bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered molecular signatures during kidney development after intrauterine growth restriction of different origins
Authors: Nüsken Eva , Fink Gregor , Lechner Felix , Voggel Jenny , Wohlfarth Maria , Sprenger Lisa , Mehdiani Nava , Weber Lutz T. , Liebau Max Christoph , Brachvogel Bent , Dötsch Jörg , Nüsken Kai-Dietrich 
Published: February 2020

Abstract
This study was performed to identify transcriptional alterations in male intrauterine growth restricted (IUGR) rats during and at the end of nephrogenesis in order to generate hypotheses which molecular mechanisms contribute to adverse kidney programming. IUGR was induced by low protein (LP) diet throughout pregnancy, bilateral uterine vessel ligation (LIG), or intrauterine stress (IUS) by sham operation. Offspring of unimpaired dams served as controls. Significant acute kidney damage was ruled out by negative results for proteins indicative of ER-stress, autophagy, apoptosis, or infiltration with macrophages. Renal gene expression was examined by transcriptome microarrays, demonstrating 53 (LP, n = 12; LIG, n = 32; IUS, n = 9) and 134 (LP, n = 10; LIG, n = 41; IUS, n = 83) differentially expressed transcripts on postnatal days (PND) 1 and 7, respectively. Reduced Pilra (all IUGR groups, PND 7), Nupr1 (LP and LIG, PND 7), and Kap (LIG, PND 1) as well as increased Ccl20, S100a8/a9 (LIG, PND 1), Ifna4, and Ltb4r2 (IUS, PND 7) indicated that inflammation-related molecular dysregulation could be a “common” feature after IUGR of different origins. Network analyses of transcripts and predicted upstream regulators hinted at proinflammatory adaptions mainly in LIG (arachidonic acid-binding, neutrophil aggregation, toll-like-receptor, NF-kappa B, and TNF signaling) and dysregulation of AMPK and PPAR signaling in LP pups. The latter may increase susceptibility towards obesity-associated kidney damage. Western blots of the most prominent predicted upstream regulators confirmed significant dysregulation of RICTOR in LP (PND 7) and LIG pups (PND 1), suggesting that mTOR-related processes could further modulate kidney programming in these groups of IUGR pups.

Key messages

Inflammation-related transcripts are dysregulated in neonatal IUGR rat kidneys.

Upstream analyses indicate renal metabolic dysregulation after low protein diet.

RICTOR is dysregulated after low protein diet and uterine vessel ligation.
Concordance as evidence in the Watson for Oncology decision-support system
Authors: Tupasela Aaro , Di Nucci Ezio 
Published: February 2020

AbstractMachine learning platforms have emerged as a new promissory technology that some argue will revolutionize work practices across a broad range of professions, including medical care. During the past few years, IBM has been testing its Watson for Oncology platform at several oncology departments around the world. Published reports, news stories, as well as our own empirical research show that in some cases, the levels of concordance over recommended treatment protocols between the platform and human oncologists have been quite low. Other studies supported by IBM claim concordance rates as high as 96%. We use the Watson for Oncology case to examine the practice of using concordance levels between tumor boards and a machine learning decision-support system as a form of evidence. We address a challenge related to the epistemic authority between oncologists on tumor boards and the Watson Oncology platform by arguing that the use of concordance levels as a form of evidence of quality or trustworthiness is problematic. Although the platform provides links to the literature from which it draws its conclusion, it obfuscates the scoring criteria that it uses to value some studies over others. In other words, the platform “black boxes” the values that are coded into its scoring system.
Pyramid Ricci flow in higher dimensions
Authors: McLeod Andrew D. , Topping Peter M. 
Published: February 2020

AbstractIn this paper, we construct a pyramid Ricci flow starting with a complete Riemannian manifold $$(M^n,g_0)$$

(

M
n

,

g
0

)

that is PIC1, or more generally satisfies a lower curvature bound $${\mathrm {K_{IC_1}}}\ge -\alpha _0$$

K

IC
1

≥
-

α
0

. That is, instead of constructing a flow on $$M\times [0,T]$$

M
×
[
0
,
T
]

, we construct it on a subset of space-time that is a union of parabolic cylinders $${{\mathbb {B}}}_{g_0}(x_0,k)\times [0,T_k]$$

B

g
0

(

x
0

,
k
)

×

[
0
,

T
k

]

for each $$k\in {{\mathbb {N}}}$$

k
∈
N

, where $$T_k\downarrow 0$$

T
k

↓
0

, and prove estimates on the curvature and Riemannian distance. More generally, we construct a pyramid Ricci flow starting with any noncollapsed $$\mathrm {IC_1}$$

IC
1

-limit space, and use it to establish that such limit spaces are globally homeomorphic to smooth manifolds via homeomorphisms that are locally bi-Hölder.
Investigating surrogate cerebrospinal fluid matrix compositions for use in quantitative LC-MS analysis of therapeutic antibodies in the cerebrospinal fluid
Authors: Fogh Jens Rose , Jacobsen Anne-Marie , Nguyen Tam T. T. N. , Rand Kasper D. , Olsen Line Rørbæk 
Published: February 2020

AbstractAs quantitative analysis of biotherapeutics in cerebrospinal fluid (CSF) with LC-MS becomes increasingly widespread, there is a need for method developments towards higher sensitivity. By using artificial CSF (aCSF) in the development phase, the consumption of costly and sparsely available CSF can be limited. The aCSF compositions tested here were made from various dilutions of bovine serum albumin (BSA) or rat plasma to mimic the total protein concentration found in CSF. Focusing on monoclonal antibodies, the aCSF was spiked with human immunoglobulin (hIgG) and prepared with the bottom-up analysis technique using LC-MS. Assuming that the composition of the aCSF would affect the digest, the response from aCSF matrices was compared with CSF from rat, monkey, and dog in terms of estimated sample concentration and matrix effects. The samples were spiked with hIgG in the range of 10 to 1000 ng/mL and volumes of 10 μL were transferred to sample preparation. The results indicate that BSA dilutions from 300 to 2000 μg/mL and rat plasma dilutions of 0.5–2% provide the most accurate concentration estimates when compared with rat CSF. 1000 μg/mL BSA did not produce significantly different concentration estimates for 500 ng/mL samples when compared with CSF from rat, monkey, and dog, and can therefore be used as aCSF for several different species.
Sonicated extracts from the Quorn fermentation co-product as oil-lowering emulsifiers and foaming agents
Authors: Lonchamp J. , Akintoye M. , Clegg P. S. , Euston S. R. 
Published: February 2020

Abstract
This study assessed the impact of sonication on the structure and properties of a functional extract (retentate 100 or R100) from the Quorn fermentation co-product (centrate). In a previous study, we reported that the R100 fraction displayed good foaming, emulsifying and rheological properties. Sonication of a R100 solution led to the breakdown of the large hyphal structures characteristic of this extract into smaller fragments. Foams prepared with sonicated R100 displayed a higher foaming ability than with untreated R100 and a high foam stability but lower than untreated R100 ones. Oil-in-water emulsions prepared with sonicated R100 displayed smaller oil droplet size distributions than with untreated R100. Confocal micrographs suggested that small fungal fragments contributed to the stabilisation of oil droplets. 50% oil-reduced R100 emulsions were prepared by mixing R100 emulsions (untreated or sonicated) with a sonicated R100 solution at a 1:1 ratio. Smaller oil droplet size distributions were reported for the oil-reduced emulsions. These results showed that the addition of small hyphal fragments or surface-active molecules and molecular aggregates released during sonication contributed to the formation and stabilisation of smaller oil droplets. This study highlighted the potential to modulate the structure, emulsifying and foaming properties of functional extracts from the Quorn fermentation co-product by sonication and the potential of these extracts as oil-lowering agents in emulsion-based products through the reduction of oil droplet size and their stabilisation.

Graphical abstract
Severity of Fontan-Associated Liver Disease Correlates with Fontan Hemodynamics
Authors: Schleiger Anastasia , Salzmann Madeleine , Kramer Peter , Danne Friederike , Schubert Stephan , Bassir Christian , Müller Tobias , Müller Hans-Peter , Berger Felix , Ovroutski Stanislav 
Published: February 2020

AbstractFontan-palliated patients are at risk for the development of Fontan-associated liver disease (FALD). In this study, we performed a detailed hemodynamic and hepatic assessment to analyze the incidence and spectrum of FALD and its association with patients' hemodynamics. From 2017 to 2019, 145 patients underwent a detailed, age-adjusted hepatic examination including laboratory analysis (FibroTest®, n = 101), liver ultrasound (n = 117) and transient elastography (FibroScan®, n = 61). The median patient age was 16.0 years [IQR 14.2], and the median duration of the Fontan circulation was 10.3 years [IQR 14.7]. Hemodynamic assessment was performed using echocardiography, cardiopulmonary exercise capacity testing and cardiac catheterization. Liver ultrasound revealed hepatic parenchymal changes in 83 patients (70.9%). Severe liver cirrhosis was detectable in 20 patients (17.1%). Median liver stiffness measured by FibroScan® was 27.7 kPa [IQR 14.5], and the median Fibrotest® score was 0.5 [IQR 0.3], corresponding to fibrosis stage ≥ 2. Liver stiffness values and Fibrotest® scores correlated significantly with Fontan duration (P1 = 0.013, P2 = 0.012). Exercise performance was significantly impaired in patients with severe liver cirrhosis (P = 0.003). Pulmonary artery pressure and end-diastolic pressure were highly elevated in cirrhotic patients (P1 = 0.008, P2 = 0.003). Multivariable risk factor analysis revealed Fontan duration to be a major risk factor for the development of FALD (P < 0.001, OR 0.77, CI 0.68–0.87). In the majority of patients, hepatic abnormalities suggestive of FALD were detectable by liver ultrasound, transient elastography and laboratory analysis. The severity of FALD correlated significantly with Fontan duration and impaired Fontan hemodynamics. A detailed hepatic assessment is indispensable for long-term surveillance of Fontan patients.
Cannings models, population size changes and multiple-merger coalescents
Authors: Freund Fabian 
Published: February 2020

AbstractMultiple-merger coalescents, e.g. $$\varLambda $$Λ-n-coalescents, have been proposed as models of the genealogy of n sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman’s n-coalescent. $$\varLambda $$Λ-n-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size $$N\rightarrow \infty $$N→∞. As established for Kingman’s n-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. For $$\varLambda $$Λ-n-coalescents, this has been explicitly shown for only a limited subclass of $$\varLambda $$Λ-n-coalescents and exponentially growing populations. This article gives a more general construction of time-changed $$\varLambda $$Λ-n-coalescents as limits of specific Cannings models with rather arbitrary time changes.
Prevalence and clinical presentation of lymphoproliferative disorder in patients with primary Sjögren’s syndrome
Authors: Sebastian Agata , Madej Marta , Sebastian Maciej , Butrym Aleksandra , Woytala Patryk , Hałoń Agnieszka , Wiland Piotr 
Published: February 2020

AbstractLymphomas are one of the serious complications of the primary Sjörgen’s Syndrome (pSS). The aim of the study was to evaluate the frequency of lymphoma in pSS. The singe-center retrospective study included 198 Caucasian patients, who met diagnostic criteria for pSS. The type of lymphoproliferative disorder was classified according to the WHO 2016 classification. The mean time of observation, after pSS diagnosis, was 48 weeks. Focus score (FS) ≥ 1 was present in 85% of the patients, and anti-SSA antibodies were detected in 84%. Rheumatoid factor was detected in 130 (65%) patients. Mean disease activity index, according to EULAR Sjörgen’s Syndrome disease activity index (ESSDAI), was 8.3 points at the moment of pSS diagnosis. Complement C3 was decreased in 14% of the patients, while 10% showed reduced complement C4. Four patients (2%) were diagnosed with a lymphoma. Most of the patients were diagnosed with mucosa-associated lymphoid tissue lymphoma (MALT), in whom the tumour was located in the parotid gland, and in one patient the stomach was involved. Finally, one patient was diagnosed with a rare B-cell small lymphocytic lymphoma located in the lungs. In this article, we present detailed characteristics of each case. In analysed population the frequency of lymphoma in the course of pSS in patients with pSS is 2%. The variety of lymphoma types in pSS patients imposes individual monitoring in each patient at every check-up visit for disease activity.
Impact of different earthworm ecotypes on water stable aggregates and soil water holding capacity
Authors: Hallam Jamal , Hodson Mark E. 
Published: February 2020

AbstractWe carried out mesocosm experiments using either the anecic earthwormLumbricus terrestrisor the endogeic earthwormAllolobophora chloroticaand loam, silt loam and sandy loam soils to investigate the differing impact of these earthworm of different ecotypes on aggregate formation (percentage water stable aggregates, %WSA) and soil water holding capacity (WHC), two soil properties that underpin many of the ecosystem services provided by soils. Earthworms significantly increased %WSA (by 16–56% and 19–63% relative to earthworm-free controls forL. terrestrisandA. chlorotica, respectively). ForL. terrestris, this increase was significantly greater in the upper 6.5 cm of the soil where their casts were more obviously present.Allobophora chloroticatreatments significantly increased WHC by 7–16%.L. terrestrisonly caused a significant increase in WHC (of 11%) in the upper 6.5 cm of the sandy loam soil. Linear regression indicated a consistent relationship between increases in %WSA and WHC for both earthworm species. However, for a given %WSA, WHC was higher forA. chloroticathanL. terrestrislikely due to the known differences in their burrow structure. Overall, earthworms increased soil %WSA and WHC but the significant species/ecotype differences need to be considered in discussions of the beneficial impacts of earthworms to soil properties.
Quantitative serological antibody testing for suspected neuroborreliosis
Authors: Schneider Christian , Gielen Jörg , Röth Philip , Albrecht Philipp , Schroeter Michael , Fink Gereon R. , Wunderlich Gilbert , Lehmann Helmar C. 
Published: February 2020

Abstract
Objective
To assess the importance of serum IgG/IgM antibody titers for the differentiation of Lyme neuroborreliosis (LNB) from its mimics.

Method
This was a retrospective, cross-sectional study conducted at two German neurological centers. Serological parameters (ELISA or CLIA analysis) and clinical presentation of 28 patients with definite LNB were compared to those of 36 patients with neurological symptoms mimicking LNB (mimics). Analysis was performed using receiver operating characteristic (ROC) and binary logistic regression.

Results
Elevated IgG-titers had a high sensitivity for neuroborreliosis in both centers (0.95 and 1.0). The optimal cutoff-values were set to 26.35 in center A (ELISA), and 64.0 in center B (CLIA). Diagnostic specificity was 0.41 and 0.89 in this constellation. Elevated IgM-titers showed a high diagnostic specificity for a cutoff at 68.10 (A) and 47.95 (B) (0.93 and 0.89). Sensitivity was 0.45 and 0.5. Overall diagnostic accuracy was low in both centers (A: IgG AUC = 0.665, IgM AUC = 0.629; B: IgG AUC = 0.917, IgM AUC = 0.556). In logistic regression of antibody titers and clinical measures, prediction of LNB was significantly better than the “null hypothesis”. Clinical measures showed the highest odds ratio.

Conclusion
Data show that in addition to the clinical presentation of patients with symptoms suggesting central or peripheral nervous system manifestation, serum IgG- and IgM-titers help to identify LNB-patients. The results should guide physicians counseling patients with suspected LNB about further diagnostic steps and treatment.
Parasitic infections represent a significant health threat among recent immigrants in Chicago
Authors: Herrick Jesica A. , Nordstrom Monica , Maloney Patrick , Rodriguez Miguel , Naceanceno Kevin , Gallo Gloria , Mejia Rojelio , Hershow Ron 
Published: February 2020

AbstractParasitic infections are likely under-recognized among immigrant populations in the USA. We conducted a cross-sectional study to evaluate if such infections have health impacts among recent immigrants in Chicago and to identify predictive factors for parasitic infections. A total of 133 recent immigrants were enrolled, filling out a standardized medical questionnaire and providing blood and stool samples. Appriximately 12% of subjects (15/125) who provided a blood or stool sample for testing were found to have evidence of current or prior infection with a pathogenic parasite, of whichToxocaraspp.(8 subjects, 6.4%) andStrongyloides stercoralis(5 subjects, 4%) were most commonly identified. Parasitic infection was more likely among subjects who had immigrated within the previous 2 years and those with a self-reported history of worms in the stool. The most useful surrogate markers identified for parasitic infections were an elevated immunoglobulin E level (seen in 46.7% (7/15) of subjects with parasitic infections and 20% (22/110) of uninfected individuals,p = 0.04) and the presence ofBlastocystis hominiscysts on Ova & Parasite exam (detected in 38.5% (5/13) of subjects with parasitic infections who provided a stool sample and 5.1% (5/98) of uninfected subjects,p = 0.002). Our study found that parasitic infections may be common in recent US immigrants, which highlights an important health disparity among a vulnerable population that merits further study. Additionally, clinical risk factors, symptoms, and laboratory findings traditionally thought to be associated with parasites were commonly found but not predictive of infection in this study population.
Age and sex differences in numerical responses, dietary shifts, and total responses of a generalist predator to population dynamics of main prey
Authors: Masoero Giulia , Laaksonen Toni , Morosinotto Chiara , Korpimäki Erkki 
Published: February 2020

AbstractFluctuations in the abundance of main prey species might shape animal communities, by inducing numerical responses and dietary shifts in predators. Whether numerical responses and dietary shifts differ among individuals of different age and sex has so far gained little attention. These differences could affect how much predators consume main and alternative prey, thus causing variation in predation pressure on main and alternative prey species. We studied the effect of fluctuating main prey abundance (voles) in autumn on the age and sex composition of a food-hoarding population of Eurasian pygmy owls Glaucidium passerinum (327 individuals), and on the species composition of their food stores in western Finland during 2003–2017 (629 food stores). Numbers of yearlings (< 1-year old) of both sexes and adult (+ 1-year old) females increased with increasing vole abundance. During low vole abundance, adult owls stored more small birds and less small mammals than yearlings. Females stored more small mammals than males and showed a tendency to store less birds. The amount of consumed birds (the most important alternative prey), and in particular of crested, willow, great, and blue tits, increased with low vole densities. Our results show that numerical, functional, and total responses of pygmy owls, and probably also other vertebrate predators, to the availability of the main prey in winter are shaped by the age and sex composition of the predator population, which both show large spatio-temporal variation in boreal forests.
Embedding Small Digraphs and Permutations in Binary Trees and Split Trees
Authors: Albert Michael , Holmgren Cecilia , Johansson Tony , Skerman Fiona 
Published: February 2020

AbstractWe investigate the number of permutations that occur in random labellings of trees. This is a generalisation of the number of subpermutations occurring in a random permutation. It also generalises some recent results on the number of inversions in randomly labelled trees (Cai et al. in Combin Probab Comput 28(3):335–364, 2019). We consider complete binary trees as well as random split trees a large class of random trees of logarithmic height introduced by Devroye (SIAM J Comput 28(2):409–432, 1998.10.1137/s0097539795283954). Split trees consist of nodes (bags) which can contain balls and are generated by a random trickle down process of balls through the nodes. For complete binary trees we show that asymptotically the cumulants of the number of occurrences of a fixed permutation in the random node labelling have explicit formulas. Our other main theorem is to show that for a random split tree, with probability tending to one as the number of balls increases, the cumulants of the number of occurrences are asymptotically an explicit parameter of the split tree. For the proof of the second theorem we show some results on the number of embeddings of digraphs into split trees which may be of independent interest.
Subgraph Complementation
Authors: Fomin Fedor V. , Golovach Petr A. , Strømme Torstein J. F. , Thilikos Dimitrios M. 
Published: February 2020

AbstractA subgraph complement of the graph G is a graph obtained from G by complementing all the edges in one of its induced subgraphs. We study the following algorithmic question: for a given graph G and graph class $${\mathscr {G}}$$G, is there a subgraph complement of G which is in $${\mathscr {G}}$$G? We show that this problem can be solved in polynomial time for various choices of the graphs class $${\mathscr {G}}$$G, such as bipartite, d-degenerate, or cographs. We complement these results by proving that the problem is $${{\mathrm{NP}}}$$NP-complete when $${\mathscr {G}}$$G is the class of regular graphs.
Placing Labels in Road Maps: Algorithms and Complexity
Authors: Gemsa Andreas , Niedermann Benjamin , Nöllenburg Martin 
Published: February 2020

AbstractA road map can be interpreted as a graph embedded in the plane, in which each vertex corresponds to a road junction and each edge to a particular road section. In this paper, we consider the computational cartographic problem to place non-overlapping road labels along the edges so that as many road sections as possible are identified by their name, i.e., covered by a label. We show that this is -hard in general, but the problem can be solved in $$O(n^3)$$O(n3) time if the road map is an embedded tree with n vertices and constant maximum degree. This special case is not only of theoretical interest, but our algorithm in fact provides a very useful subroutine in exact or heuristic algorithms for labeling general road maps.