bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of soil organic and inorganic carbon at different moisture contents with dry ground VNIR: a comparative study of different approaches
Authors: Wijewardane N. K. , Ge Y. , Morgan C. L. S. 
Published: July 2016

Visible and near infrared reflectance spectroscopy (VNIR) is a rapid and multi‐sensing technology that can provide spatially dense soil data for many disciplines. Soil moisture is the main barrier to the use of this technology in the field. The objective of this study was to compare the effectiveness of five approaches, external parameter orthogonalization (EPO), direct standardization (DS), global moisture modelling (GMM), slope bias correction (SB) and selective wavelength modelling (SWM), to enable models based on dry ground VNIR spectra of soil to be applied directly to moist spectra to predict organic carbon (OC) and inorganic carbon (IC). A total of 352 archived soil samples were selected and scanned, and of these 185 samples were used to develop dry ground models. The remaining 167 samples were rewetted to eight different moisture contents for the development (100) and validation (67) of the five moisture‐correction approaches. The results showed that EPO, DS and GMM account satisfactorily for the effect of moisture in soil spectra. They improved the prediction of OC substantially with an increase in R2 from almost zero for no correction to over 0.5, and an RPIQ (ratio of performance to interquartile range) from 0.38 to over 1.7. Improvement was also achieved with EPO, DS and GMM for IC; RPIQ increased from 0.53 to over 1.2. External parameter orthogonalization and DS showed that their effectiveness in moisture correction depended on the moisture content of the sample (larger moisture contents decrease the effectiveness), whereas this dependence was not observed for the moisture‐explicit DS and GMM methods. We concluded that EPO, DS and GMM are all viable approaches for moisture correction for VNIR‐based proximal soil sensors.HighlightsAccounting for the effect of soil moisture on soil spectra is essential for in situ VNIR‐based soil sensors.
Five methods to remove the effect of moisture on VNIR modelling of soil OC and IC are investigated.
EPO, DS (with two implementations) and GMM showed promising results for moisture correction.
Correction done with moisture‐explicit DS and GMM showed little dependence with moisture content.
Systemic disease manifestations associated with epilepsy in tuberous sclerosis complex
Authors: Jeong Anna , Wong Michael 
Published: July 2016

SummaryObjectiveEpilepsy is one of the most disabling symptoms of tuberous sclerosis complex (TSC) and is a leading cause of morbidity and mortality in affected individuals. The relationship between systemic disease manifestations and the presence of epilepsy has not been thoroughly investigated. This study utilizes a multicenter TSC Natural History Database including 1,816 individuals to test the hypothesis that systemic disease manifestations of TSC are associated with epilepsy.MethodsUnivariate analysis was used to identify patient characteristics (e.g., age, gender, race, and TSC mutation status) associated with the presence of epilepsy. Individual logistic regression models were built to examine the association between epilepsy and each candidate systemic or neurologic disease variable, controlling for the patient characteristics found to be significant on univariate analysis. Finally, a multivariable logistic regression model was constructed, using the variables found to be significant on the individual analyses as well as the patient characteristics that were significant on univariate analysis.ResultsNearly 88% of our cohort had a history of epilepsy. After adjusting for age, gender, and TSC mutation status, multiple systemic disease manifestations including cardiac rhabdomyomas (odds ratio [OR] 2.3, 95% confidence interval [CI] 1.3–3.9, p = 0.002), retinal hamartomas (OR 2.1, CI 1.0–4.3, p = 0.04), renal cysts (OR 2.1, CI 1.3–3.4, p = 0.002), renal angiomyolipomas (OR 3.0, CI 1.8–5.1, p < 0.001), shagreen patches (OR 1.7, CI 1.0–2.7, p = 0.04), and facial angiofibromas (OR 1.7, CI 1.1–2.9, p = 0.03) were associated with a higher likelihood of epilepsy. In the multivariable logistic regression model, cardiac rhabdomyomas (OR 1.9, CI 1.0–3.5, p = 0.04) remained significantly associated with the presence of epilepsy.SignificanceThe identification of systemic disease manifestations such as cardiac rhabdomyomas that confer a higher risk of epilepsy development in TSC could contribute to disease prognostication and assist in the identification of individuals who may receive maximal benefit from potentially novel, targeted, preventative therapies.
Suspected new‐onset autoimmune temporal lobe epilepsy with amygdala enlargement
Authors: Malter Michael P. , Widman Guido , Galldiks Norbert , Stoecker Winfried , Helmstaedter Christoph , Elger Christian E. , Wagner Jan 
Published: July 2016

SummaryObjectiveRecent reports define temporal lobe epilepsy with amygdala enlargement (TLE‐AE) as a distinct electroclinical syndrome comparable to TLE with hippocampal sclerosis. In this retrospective observational study, we present the largest consecutive series of patients with new‐onset TLE‐AE to date and describe clinical characteristics and seizure outcome, and we aim to explore underlying autoimmune mechanisms within this syndrome.MethodsWe reviewed all consecutive patients between 2004 and 2014 at our tertiary epilepsy center at the University of Bonn, Germany, with new‐onset (<5 years) TLE‐AE, negative serum antibody (ab) test results, and with available follow‐up data for at least 12 months.ResultsWe identified 40 patients (23 male) with TLE‐AE with a median age at epilepsy onset of 51 years (range 10–73) and a median disease duration of 11 months (range 0.5–55) at first presentation. At follow‐up, 50% of the entire cohort achieved seizure freedom. Of interest, patients with remittent features of AE at follow‐up (N = 24) had a superior outcome compared to those with stable magnetic resonance imaging (MRI) features of AE (N = 16): 17 (71%) of 24 were seizure‐free for at least 6 months compared to 3 (19%) of 16, respectively (p = 0.003). MRI volumetry confirmed significantly enlarged amygdalae in TLE‐AE in relation to healthy controls, and additionally showed significantly greater volume reductions in patients with remittent AE compared to those with stable AE.SignificanceTLE‐AE is a clinical syndrome beginning mostly in middle age, and in addition to its known association with ab‐positive limbic encephalitis, it occurs in an ab‐negative condition. Remission of AE in the course of the disease could be identified as a predictor for a favorable clinical outcome and is suspicious of an autoimmune etiology, although we could not confirm this hypothesis unequivocally with currently available noninvasive diagnostic tools.
The intriguing CP12‐like tail of adenylate kinase 3 from Chlamydomonas reinhardtii
Authors: Thieulin‐Pardo Gabriel , Schramm Antoine , Lignon Sabrina , Lebrun Régine , Kojadinovic Mila , Gontero Brigitte 
Published: July 2016

Adenylate kinases (ADK) are key enzymes that maintain the energetic balance in cellular compartments by catalyzing the reaction: AMP + ATP↔2 ADP. Here, we analyzed the chloroplast ADK 3 from the green alga, Chlamydomonas reinhardtii for the first time. This enzyme bears a C‐terminal extension that is highly similar to the C‐terminal end of the intrinsically disordered protein CP12 that plays a major role in the redox regulation of key enzymes of the Calvin–Benson cycle like glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) and phosphoribulokinase. The only other known example of a CP12‐like extension is found in the GapB isoform of GAPDH, where it is responsible for the autonomous redox regulation of the higher plant A2B2 GAPDH. In this study, we show that the CP12‐like tail is not involved in the redox regulation of ADK 3, but contributes greatly to its stability, and is essential for the post‐translational modification of the Cys221 residue by glutathione. This report highlights the fact that the C‐terminal part of the CP12 protein can act as a moonlighting, intrinsically disordered module conferring additional capabilities to the proteins to which it is added.EnzymesAdenylate kinase (ADK, EC 2.7.4.3) and glyceraldehyde 3‐phosphate dehydrogenase (GAPDH, EC 1.2.1.13)
A simplified extreme method for determining double‐K fracture parameters of concrete using experimental peak load
Authors: Qing L.B. , Nie Y.T. , Wang J , Hu Y 
Published: July 2016

AbstractA simplified approach to obtain the double‐K fracture parameters of concrete for three‐point bending beams was proposed based on the extreme method. With the proposed method, the double‐K parameters can be easily obtained by the experimental peak load. This method requires fewer parameters or tests than the double‐K method and the peak load method. It also avoids complicated numerical integral compared with the traditional extreme method. The double‐K parameters obtained by the proposed method are slightly smaller than those by the double‐K method, and they do not seem to be influenced by the initial crack length to depth ratio.
The reliability of histological grade in breast cancer core needle biopsies depends on biopsy size: a comparative study with subsequent surgical excisions
Authors: Focke Cornelia M , Decker Thomas , van Diest Paul J 
Published: July 2016

AimsIn breast cancer patients undergoing neoadjuvant chemotherapy, histological grading needs to be performed on core needle biopsies (CNBs) that may not be representative of the whole tumour when they are small. Our aim was to study the influence of biopsy size on agreement rates for histological grade between CNBs and subsequent surgical excision biopsies (SEBs).Methods and resultsWe calculated agreement and Cohen's κ between CNBs and SEBs of 300 early‐stage breast cancers. The number of cores, total core length, total tumour length and tumour/tissue ratio were assessed for each CNB set. Agreement rates for grade were calculated for different classes of core number and tumour/tissue ratio, and for total core lengths and tumour lengths per CNB set in 5–15‐mm intervals. Agreement on grade between CNBs and SEBs was 73% (κ = 0.59), with underestimation of grade in CNBs in 26% of cases and overestimation in 1% of cases. There was significantly higher concordance between CNBs and SEBs at a total core length of ≥50 mm than at a total core length of <50 mm (83% versus 68% agreement, P = 0.007), at a tumour length of ≥15 mm than at tumour length of <15 mm in CNBs (79% versus 67% agreement, P = 0.036), and at three or more cores than at fewer than three cores (75% versus 58% agreement, P = 0.048). The tumour/tissue ratio, pathological tumour size and radiological tumour size were not statistically different between concordant and discordant cases.ConclusionsAgreement rates for histological grade in CNBs versus SEBs improve with increasing biopsy sample size.
Recent progress in the research about Propionibacterium acnes strain diversity and acne: pathogen or bystander?
Authors: Kwon Hyuck Hoon , Suh Dae Hun 
Published: July 2016

AbstractRecent progress has steadily reported the existence of the diverse strains of Propionibacterium acnes, and these studies have contributed to the elucidation of their contradictory roles between normal commensals and pathogens. In this review, the authors aimed to provide an update on the recent understanding of research about P. acnes strain diversity and acne, analyzing the potential implications for clinical applications. Before the era of genomic research, P. acnes was known to be distinguished based on serological agglutination tests, cell wall sugar analysis, or fermentation traits. Since the complete genome sequence of P. acnes was first deciphered, genetic studies based on sequence data have expanded with the introduction of more refined and precise DNA‐based typing methods, including multilocus sequence typing and metagenomics. These sophisticated techniques have revealed that P. acnes consists of phylogenetically distinct cluster groups with various pathogenic traits, including elicitation of inflammation, protein secretome profile, and unique distribution patterns in various skin loci. In following large‐scale studies from patients’ acne samples have revealed that specific sequence types are included within the phylogenetic divisions and further suggested that particular P. acnes strains play an etiologic role in acne while others are associated with health, providing a firm platform for evidential‐based research into the exact role of this organism in acne. We strongly believe that future research would provide fruitful results in not only clarifying the apparent controversy with respect to roles of P. acnes but also developing therapeutic drugs by pinpointing specific targets of the pathogenic strain only.
Ongoing outbreak of cutaneous leishmaniasis in northwestern Yemen: clinicoepidemiologic, geographic, and taxonomic study
Authors: Khatri Mishri Lal , Di Muccio Trentina , Fiorentino Eleonora , Gramiccia Marina 
Published: July 2016

AbstractBackgroundCutaneous leishmaniasis (CL) is widespread in Yemen but has not been fully documented.ObjectivesThis study aimed to investigate the clinicoepidemiologic and geographic aspects of CL in northwest Yemen and the taxonomic profile of the causative Leishmania species.MethodsAll CL cases diagnosed at the Dermatology Clinic of the Saudi Hospital at Hajjah during 1997–2012 were reviewed. Diagnoses were based on clinical, microscopic and, occasionally, histopathologic examinations. Leishmania species identification was carried out in 712 microscopically positive samples by multi‐locus enzyme electrophoresis and polymerase chain reaction–restriction fragment length polymorphism.ResultsDuring the surveillance period, 1343 cases of CL were diagnosed. Lesions per patient ranged from one to 71, but most patients had a single facial lesion, classified as representing the “dry type” in 1315 (97.9%) and “wet type” in 28 (2.1%) patients. Leishmania typing in 576 cases identified Leishmania tropica as the main species responsible (n = 529), followed by Leishmania infantum (n = 20), Leishmania donovani (n = 11), and members of the L. donovani complex (n = 8). Atypical molecular patterns were observed in eight CL cases diagnosed in areas in which the three Leishmania species were found sympatrically.ConclusionsCutaneous leishmaniasis appears to be endemic in northwest Yemen, where its incidence has recently increased abruptly. The disease presents clinically as the “dry type” and is caused mainly by L. tropica and occasionally by L. infantum, L. donovani, and L. donovani complex species. A sympatric diffusion of the three species is present in some governorates.
Evaluation of the correlation between serum levels of vitamin D and vitamin D receptor gene polymorphisms in an Egyptian population
Authors: Sobeih Shereen , Mashaly Heba M. , Gawdat Heba , Amr Khalda , Hamid Mahmoud Fawzy Abdel , Shaalan Eman 
Published: July 2016

AbstractBackgroundVitiligo is an autoimmune depigmentation disorder. Polymorphisms in the vitamin D receptor (VDR) have been found to be associated with vitiligo.ObjectivesTo evaluate the potential association between VDR gene polymorphisms (ApaI, TaqI, and FokI) and vitiligo susceptibility, and to detect if there is correlation between serum 25‐hydroxyvitamin D [25(OH)D] levels and vitiligo and between VDR gene polymorphisms and 25(OH)D levels in vitiligo.Materials and methodsSeventy‐five patients with vitiligo and 75 age and sex‐matched controls were subjected to detailed history taking and dermatological examination to determine the extent and clinical type of vitiligo. A blood sample (5 ml) was retrieved to investigate VDR gene polymorphisms and serum 25(OH)D level.ResultsOur results showed that the serum level of vitamin D is statistically significantly lower in patients than controls. The frequency of the ApaI variant a allele, the variant genotype (aa), and the variant genotype (tt) were significantly higher among the vitiligo cases than among controls. Our study also showed that the serum 25(OH)D levels were not significantly different among the different ApaI, TaqI, and FokI genotypes.ConclusionThe present study showed that serum level of 25(OH)D is statistically significantly lower in patients than controls, so screening for vitamin D deficiency seems of value in patients with vitiligo for the possibility of vitamin D supplementation. We also report that VDR gene polymorphisms may be a risk for the development of vitiligo in an Egyptian population.
IgG4‐related skin disease may have distinct systemic manifestations: a systematic review
Authors: Bennett Adam E. , Fenske Neil A. , Rodriguez‐Waitkus Paul , Messina Jane L. 
Published: July 2016

AbstractIgG4‐related disease (IgG4‐RD) is an increasingly prevalent protean multisystem disorder characterized by single or multi‐organ infiltration of IgG4‐bearing plasma cells. Skin involvement has been recognized and is relevant to proper diagnosis. A systematic literature review of 50 cases involving the skin reveals that patients with IgG4‐related skin disease show predominant involvement of the head and neck and have a distinct pattern of systemic involvement, also favoring the head and neck – lymphatics, orbit, salivary, and lacrimal glands – but generally lacking pancreaticobiliary involvement (16% of cases), which by contrast is a predominant manifestation in systemic IgG4‐RD (60% with pancreaticobiliary involvement). We summarize clinical and pathologic descriptive data from this systematic review. We review differential diagnosis and propose a diagnostic scheme for stratifying probability of disease based upon comprehensive integration of clinical, histopathologic, and laboratory data. Plasmacyte infiltration and storiform fibrosis are prominent in IgG4‐related skin disease, but obliterative venulitis is less common than in the prototypical IgG4‐related disease manifestation of autoimmune pancreatitis. IgG4 tissue and serum values, with a mean (±95% CI) in the reviewed cases of 132.8 ± 32.6 IgG4‐positive plasma cells per high‐power field and 580 ± 183.8 mg/dl, respectively, are incorporated into the suggested criteria. The distinct set of manifestations identified by this systematic review and the proposed diagnostic considerations, while requiring further validation in prospective studies, highlight the need to consider that IgG4‐related skin disease defines a unique systemic disease complex along the spectrum of IgG4‐RD.
Postoperative urinary incontinence exacerbates nocturia‐specific quality of life after robot‐assisted radical prostatectomy
Authors: Haga Nobuhiro , Aikawa Ken , Hoshi Seiji , Yabe Michihiro , Akaihata Hidenori , Hata Junya , Satoh Yuichi , Ogawa Soichiro , Ishibashi Kei , Kojima Yoshiyuki 
Published: July 2016

ObjectivesTo elucidate the effect of postoperative urinary incontinence on nocturia‐related quality of life after robot‐assisted radical prostatectomy.MethodsA total of 100 consecutive patients who underwent robot‐assisted radical prostatectomy completed a nocturia quality of life questionnaire score and a frequency‐volume chart before and after surgery. These patients were divided into two groups by continence status (continent and incontinent) according to the number of pad exchanges per day and the 1‐h pad test after surgery. Assessment was carried out before surgery, and then at 3 and 12 months after surgery.ResultsThe Nocturia Quality of Life questionnaire total score and the Bother/Concern subscore were significantly lower in incontinent patients at 3 and 12 months after surgery (Nocturia Quality of Life questionnaire total score: Bother/Concern subscores P = 0.006: P = 0.04 at 3 months after surgery; and P = 0.04: P = 0.02 at 12 months). Both nocturnal maximum voided volume and nocturnal frequency were not significantly different between continent and incontinent patients. On multivariate analysis, nocturnal urinary frequency (P = 0.01) and urinary incontinence (P = 0.005) were significantly associated with nocturia‐specific quality of life.ConclusionsAlthough the number of nocturia episodes was not significantly different between the continent and incontinent patients after surgery, the Nocturia Quality of Life questionnaire score was significantly worse in incontinent patients. In these patients, other than the number of nocturia episodes, psychological stress might worsen the Nocturia Quality of Life questionnaire score. Therefore, prevention of post‐prostatectomy incontinence might be important to avoid aggravating the Nocturia Quality of Life questionnaire score.
How does forest species specialization affect the application of the island biogeography theory in fragmented landscapes?
Authors: Dondina Olivia , Orioli Valerio , D'Occhio Pamela , Luppi Massimiliano , Bani Luciano 
Published: July 2016

AbstractAimOverall species richness in habitat remnants is seldom explained by the island biogeography theory (IBT). In this study, we tested the effectiveness of theIBTin explaining species richness of forest birds with or without considering the effect of the different forest specialization of species (generalist,edgeandinterior; community analysis). We also identified single species and groups of species that could serve as indicators of different fragmentation degrees (indicator species analysis).LocationBroadleaved forests in western Lombardy (northern Italy).MethodsWe evaluated bird species richness in 344 forest fragments. Fragment area (FA), distance from the nearest source area (> 1000 ha) (DSA) and number of neighbouring fragments (NF) were calculated for each fragment. Using Poisson generalized linear models, we compared a model that evaluated the relationships between fragment covariates and species richness to a model that also considered the effect of forest species specialization on each relationship. Moreover, we investigated the association between each species and particular fragmentation conditions by calculating the IndVal index.ResultsThe application of theIBTto species richness performed significantly better if we took into account forest species specialization when evaluating the effect of fragment covariates. In particular, the positive effects ofFAandNFand the negative effect ofDSAwere significantly stronger oninteriorspecies rather than ongeneralistandedgespecies. Using the IndVal index we identified six species in three groups strongly associated with specific fragmentation degrees.Main conclusionsThe results showed the strong influence of the specialization of species on their distribution in fragmented landscapes.Interiorspecies were the best candidates as a proxy of fragmentation effects. However, the indicator species analyses revealed that not allinteriorspecies showed the same sensitivity to fragment covariates.