Published: March 2016

Abstract
Background
Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks.
There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free —an aspect that could potentially drive away members of the scientific community.

Results
We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources.

Conclusions
Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We strongly believe that our efforts not only decrease the turnaround time to obtain scientific results but also have a positive impact on reproducibility, thus elevating the quality of obtained scientific results.
Characterization of mesenchymal stem cells and fibrochondrocytes in three-dimensional co-culture: analysis of cell shape, matrix production, and mechanical performance
Authors: McCorry Mary Clare , Puetzer Jennifer L. , Bonassar Lawrence J. 
Published: March 2016

AbstractBackgroundBone marrow mesenchymal stem cells (MSCs) have shown positive therapeutic effects for meniscus regeneration and repair. Preliminary in vitro work has indicated positive results for MSC applications for meniscus tissue engineering; however, more information is needed on how to direct MSC behavior. The objective of this study was to examine the effect of MSC co-culture with primary meniscal fibrochondrocytes (FCCs) in a three-dimensional collagen scaffold in fibrochondrogenic media. Co-culture of MSCs and FCCs was hypothesized to facilitate the transition of MSCs to a FCC cell phenotype as measured by matrix secretion and morphology.MethodsMSCs and FCCs were isolated from bovine bone marrow and meniscus, respectively. Cells were seeded in a 20 mg/mL high-density type I collagen gel at MSC:FCC ratios of 0:100, 25:75, 50:50, 75:25, and 100:0. Constructs were cultured for up to 2 weeks and then analyzed for cell morphology, glycosaminoglycan content, collagen content, and production of collagen type I, II, and X.ResultsCells were homogeneously mixed throughout the scaffold and cells had limited direct cell–cell contact. After 2 weeks in culture, MSCs transitioned from a spindle-like morphology toward a rounded phenotype, while FCCs remained rounded throughout culture. Although MSC shape changed with culture, the overall size was significantly larger than FCCs throughout culture. While 75:25 and 100:0 (MSC mono-culture) culture groups produced significantly more glycosaminoglycan (GAG)/DNA than FCCs in mono-culture, GAG retention was highest in 50:50 co-cultures. Similarly, the aggregate modulus was highest in 100:0 and 50:50 co-cultures. All samples contained both collagen types I and II after 2 weeks, and collagen type X expression was evident only in MSC mono-culture gels.ConclusionsMSCs shift to a FCC morphology in both mono- and co-culture. Co-culture reduced hypertrophy by MSCs, indicated by collagen type X. This study shows that MSC phenotype can be influenced by indirect homogeneous cell culture in a three-dimensional gel, demonstrating the applicability of MSCs in meniscus tissue engineering applications.
Fuzzy quasi-triangular spaces, fuzzy sets of Pompeiu-Hausdorff type, and another extensions of Banach and Nadler theorems
Authors: Włodarczyk Kazimierz 
Published: March 2016

AbstractLet $\mathcal{A}$
A
be an index set, and $C=\{C_{\alpha}\}_{\alpha\in \mathcal{A}}\in{}[1;\infty)^{\mathcal{A}}$
C
=

{

C
α

}

α
∈
A

∈
[
1
;
∞

)
A

. Fuzzy quasi-triangular space is defined to be $(X,\mathcal{M}_{C;\mathcal{A}},\ast)$
(
X
,

M

C
;
A

,
∗
)
, where X is a nonempty set, a fuzzy family $\mathcal{M}_{C;\mathcal{A}}=\{M_{\alpha }:X\times X\times(0;\infty)\rightarrow(0;1],\alpha\in\mathcal{A}\}$

M

C
;
A

=
{

M
α

:
X
×
X
×
(
0
;
∞
)
→
(
0
;
1
]
,
α
∈
A
}
satisfies $\forall_{\alpha\in\mathcal{A}}\forall_{x,y,z\in X}\forall _{t,s\in(0;\infty)}\{M_{\alpha}(x,y,t)\ast M_{\alpha}(y,z,s)\leq M_{\alpha}(x,z,C_{\alpha}(t+s))\}$

∀

α
∈
A

∀

x
,
y
,
z
∈
X

∀

t
,
s
∈
(
0
;
∞
)

{

M
α

(
x
,
y
,
t
)
∗

M
α

(
y
,
z
,
s
)
≤

M
α

(
x
,
z
,

C
α

(
t
+
s
)
)
}
, and ∗ is the continuous t-norm $\ast:[0;1]\times{}[0;1]\rightarrow{}[0;1]$
∗
:
[
0
;
1
]
×
[
0
;
1
]
→
[
0
;
1
]
. In $(X,\mathcal{M}_{C;\mathcal{A}},\ast)$
(
X
,

M

C
;
A

,
∗
)
, left (right) $\mathcal{G}$
G
-families and $\mathcal{W}$
W
-families $\mathcal{K}_{C;\mathcal{A}}$

K

C
;
A

generated by $\mathcal{M}_{C;\mathcal{A}}$

M

C
;
A

($\mathcal{K}_{C;\mathcal{A}}$

K

C
;
A

generalize $\mathcal {M}_{C;\mathcal{A}}$

M

C
;
A

) are defined and described. Using families $\mathcal {K}_{C;\mathcal{A}}$

K

C
;
A

, three kinds of left (right) fuzzy sets of Pompeiu-Hausdorff type on $2^{X}\times2^{X}\times(0;\infty)$

2
X

×

2
X

×
(
0
;
∞
)
are introduced. Using these fuzzy sets, three kinds of left (right) set-valued fuzzy contractions $T:X\rightarrow2^{X}$
T
:
X
→

2
X

are constructed, and for such fuzzy contractions, conditions guaranteeing the existence of periodic points and left (right) $\mathcal {M}_{C;\mathcal{A}}$

M

C
;
A

-convergence to these periodic points of dynamic processes $(w^{m}:m\in\{0\}\cup\mathbb{N})$
(

w
m

:
m
∈
{
0
}
∪
N
)
, $w^{m}\in T(w^{m-1})$

w
m

∈
T
(

w

m
−
1

)
for $m\in \mathbb{N}$
m
∈
N
, starting at $w^{0}\in X$

w
0

∈
X
, are established. Moreover, in $(X,\mathcal {M}_{C;\mathcal{A}},\ast)$
(
X
,

M

C
;
A

,
∗
)
, using left (right) $\mathcal{G}$
G
-families and $\mathcal{W}$
W
-families $\mathcal{K}_{C;\mathcal{A}}$

K

C
;
A

generated by $\mathcal{M}_{C;\mathcal{A}}$

M

C
;
A

, two kinds of left (right) single-valued fuzzy contractions $T:X\rightarrow X$
T
:
X
→
X
are constructed, and for such fuzzy contractions, the convergence, existence, approximation, uniqueness, periodic point, and fixed point result is also obtained. Examples are provided.