bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giant Brunner's gland hamartoma diagnosed via endoscopic mucosal resection: A case report
Authors: Naito Sakiko , Fukuzawa Masakatsu , Nakamura Shunsuke , Kono Shin , Matsubayashi Jun , Itoi Takao 
Published: October 2021

AbstractWe report the case of a patient with a giant Brunner's gland hamartoma that was pathologically diagnosed by endoscopic mucosal resection. A 69‐year‐old woman presented with intermittent abdominal pain, and imaging revealed a smooth saccular submucosal tumor, 40 mm in diameter, on the anterior wall of the duodenal bulb. Brunner's gland and smooth muscle tissue were observed on endoscopic ultrasound‐guided fine‐needle aspiration biopsy, which resulted in the preoperative diagnosis of a duplication cyst. However, subsequent endoscopic mucosal resection established a final histopathological diagnosis of Brunner's gland hamartoma.
North Atlantic minke whale (Balaenoptera acutorostrata) feeding habits and migrations evaluated by stable isotope analysis of baleen
Authors: Eerkes‐Medrano Dafne , Aldridge David C. , Blix Arnoldus S. 
Published: October 2021

AbstractIsotopic analyses of the incrementally growing baleen in Mysticeti have been used to learn about their feeding and movement patterns. Using methods previously applied to Pacific minke whales, stable δ15N and δ13C isotope values were measured along the baleen plates of male and female minke whales from two locations in the Northeast Atlantic. The sample sizes used in this study are comparable to those previously used in the literature, and, although limited in size, the evidence suggests differences in isotopic signatures between whales caught at different locations. Both the δ15N and δ13C data suggest whales at the higher latitude site of Svalbard have a narrower diet than the whales from Lofoten/Vesterålen in Norway. Across all whales, the δ15N data indicate the whales primarily prey on fish for much of the year, only switching to zooplankton during the spring bloom. The δ13C data fail to confirm whether the whales migrate over long distances.
Using machine learning to model nontraditional spatial dependence in occupancy data
Authors: Mohankumar Narmadha M. , Hefley Trevor J. 
Published: October 2021

AbstractSpatial models for occupancy data are used to estimate and map the true presence of a species, which may depend on biotic and abiotic factors as well as spatial autocorrelation. Traditionally researchers have accounted for spatial autocorrelation in occupancy data by using a correlated normally distributed site‐level random effect, which might be incapable of modeling nontraditional spatial dependence such as discontinuities and abrupt transitions. Machine learning approaches have the potential to model nontraditional spatial dependence, but these approaches do not account for observer errors such as false absences. By combining the flexibility of Bayesian hierarchal modeling and machine learning approaches, we present a general framework to model occupancy data that accounts for both traditional and nontraditional spatial dependence as well as false absences. We demonstrate our framework using six synthetic occupancy data sets and two real data sets. Our results demonstrate how to model both traditional and nontraditional spatial dependence in occupancy data, which enables a broader class of spatial occupancy models that can be used to improve predictive accuracy and model adequacy.
Heparanase is a regulator of natural killer cell activation and cytotoxicity
Authors: Mayfosh Alyce J , Goodall Katharine J , Nguyen Tien , Baschuk Nikola , Hulett Mark D 
Published: October 2021

AbstractHeparanase is the only mammalian enzyme capable of cleaving heparan sulfate, a glycosaminoglycan of the extracellular matrix and cell surfaces. Most immune cells express heparanase that contributes to a range of functions including cell migration and cytokine expression. Heparanase also promotes natural killer (NK) cell migration; however, its role in other NK cell functions remains to be defined. In this study, heparanase-deficient (Hpse–/–) mice were used to assess the role of heparanase in NK cell cytotoxicity, activation, and cytokine production. Upon challenge with the immunostimulant polyinosinic:polycytidylic acid (poly(I:C)), NK cells isolated from Hpse–/– mice displayed impaired cytotoxicity against EO771.LMB cells and reduced levels of activation markers CD69 and NKG2D. However, in vitro cytokine stimulation of wild-type and Hpse–/– NK cells resulted in similar CD69 and NKG2D expression, suggesting the impaired NK cell activation in Hpse–/– mice results from elements within the in vivo niche. NK cells are activated in vivo by dendritic cells (DCs) in response to poly(I:C). Poly(I:C)-stimulated Hpse–/– bone marrow DCs (BMDCs) expressed less IL-12, and when cultured with Hpse–/– NK cells, less MCP-1 mRNA and protein was detected. Although cell-cell contact is important for DC-mediated NK cell activation, co-cultures of Hpse–/– BMDCs and NK cells showed similar levels of contact to wild-type cells, suggesting heparanase contributes to NK cell activation independently of cell-cell contact with DCs. These observations define a role for heparanase in NK cell cytotoxicity and activation and have important implications for how heparanase inhibitors currently in clinical trials for metastatic cancer may impact NK cell immunosurveillance.
Iterative differential autoregressive spectrum estimation for Raman spectrum denoising
Authors: Guo Yixin , Jin Weiqi , Guo Zongyu , He Yuqing 
Published: October 2021

AbstractAlthough ultraviolet (UV) laser Raman spectroscopy offers the benefits of stronger signals, partial separation of fluorescence and Raman spectra, and increased eye safety, it suffers from excessive noise, poor resolution, low maturity level, and small intensities of remotely acquired signals and therefore needs to be used in combination with effective denoising techniques. Herein, a denoising approach denoted as iterative differential autoregressive spectrum estimation was developed relying on the assumption that more detailed Raman peaks can be obtained by dividing the Raman spectrum into multiple layers with different intensity levels and estimating the energy distribution of each layer. Specifically, each layer was computed from the difference between the upper layer spectrum and its autoregressive model estimation spectrum, and the energy distribution at progressively lower intensity levels was considered. Compared with traditional techniques, our method exhibited good noise suppression performance and an excellent Raman peak restoration ability while offering the advantages of decreased spectral resolution loss and stable robustness. Cutoff optimization strategies were proposed to improve convergence and noise suppression ability and thus decrease the calculation time to 0.18 s and meet the needs of remote Raman spectrometers for real‐time denoising under the condition of long integration. The developed technique paves the way to Raman spectrum denoising based on power spectrum estimation, has a strong adaptive potential, and can be extended to other applications.
Distribution evaluation of tacrolimus in the ascitic fluid of liver transplant recipients with liver cirrhosis by a sensitive ultra‐performance liquid chromatography‐tandem mass spectrometry method
Authors: Yang Na , Du Yao , He Jun , Ge Jiajia , Wang Min , Sun Runbin , Zhu Huaijun , Ge Weihong 
Published: October 2021

AbstractTacrolimus has a narrow therapeutic index and large individual differences in pharmacokinetics. The distribution of tacrolimus in ascitic fluid and its influence on whole‐blood tacrolimus were unclear. In this study, a sensitive ultra‐performance liquid chromatography‐tandem mass spectrometry method was established and validated for the quantification of tacrolimus in the ascitic fluid of liver transplant recipients. Chromatographic separation was achieved on an Agilent ZORBAX Eclipse Plus Phenyl‐Hexyl column (2.1 × 100 mm, 3.5 μm). Mass spectrometry was performed in multiple reaction monitoring conditions of transitions m/z 821.4→768.5 for tacrolimus. The concentrations of tacrolimus in the ascitic fluid range from 0.2 to 3.0 ng/mL, accounting for 1.19–31.87% of whole‐blood tacrolimus concentrations. A linear mixed model showed a statistically significant positive correlation between the steady‐state trough blood concentration of tacrolimus and the corresponding amount of tacrolimus excreted in the ascitic fluid for 24 consecutive hours, especially after normalization by daily dose per unit body weight. These data suggested that the distribution of tacrolimus in the ascitic fluid has great individual differences. The whole‐blood tacrolimus concentration, dose per unit body weight, and other confounding factors may contribute to the excretion of tacrolimus in ascitic fluid, but the influence of tacrolimus excretion in drained ascitic fluid on the whole‐blood tacrolimus concentration is negligible.
Mechanism of activation and the rewired network: New drug design concepts
Authors: Nussinov Ruth , Zhang Mingzhen , Maloney Ryan , Tsai Chung‐Jung , Yavuz Bengi Ruken , Tuncbag Nurcan , Jang Hyunbum 
Published: October 2021

AbstractPrecision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same‐allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure‐based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor‐specific network, ushering innovative considerations in precision medicine.
Forensic advisors: The missing link
Authors: Bitzer Sonja , Miranda Michelle D. , Bucht Rebecca E. 
Published: October 2021

AbstractIn this paper we advocate for the re‐establishment of the generalist role in forensic science systems in the form of a forensic advisor. The generalist can be defined as an individual possessing a broad scientific knowledge base coupled with comprehensive knowledge of forensic science, criminalistics, traces, crime scene and criminal investigations. The forensic advisor's role is that of a collaborative, non‐competitive effort intended to provide scientific consultation with the myriad actors in the investigative process to advance justice and aid in crime prevention efforts. The generalist forensic scientist, in the role of forensic advisor, helps bridge gaps and break down silos by facilitating communication between actors and overseeing the potential contribution of traces in investigatory efforts. The purposes of this paper are to address the current status of forensic advisors within existing organisational frameworks; to propose roles and responsibilities of the forensic advisor; to delineate the key attributes of the forensic advisor; and to present challenges to implementing this advisor role within a jurisdiction. In developing the roles and responsibilities of the forensic advisor, we examine front‐end, midpoint and back‐end stages of an investigation. Despite organizational challenges explored in this article, the introduction of forensic advisors can serve to diversify the contribution of forensic science and improve the efficiency of the delivery of forensic science services.This article is categorized under:
Crime Scene Investigation > Crime Scene Examination
Crime Scene Investigation > From Traces to Intelligence and Evidence
Jurisprudence and Regulatory Oversight > Interdisciplinary Collaboration
Complex Langevin dynamics and supersymmetric quantum mechanics
Authors: Joseph Anosh , Kumar Arpith 
Published: October 2021

Abstract
Using complex Langevin method we probe the possibility of dynamical supersymmetry breaking in supersymmetric quantum mechanics models with complex actions. The models we consider are invariant under the combined operation of parity and time reversal, in addition to supersymmetry. When actions are complex traditional Monte Carlo methods based on importance sampling fail. Models with dynamically broken supersymmetry can exhibit sign problem due to the vanishing of the partition function. Complex Langevin method can successfully evade the sign problem. Our simulations suggest that complex Langevin method can reliably predict the absence or presence of dynamical supersymmetry breaking in these one-dimensional models with complex actions.
Illuminating entanglement shadows of BTZ black holes by a generalized entanglement measure
Authors: Gerbershagen Marius 
Published: October 2021

Abstract
We define a generalized entanglement measure in the context of the AdS/CFT correspondence. Compared to the ordinary entanglement entropy for a spatial subregion dual to the area of the Ryu-Takayanagi surface, we take into account both entanglement between spatial degrees of freedom as well as between different fields of the boundary theory. Moreover, we resolve the contribution to the entanglement entropy of strings with different winding numbers in the bulk geometry. We then calculate this generalized entanglement measure in a thermal state dual to the BTZ black hole in the setting of the D1/D5 system at and close to the orbifold point. We find that the entanglement entropy defined in this way is dual to the length of a geodesic with non-zero winding number. Such geodesics probe the entire bulk geometry, including the entanglement shadow up to the horizon in the one-sided black hole as well as the wormhole growth in the case of a two-sided black hole for an arbitrarily long time. Therefore, we propose that the entanglement structure of the boundary state is enough to reconstruct asymptotically AdS3 geometries up to extremal surface barriers.
Estimating a gradual parameter change in an AR(1)-process
Authors: Hušková Marie , Prášková Zuzana , Steinebach Josef G. 
Published: October 2021

AbstractWe discuss the estimation of a change-point $$t_0$$

t
0

at which the parameter of a (non-stationary) AR(1)-process possibly changes in a gradual way. Making use of the observations $$X_1,\ldots ,X_n$$

X
1

,
…
,

X
n

, we shall study the least squares estimator $$\widehat{t}_0$$

t
^

0

for $$t_0$$

t
0

, which is obtained by minimizing the sum of squares of residuals with respect to the given parameters. As a first result it can be shown that, under certain regularity and moment assumptions, $$\widehat{t}_0/n$$

t
^

0

/
n

is a consistent estimator for $$\tau _0$$

τ
0

, where $$t_0 =\lfloor n\tau _0\rfloor $$

t
0

=

⌊
n

τ
0

⌋

, with $$0<\tau _0<1$$

0
<

τ
0

<
1

, i.e., $$\widehat{t}_0/n \,{\mathop {\rightarrow }\limits ^{P}}\,\tau _0$$

t
^

0

/
n

→
P

τ
0

$$(n\rightarrow \infty )$$

(
n
→
∞
)

. Based on the rates obtained in the proof of the consistency result, a first, but rough, convergence rate statement can immediately be given. Under somewhat stronger assumptions, a precise rate can be derived via the asymptotic normality of our estimator. Some results from a small simulation study are included to give an idea of the finite sample behaviour of the proposed estimator.
Lymphocyte subsets in the peripheral blood are disturbed in systemic sclerosis patients and can be changed by immunosuppressive medication
Authors: Gernert Michael , Tony Hans-Peter , Schwaneck Eva Christina , Gadeholt Ottar , Fröhlich Matthias , Portegys Jan , Strunz Patrick-Pascal , Schmalzing Marc 
Published: October 2021

AbstractSystemic sclerosis (SSc) is a severe chronic disease with a broad spectrum of clinical manifestations. SSc displays disturbed lymphocyte homeostasis. Immunosuppressive medications targeting T or B cells can improve disease manifestations. SSc clinical manifestations and immunosuppressive medication in itself can cause changes in lymphocyte subsets. The aim of this study was to investigate peripheral lymphocyte homeostasis in SSc with regards to the immunosuppression and to major organ involvement. 44 SSc patients and 19 healthy donors (HD) were included. Immunophenotyping of peripheral whole blood by fluorescence-activated cell sorting was performed. Cytokine secretions of stimulated B cell cultures were measured. SSc patients without immunosuppression compared to HD displayed lower γδ T cells, lower T helper cells (CD3+/CD4+), lower transitional B cells (CD19+/CD38++/CD10+/IgD+), lower pre-switched memory B cells (CD19+/CD27+/IgD+), and lower post-switched memory B cells (CD19+/CD27+/IgD−). There was no difference in the cytokine production of whole B cell cultures between SSc and HD. Within the SSc cohort, mycophenolate intake was associated with lower T helper cells and lower NK cells (CD56+/CD3−). The described differences in peripheral lymphocyte subsets between SSc and HD generate further insight in SSc pathogenesis. Lymphocyte changes under effective immunosuppression indicate how lymphocyte homeostasis in SSc might be restored.
Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses
Authors: Upadhyay Rakesh K. , Shao Jonathan , Mattoo Autar K. 
Published: October 2021

Abstract
Main conclusion
Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH.

Abstract
Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant.
Protein carbonylation in food and nutrition: a concise update
Authors: Estévez Mario , Díaz-Velasco Silvia , Martínez Remigio 
Published: October 2021

AbstractProtein oxidation is a topic of indisputable scientific interest given the impact of oxidized proteins on food quality and safety. Carbonylation is regarded as one of the most notable post-translational modifications in proteins and yet, this reaction and its consequences are poorly understood. From a mechanistic perspective, primary protein carbonyls (i.e. α-aminoadipic and γ-glutamic semialdehydes) have been linked to radical-mediated oxidative stress, but recent studies emphasize the role alternative carbonylation pathways linked to the Maillard reaction. Secondary protein carbonyls are introduced in proteins via covalent linkage of lipid carbonyls (i.e. protein-bound malondialdehyde). The high reactivity of protein carbonyls in foods and other biological systems indicates the intricate chemistry of these species and urges further research to provide insight into these molecular mechanisms and pathways. In particular, protein carbonyls are involved in the formation of aberrant and dysfunctional protein aggregates, undergo further oxidation to yield carboxylic acids of biological relevance and establish interactions with other biomolecules such as oxidizing lipids and phytochemicals. From a methodological perspective, the routine dinitrophenylhydrazine (DNPH) method is criticized not only for the lack of accuracy and consistency but also authors typically perform a poor interpretation of DNPH results, which leads to misleading conclusions. From a practical perspective, the biological relevance of protein carbonyls in the field of food science and nutrition is still a topic of debate. Though the implication of carbonylation on impaired protein functionality and poor protein digestibility is generally recognized, the underlying mechanism of such connections requires further clarification. From a medical perspective, protein carbonyls are highlighted as markers of protein oxidation, oxidative stress and disease. Yet, the specific role of specific protein carbonyls in the onset of particular biological impairments needs further investigations. Recent studies indicates that regardless of the origin (in vivo or dietary) protein carbonyls may act as signalling molecules which activate not only the endogenous antioxidant defences but also implicate the immune system. The present paper concisely reviews the most recent advances in this topic to identify, when applicable, potential fields of interest for future studies.