bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practical investigation of suitable decoding techniques for spectral amplitude coding optical code division multiple access‐based vibration sensing
Authors: Taiwo Ambali , Moghaddasi Majid , Kuje Danjuma , Idriss Yahaya , Mokhtar Makhfudza 
Published: April 2016

A suitable decoding technique for spectral amplitude coding optical code division multiple access (SAC‐OCDMA)‐based secured distributed vibration sensor is investigated. The study is carried out to identify the most appropriate techniques for receiving the transmitted vibration signal in SAC‐OCDMA‐based system. The techniques which are direct decoding, complementary and logical AND decoding are compared based on the level of crosstalk, number of components used and supported transmission distance in multiplexed vibration sensing using both simulation and experiment. The results show direct decoding capable of supporting 55 km unlike the other two which are 44 and 38 km, respectively. Aside that, direct decoding techniques could be implemented with less number of components and has optimal signal‐to‐noise ratio while still preventing the system again the ‘man in the middle’ attack.
The Paradoxical Significance of Headache in Hypertension
Authors: Courand Pierre-Yves , Serraille Michaël , Girerd Nicolas , Demarquay Genevieve , Milon Hugues , Lantelme Pierre , Harbaoui Brahim 
Published: April 2016

Abstract

BACKGROUND
The cardiovascular prognostic value of various types of headache, particularly migraine, in the general population remains controversial. The aim of the present study was to assess their prognostic value for all-cause, cardiovascular and stroke mortalities in hypertensive patients.

METHODS
A total of 1,914 hypertensive individuals were first categorized according to the absence or presence of headache and thereafter according to the 3 subtypes of headache: migraine, daily headache, and other headache.

RESULTS
Multiple regression analysis demonstrated that all headache types were predicted by gender (women), diastolic blood pressure, absence of diabetes, secondary hypertension, and a trend for severe retinopathy. After 30 years of follow-up, 1,076 deaths were observed, 580 of whom were from cardiovascular cause and 97 from acute stroke. In a multivariable Cox model adjusted for major confounders, patients having headache had a decreased risk for all-cause mortality (hazard ratio (HR) 0.82; 95% confidence interval (CI) 0.73–0.93) and cardiovascular mortality (HR 0.80; 95% CI 0.68–0.95), but not for stroke mortality (HR 1.00; 95% CI 0.70–1.43). When considering only patients with headache, “daily headache” had a nonsignificant better prognostic value for all-cause and cardiovascular mortality than “other headache” (HR 0.83; 95% CI 0.68–1.01; HR 0.89; 95% CI 0.69–1.16, respectively) and “migraine” (HR 0.85; 95% CI 0.65–1.11; HR 0.78; 95% CI 0.55–1.10, respectively).

CONCLUSION
Presence of nonspecific headache in hypertensive patients has a paradoxical significance in that it is associated with a high-risk profile but does not result in a worse prognosis over the long term.
Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins
Authors: Ziegler Zachary , Schmidt Molly , Gurry Thomas , Burger Virginia , Stultz Collin M. 
Published: April 2016

Abstract
Summary: Intrinsically disordered proteins (IDPs) play central roles in many biological processes. Consequently, an accurate description of the disordered state is an important step towards a comprehensive understanding of a number of important biological functions. In this work we describe a new web server, Mollack, for the automated construction of unfolded ensembles that uses both experimental and molecular simulation data to construct models for the unfolded state. An important aspect of the method is that it calculates a quantitative estimate of the uncertainty in the constructed ensemble, thereby providing an objective measure of the quality of the final model. Overall, Mollack facilitates structure-function studies of disordered proteins.
Availability and Implementation: http://cmstultz-mollack.mit.edu
Contact: cmstultz@mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sparse group factor analysis for biclustering of multiple data sources
Authors: Bunte Kerstin , Leppäaho Eemeli , Saarinen Inka , Kaski Samuel 
Published: April 2016

Abstract
Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments. These biclustering techniques have focused on one data source, often gene expression data. We present a Bayesian approach for joint biclustering of multiple data sources, extending a recent method Group Factor Analysis to have a biclustering interpretation with additional sparsity assumptions. The resulting method enables data-driven detection of linear structure present in parts of the data sources.
Results: Our simulation studies show that the proposed method reliably infers biclusters from heterogeneous data sources. We tested the method on data from the NCI-DREAM drug sensitivity prediction challenge, resulting in an excellent prediction accuracy. Moreover, the predictions are based on several biclusters which provide insight into the data sources, in this case on gene expression, DNA methylation, protein abundance, exome sequence, functional connectivity fingerprints and drug sensitivity.
Availability and Implementation: http://research.cs.aalto.fi/pml/software/GFAsparse/
Contacts: kerstin.bunte@googlemail.com or samuel.kaski@aalto.fi
DJ-1 linked parkinsonism (PARK7) is associated with Lewy body pathology
Authors: Taipa Ricardo , Pereira Conceição , Reis Inês , Alonso Isabel , Bastos-Lima António , Melo-Pires Manuel , Magalhães Marina 
Published: April 2016

AbstractMutations in DJ-1 (encoded by PARK7) are a very rare cause of early-onset recessive Parkinson’s disease. We describe a patient with early-onset parkinsonism, starting at the age of 22, with poor response to levodopa and additional features in progression (dystonia, pyramidal signs and dementia), who died when he was 49 years old. The neuropathological study showed severe substantia nigra and locus coeruleus neuronal loss, with diffuse Lewy body pathology (Lewy bodies, aberrant neurites, grain-like structures, spheroids and scattered glial pathology). Genetic analysis revealed a novel c.515T &gt; A; p.L172Q mutation in the PARK7 gene. To evaluate the pathogenicity of this new mutation we explored DJ-1 expression levels in vitro showing a massive reduction in DJ-1 protein levels due to a highly unstable and rapidly degraded L172Q mutant. DJ-1 immunohistochemistry of brain tissue revealed no staining in our case. This is the first neuropathological report of a brain from DJ-1-linked parkinsonism that, although based on a single case study, suggests that DJ-1 mutations are causative of α-synucleinopathy. These results can help in the understanding of Parkinson’s disease pathophysiology, promote research studies to increase the knowledge on the pathways involved in the neurodegeneration process, and pave the way for new therapeutic interventions.
Developing a digital data collection platform to measure the prevalence of sepsis in Wales
Authors: Sharif B , Lundin RM , Morgan P , Hall JE , Dhadda A , Mann C , Donoghue D , Brownlow E , Hill F , Carr G , Turley H , Hassall J , Atkinson M , Jones M , Martin R , Rollason S , Ibrahim Y , Kopczynska M , Szakmany T 
Published: April 2016

Abstract
Objective To develop a secure, efficient, and easy-to-use data collection platform to measure the prevalence of sepsis in Wales over 24 hours.
Materials and Methods Open Data Kit was used on Android devices with Google App Engine and a digital data collection form.
Results A total of 184 students participated in the study using 59 devices across 16 hospitals, 1198 datasets were submitted, and 97% of participants found the Open Data Kit form easy to use.
Discussion We successfully demonstrated that by combining a reliable Android device, a free open-source data collection framework, a scalable cloud-based server, and a team of 184 medical students, we can deliver a low-cost, highly reliable platform that requires little training or maintenance, providing results immediately on completion of data collection.
Conclusion Our platform allowed us to measure, for the first time, the prevalence of sepsis in Wales over 24 hours.
Relativistic radiative transfer and relativistic spherical shell flows
Authors: Fukue Jun 
Published: April 2016

Abstract
We examine a radiatively driven spherical flow from a central object, whose thickness is smaller than the radius of the central object, and a plane-parallel approximation can be used—a spherical shell flow. We first solve the relativistic radiative transfer equation iteratively, using a given velocity field, and obtain specific intensities as well as moment quantities. Using the obtained comoving flux, we then solve the relativistic hydrodynamical equation, and obtain a new velocity field. We repeat these double iteration processes until both the intensity and velocity profiles converge. We found that the flow speed v(τ) is roughly approximated as β ≡ v/c = βs(1 − τ/τb), where τ is the optical depth, τb the flow total optical depth, and c the speed of light. We further found that the flow terminal speed vs is roughly expressed as $\beta _{\rm s} \equiv v_{\rm s}/c = (\Gamma \hat{F}_0-1)\tau _{\rm b}/\dot{m}\,$, where Γ is the central luminosity normalized by the Eddington luminosity, $\hat{F}_0$ the comoving flux normalized by the incident flux, and of the order of unity, and $\dot{m}$  the mass-loss rate normalized by the critical mass loss.
CO-to-H2 conversion factor of molecular clouds using X-ray shadows
Authors: Sofue Yoshiaki , Kataoka Jun 
Published: April 2016

Abstract
A new method to determine the CO-to-H2 conversion factor XCO using absorption of diffuse X-ray emission by local molecular clouds was developed. It was applied to the Ophiuchus (G353+17) and Corona Australis (G359−18) clouds using CO line and soft X-ray archival data. We obtained a value XCO = 1.85 ± 0.45 × 1020 H2 cm−2 (K km s−1)−1 as the average of least-χ2 fitting results for R4 (0.7 keV) and R5 (0.8 keV) bands.
Does research matter in residency applications? A single institution’s experience
Authors: Larson Eric , Wojcik Jonathan , Cannada Lisa K. 
Published: April 2016

Background:
Orthopaedic surgery has become one of the most competitive specialties for medical students to pursue. With increasing numbers of well-qualified applicants applying into the field, it has become essential for students to distinguish themselves, and one effective way of doing so is through research involvement.

Methods:
Saint Louis University (SLU) graduates from 2010-2015 who successfully matched into orthopaedic surgery were contacted and asked about their involvement in research, what field that research was in, whether it led to any publications or presentations, and which faculty member oversaw the project.

Results:
Between 2010 and 2015, 41 students matched into orthopaedic surgery from SLU out of a total of 42 who had applied, yielding a 97.6% match rate. Sixty-eight percent (26/38) of the graduates who responded to our survey took part in a total of 45 orthopaedic surgery research projects. This research resulted in 19 publications and 28 presentations. Thirty-three projects were done through the SLU Department of Orthopaedics and 12 projects were done at an outside facility. Of the 12 graduates who responded to the survey and denied orthopaedic research, eight took part in research projects through other departments.

Conclusions:
SLU’s match rate into orthopaedics over the last 6 years (97.6%) is significantly above the national average for the same period of time (75.6%). Thirty-four of 38 (89.5%) of our graduates were engaged in research during medical school, which is well above the reported national average for medical students (57%). We believe this strong research involvement accounts for our high match rate into orthopaedics.
Cutaneous, Purpuric Painful Nodules Upon Addition of Ibrutinib to RCVP Therapy in a CLL Patient: A Distinctive Reaction Pattern Reflecting Iatrogenic Th2 to Th1 Milieu Reversal
Authors: Mulvey Joseph Justin , Nuovo Gerard J. , Magro Cynthia M. 
Published: April 2016

Abstract:
A 70-year-old white man with stage C chronic lymphocytic leukemia who was being successfully treated with ibrutinib and rituximab developed bilateral, purpuric, painful cutaneous nodules. Biopsies of these nodules did not reveal the usual Th2 milieu of chronic lymphocytic leukemia but instead exhibited a Th1-rich lymphocytic infiltrate with resultant neutrophil and granulomatous inflammation. The eruption resolved with drug cessation emphasizing the potential importance of this drug in treating conditions associated with Th2 dysregulation.
Acquired Localized Longitudinal Pachyonychia and Onychomatrical Tumors: A Comparative Study to Onychomatricomas (5 Cases) and Onychocytic Matricomas (4 Cases)
Authors: Perrin Christophe , Cannata Giuseppe Emilio , Langbein Lutz , Ambrosetti Damien , Coutts Michael , Balaguer Thierry , Garzon Jean-Marc , Michiels Jean-François 
Published: April 2016

Background:
Besides onychomatricoma (OM), which shows a clinical band pattern of nail plate thickening, 2 new onychomatrical tumors with this clinical feature have recently been described: onychocytic matricoma (OCM) and in situ onychocytic carcinoma.

Objective:
The purpose of this study was to present 4 cases of OCMs and compare their clinical and histopathologic characteristics with usual OMs.

Methods:
We studied 4 cases of OCMs with nail clipping in 3 cases and an extensive immunohistochemical study for hair-related keratins and epithelial keratins. Nail clipping of OCMs was compared with the distal nail plate of 5 cases of OMs.

Results:
All cases showed an acquired localized longitudinal band pattern of a thickened nail plate with yellow discoloration in 2 cases and a black streak in 2 cases. All cases showed a V-shaped keratogenous epithelial tumor with a papillomatous pattern of growth. The nail plate was thickened with small holes in a honeycomb pattern. In contrast, the 5 OMs showed the classical pattern of a panonychoma fibropapilliferum. The nail plate showed large cavities in a honeycomb pattern.

Conclusions:
This case series raises awareness of the clinical value of longitudinal pachyonychia coupled with nail clipping in the early detection of onychomatrical tumors as generic diagnosis with a limited differential diagnosis and a simple therapeutic approach. Nail clipping could be an aid in the surgical planning of onychomatrical tumor. A diagnosis of a benign growth could be suggested when the average dimensions of cavities are superior to 0.15 mm sparing the patient from an excisional procedure with its risk of subsequent permanent nail dystrophy. In contrast, nail clipping with a honeycomb pattern of minute cavities with average dimension inferior to 0.10 mm should prompt a biopsy of the distal matrix to rule out a malignant lesion.
Rosacea-Like Leukemia Cutis: A Case Report
Authors: Cruz Manzano Mariana , Ramírez García Lilliana , Sánchez Pont Julio E. , Velázquez Mañana Ana I. , Sánchez Jorge L. 
Published: April 2016

Abstract:
Leukemia cutis describes the infiltration and dissemination of neoplastic leukemic cells into the epidermis, dermis, or subcutis, resulting in clinically identifiable cutaneous lesions. Depending on the type of leukemia, a wide range of clinical and histopathological findings may be encountered. This report describes a patient with a rosacea-like eruption as a unique clinical presentation of T-cell prolymphocytic leukemia.
Morpheaform Basal Cell Carcinomas With Areas of Predominantly Single-Cell Pattern of Infiltration: Diagnostic Utility of p63 and Cytokeratin
Authors: East Ellen , Fullen Douglas R. , Arps David , Patel Rajiv M. , Palanisamy Nallasivam , Carskadon Shannon , Harms Paul W. 
Published: April 2016

Background:Morpheaform basal cell carcinoma (BCC) is a variant of BCC characterized by narrow strands and nests of basaloid cells with dense sclerotic stroma. The histologic extent often exceeds the clinical impression, leading to high recurrence rates after standard excision. The authors encountered a case with single-cell invasion distant from the main tumor. To date a systematic review of single-cell infiltration in morpheaform BCC has yet to be performed.Design:Ten morpheaform BCCs, 10 nonmorpheaform aggressive BCCs, 5 desmoplastic trichoepitheliomas, and 2 microcystic adnexal carcinomas were identified by database search and confirmed on hematoxylin and eosin. Cases were evaluated by hematoxylin and eosin, immunohistochemical staining for p63, and (in a subset) broad-spectrum cytokeratin. Single-cell pattern was defined as individual cells, 2-cell clusters, or single-file invasion.Results:Three types of single-cell pattern were identified: intratumoral (single cells within the main tumor mass), peripheral, and distant. Single cells were typically a minor component relative to larger tumor nodules and strands. Eight of the 10 cases of morpheaform BCC demonstrated areas of single-cell pattern: 3 intratumoral, 3 peripheral, and 2 with distant spread (0.75 and 1.0 mm from the main tumor). Eight of the 10 aggressive BCC demonstrated a peripheral single-cell pattern. Rare intratumoral single cells were identified in 3/5 desmoplastic trichoepitheliomas and 1/2 microcystic adnexal carcinomas.Conclusion:Single-cell pattern is frequently a component of morpheaform BCC. Tumor cells at a significant distance from the main component were unique to morpheaform BCC. Thus, when evaluating margins for morpheaform BCC, increased caution is recommended, and immunohistochemical stains for p63 or cytokeratins may be helpful.
Cutaneous Osteoblastic Osteosarcoma: Report of 2 New Cases Integrated With SATB2 Immunohistochemistry and Review of the Literature
Authors: Falconieri Giovanni , Cataldi Palmina , Kavalar Rajko , Štitič Vesna , Luzar Boštjan 
Published: April 2016

Abstract:We report 2 cases of primary dermal osteosarcoma. The patients were an 88-year-old man and a 72-year-old man complaining of masses occurring in the ear pavilion and the palm, deemed suspicious for basal cell carcinoma and metastatic colonic carcinoma, and were treated by resection. Microscopically, both featured a dermal lesion mostly composed of atypical spindle cells within a fibrous to hyaline matrix often showing mineralization. Osteoid material was rimmed by atypical tumor cells and was also associated with osteoclast-like giant cells. Tumor cells were positive for SATB2 and negative for markers of epithelial (low-molecular and high-molecular weight cytokeratins, epithelial membrane antigen, p63), melanocytic (S100 protein, HMB45, Melan A), and skeletal/smooth muscle differentiation (desmin, myogenin). No further therapy has been administered. Follow-up at 6 (case 1) and 8 months (case 2) was uneventful. A brief differential diagnosis discussing cutaneous tumors capable of showing osseous differentiation is summarized, along with a review of the pertinent literature. The specificity and sensitivity of SATB2 is also shortly addressed.
Loss of Fumarate Hydratase and Aberrant Protein Succination Detected With S-(2-Succino)-Cysteine Staining to Identify Patients With Multiple Cutaneous and Uterine Leiomyomatosis and Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome
Authors: Llamas-Velasco Mar , Requena Luis , Adam Julie , Frizzell Norma , Hartmann Arndt , Mentzel Thomas 
Published: April 2016

Aims:
Hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome is an autosomal dominant disorder caused by heterozygotic germline mutations in fumarate hydratase (FH) with incomplete penetrance, and clinically challenging to diagnose. Immunohistochemical stainings may favor an earlier diagnosis.

Methods and Results:
The authors have tested 31 smooth muscle neoplasms. Ten of the 13 lesions from patients with HLRCC syndrome showed negative FH staining. Most sporadic piloleiomyomas presented strongly positive FH staining although 5 cases were negative. Sensitivity of FH staining in our series is 83.3% but specificity is 75%. Anti-S-(2-succino)-cysteine (2SC) showed the opposite intensity staining pattern and showed great correlation with anti-FH (rho spearman = −0.797). Anti-2SC staining increased the diagnostic accuracy in 19% of the cases.

Limitations:
The main limitation of this study is the lack additional clinical data to further classify the cases as the case inclusion was histopathological.

Conclusions:
Negative FH staining could indicate a high risk of HLRCC but it could also suggest the presence of a syndrome in up to 25% of sporadic cases. Thus, when there is a doubtful case, anti-2SC may be added to exclude the syndrome if a negative staining is found.
Diffuse Dermal Angiomatosis of the Breast With an Apparent Etiology of Underlying Calcified Thrombosed Artery With Adjacent Fat Necrosis
Authors: Strausburg Matthew B. , Gehlhausen Jeff , Ludwig Kandice , Warren Simon 
Published: April 2016

Abstract:
In this report, the authors present a case of diffuse dermal angiomatosis (DDA) with an underlying mass lesion of the breast, which proved to be a large calcified, thrombosed artery with adjacent fat necrosis. Histologically, DDA consists of hyperplastic vessels, which diffusely infiltrate the papillary and reticular dermis forming small vascular lumina. The condition is associated with various underlying conditions, many of which result in local tissue ischemia. In the past, DDA was most commonly reported on the lower extremities; however, it seems that this entity is more common on the breast than previously recognized. Various treatments have proven beneficial, including revascularization, oral corticosteroids, smoking cessation, and isotretinoin. In this case, our patient benefited from primary excision of the affected area.
Screening for and validation of a hepatic fibrosis-related pathway induced by insulin-like growth factor-binding protein-related protein 1
Authors: Guo XiaoHong , Zhang HaiYan , Zhang QianQian , Li XiuQing , Liu LiXin 
Published: April 2016

Objective
Our previous studies characterized insulin-like growth factor-binding protein-related protein 1 (IGFBPrP1) as a molecule that promotes hepatic fibrogenesis, but its mechanism has not been fully elucidated. Here, we have investigated the effect of IGFBPrP1 on gene expression in the hepatic fibrosis-related pathway.

Materials and methods
Sprague–Dawley rats received injections of an adenovirus carrying IGFBPrP1 or EGFP cDNA into their tail veins. In hepatic preparations, hepatic stellate cell activation was determined by α-smooth muscle actin expression and hepatic fibrosis by Sirius red staining and hydroxyproline content analysis. IGFBPrP1-inducible genes of the hepatic fibrosis-related pathway were assessed by PCR array. Expression of IGFBPrP1 and transforming growth factor β1 (TGFβ1) and array results were evaluated by quantitative real-time PCR and western blotting.

Results
IGFBPrP1-overexpressing rats showed an increase in α-smooth muscle actin expression and collagen and hydroxyproline content in the liver. The PCR array results indicated that some genes were upregulated and some were downregulated in Ad-IGFBPrP1-infected rats. Among these, Egr1, MAP2K2 (MEK2) and MAPK3 (ERK1) expression increased, whereas PTEN and Hhip mRNA expression decreased. Egr1 protein levels increased and peaked 2 weeks after infection and then decreased gradually. PTEN protein decreased gradually in Ad-IGFBPrP1-infected rats with a concurrent increase in the degree of hepatic fibrosis. TGFβ1 levels increased during hepatic fibrosis development in liver tissues.

Conclusion

Egr1, PTEN, Hhip, MAP2K2 (MEK2) and MAPK3 (ERK1) were identified as candidate genes of the IGFBPrP1-induced hepatic fibrosis-related pathway. IGFBPrP1 promoted hepatic fibrosis mainly by enhancing the TGFβ1 expression that it triggered.