bluuebunny/crossref_metadata_2025 huggingface dataset:
Tandem mass tagging combined with liquid chromatography–tandem mass spectrometry technique to detect protein markers in gastroesophageal junction adenocarcinoma
Authors: Zheng Xiuli , Bi Yanna , Yang Tianshuo , Zhao Lianmei , Wu Mingli , Er Limian , Liu Yao , Li Shengmian
Published: July 2022

Background

Gastroesophageal junction adenocarcinoma (GEJA) is a malignant tumor located at the junction of the esophagus and stomach, the incidence of which is increasing year by year, while screening for early biomarkers is limited. Tandem mass tagging (TMT) coupled with liquid chromatography–tandem mass spectrometry (LC/MS/MS) has been used to screen for differential proteins in various cancers.

Methods

Differential proteins in GEJA and precancerous lesions were screened using TMT–LC/MS/MS, and then proteins that met expectations were selected for trend clustering analysis, combined with GO and KEGG analysis for functional annotation of differential proteins in GEJA. Then, parallel reaction monitoring and immunohistochemistry techniques were used to validate the accuracy of the proteomics data.

Results

Our group screened the differential proteins during GEJA progression using proteomics technology, analyzed the expression trends and functional regions involved in the differential proteins during carcinogenesis, and validated the accuracy of the experimental results.

Conclusions

The screening of differential proteins in GEJA carcinogenesis based on TMT–LC/MS/MS technology provides detailed information for the elucidation of GEJA progression process, pathogenesis, early screening and screening of candidate markers.
Efficient secure state estimation against sparse integrity attack for regular linear system
Authors: Li Zishuo , Mo Yilin
Published: July 2022

We consider the problem of estimating the state of a time‐invariant linear Gaussian system in the presence of integrity attacks. The attacker can compromise out of sensors, the set of which is fixed over time and unknown to the system operator, and manipulate the measurements arbitrarily. Under the assumption that the system is regular and system matrix is non‐singular, we propose a secure estimation scheme that is resilient to ‐sparse attack as long as the system is ‐sparse detectable, which achieves the fundamental limit of secure dynamic estimation. In the absence of attack, the proposed estimation coincides with Kalman estimation with a certain probability that can be adjusted to trade‐off between performance with and without attack. Furthermore, the detectability condition checking in the designing phase and the estimation computing in the online operating phase are both computationally efficient. Two numerical examples including the IEEE 68 bus test system are provided to corroborate the results and illustrate the performance of the proposed estimator.
Synthesis of Quinoline and Polyhydroquinoline Derivatives Using Phloroglucinol Cored Amino Functionalized Dendritic Polymer as Catalyst
Authors: Vettukattil Unnikrishnan , Govindan Avudaiappan , Yousuf Naeema , Alex Saji , Krishnapillai Sreekumar
Published: July 2022

Phloroglucinol cored primary amine‐functionalized G0 dendritic polymer (PHG−G0) was effectively synthesized. The polymer was characterized by different spectroscopic and analytical techniques including Fourier transform infrared (FT‐IR) and Nuclear magnetic resonance (NMR) spectra, Thermogravimetric Analysis (TG‐DTG) and Gel Permeation Chromatography (GPC). The catalytic efficiency of the PHG−G0 was evaluated in the three‐component one‐pot green synthesis of quinoline and four component synthesis of polyhydroquinoline derivatives. Quinoline derivatives were obtained 92 % of yield within 60 minutes in water/ethanol (1 : 1) (v/v) mixture as solvent and polyhydroquinoline derivatives were obtained 90 % of yield within 30 minutes in acetonitrile as solvent under reflux conditions. High amino group capacity and high thermal stability made the PHG−G0 dendritic polymer a good base catalyst. All the quinoline and polyhydroquinoline derivatives were characterized by determining the melting point, Fourier transform infrared (FT‐IR) and Nuclear magnetic resonance (NMR) spectra. The present method is green, efficient, and cost‐effective. Catalyst can be reused up to four reaction cycles without any characteristic loss of its activity.
LOXL3‐promoted hepatocellular carcinoma progression via promotion of Snail1/USP4‐mediated epithelial‐mesenchymal transition
Authors: Li Rong , Shang Runze , Li Shunle , Ren Yifan , Shen Lin , Yang Longbao , Chen Shuo , Chen Xi , Li Junhui , Xu Meng
Published: July 2022

Lysyl‐oxidase‐like 3 (LOXL3) was reported to be essential in epithelial‐mesenchymal transition (EMT) of cancers. However, the role of LOXL3 in hepatocellular carcinoma (HCC) remained unclear. In this study, we explored clinical significance, biological functions, and regulatory mechanisms of LOXL3 in HCC. Our study found that LOXL3 expression was markedly associated with the tumor size and clinical stage of HCC, and it was highly expressed in tumor tissues of metastatic HCC patients. High expression of LOXL3 predicted a poor prognosis of HCC. TGF‐β1 treatment elevated LOXL3 protein expression and cell invasion, and reduced cell apoptosis in HCC cell lines (SMMC‐7721 and Huh‐7), while downregulation of LOXL3 reversed the promotive effects of TGF‐β1 treatment on LOXL3 protein expression and cell invasion, and the inhibitory effect on cell apoptosis. Mechanistically, LOXL3 interacted with snail family transcriptional repressor 1 (Snail1) through STRING database and RIP assay, and Snail1 bound to ubiquitin‐specific peptidase 4 (USP4) promoter by JASPAR database, luciferase reporter gene and Co‐IP assays. Overexpression of USP4 reversed the inhibitory effect of LOXL3 silence on EMT in HCC cells through deubiquitinating and stabilizing the expression of Snail1. Moreover, LOXL3‐promoted HCC EMT through Wnt/β‐catenin/Snail1 signaling pathway. In vivo study revealed that silence of LOXL3‐inhibited HCC tumor growth. In conclusion, LOXL3 silence inhibited HCC invasion and EMT through Snail1/USP4‐mediated circulation loop and Wnt/β‐catenin signaling pathway.
Retrospective analysis of liver lobe torsion in pet rabbits: 40 cases (2016–2021)
Authors: Sheen Joanne C. , Vella David , Hung Lily
Published: July 2022

Background

Liver lobe torsion (LLT) in rabbits can be under‐recognised and potentially fatal. The clinical features of cases presented to an exotic animal veterinary service in Australia were retrospectively reviewed.

Method

Medical records of confirmed rabbit LLT cases between 2016 and 2021 were reviewed for signalment, clinical signs and findings, diagnostic imaging results, management strategies and outcomes. Variables of interest were analysed for statistical association with outcome.

Results

A total of 40 rabbits were included. The mean presenting age was 56.2 months (SD 30.5). Neutered males (23/40, 57.5%) were over‐represented. Common clinical signs and findings included reduced appetite (40/40, 100%), lethargy (32/40, 80.0%), reduced faecal production (16/40, 40.0%), a doughy distended stomach (20/40, 50.0%), pale mucous membranes (19/40, 47.5%) and hypothermia (17/40, 42.5%). Anaemia and elevated plasma alanine aminotransferase and blood urea nitrogen were common clinicopathologic findings. Computed tomography (CT) was performed in 34 of 40 rabbits, confirming the presence and position of LLT (34/34, 100%), stenosis of the caudal vena cava or portal system (28/34, 82.4%) and increased free peritoneal fluid (29/34, 85.3%). Fifteen (15/40, 37.5%) rabbits were medically managed, and surgical intervention was performed in 23 of 40 (57.5%) rabbits. Overall, 30 of 40 (75.0%) rabbits survived. Surgical intervention did not confer a significant difference in outcome compared to medical management (odds ratio 0.77, 95% confidence interval 0.15‐4.10, p = 0.761).

Conclusion

CT can be an invaluable diagnostic modality for rabbit LLT. Favourable outcomes can be achieved in selected cases with medical management alone.
Growth performance and intestinal morphometric features of broiler chickens fed on dietary inclusion of yellow mealworm (Tenebrio molitor) larvae powder
Authors: Sedgh‐Gooya Shadi , Torki Mehran , Darbemamieh Maryam , Khamisabadi Hassan , Abdolmohamadi Alireza
Published: July 2022

Background

Climate change and the lack of conventional feed ingredients have made edible insects a highly nutritious alternative to feed production. The use of insects as food may help solve socio‐economic and environmental problems around the world and be in line with the United Nations Sustainable Development Goals.

Objective

In this study, the growth performance and intestinal morphology of broiler chickens were evaluated under the influence of adding different levels of Tenebrio molitor larvae meal (TM meal) to their diets.

Methods

One hundred and eighty one‐day‐old broiler chickens were divided into three treatments and five replications (12 chickens/pen). The experimental diets included a control diet and treatments containing 2.5% and 5% TM meal, which were fed to birds in the starter (0–10 days) and grower (11–25 days) stages, and during the final period (26–42 days), all birds were fed a regular finisher diet.

Results

The results showed that the diet containing TM meal had no remarkable effect on the mortality rate and feed intake of broilers (p > 0.05). In the starter period, the addition of 2.5% TM meal to broilers’ diet increased body weight gain than the control group (p ≤ 0.05). Also, the use of 2.5% TM meal in the starter period showed a significant effect on reducing the feed conversion ratio, compared to the birds fed by the control diet (p ≤ 0.05). Besides, the height of the villus, the depth of the crypt and their ratio were not altered among the different treatments (p > 0.05).

Conclusions

Overall, it can be concluded that TM meal could improve growth performance in the starter period and had no negative effects on broilers' performance and intestinal morphology in all the periods of the experiment.
Graphene Oxide‐Based Adsorbents for Organic‐Dyes Removal from Contaminated Water: A Review
Authors: Dieu Le Thu , Vinh Tran Hoang
Published: July 2022

Polluted organic dyes in water are considered as some of the most serious problems affecting humans. Adsorption techniques using traditional adsorbents such as clay, zeolite, silica, active carbon, and polymers are low cost, safe, and efficient for the treatment of organic dyes in contaminated water. However, traditional adsorbents usually have low adsorption capacity (qmax). To improve qmax, graphene oxide (GO) is considered as an excellent adsorption enhancer owing to its two‐dimensional single atomic layer material of sp2‐hybridised carbon atoms arranged in a honeycomb lattice structure with high surface area, high solubility, good chemical stability, strong mechanical strength, and excellent thermal stability. In this review, the synthesis and advantage results on improving the adsorption efficiency and qmaxwhen applying GO‐based nanocomposites as nanosorbents for organic‐dye removal are systematised and discussed in detail.
NLO JIMWLK evolution with massive quarks
Authors: Dai Lin , Lublinsky Michael
Published: July 2022

Abstract

NLO evolution of the Jalilian-Marian-Iancu-McLerran-Weigert-Leonidov-Kovner (JIMWLK) equation with massless quarks was derived a few years ago. We make a step further to compute the evolution kernels focusing on the effects due to finite quark masses. To this goal, the light-cone wave function of a fast moving dilute hadronic projectile is computed up to $$ \mathcal{O} $$
O
(g3) in QCD coupling constant. Compared with the massless case, a new IR divergence emerges, which is eventually canceled by a mass dependent counter term. Our results extend the theoretical tools used in physics of gluon saturation and aim at improving precision in future phenomenological applications.
ALPINIST: Axion-Like Particles In Numerous Interactions Simulated and Tabulated
Authors: Jerhot Jan , Döbrich Babette , Ertas Fatih , Kahlhoefer Felix , Spadaro Tommaso
Published: July 2022

Abstract

Proton beam dump experiments are among the most promising strategies to search for light and feebly interacting states such as axion-like particles (ALPs). The interpretation of these experiments is however complicated by the wide range of ALP models and the multitude of different production and decay channels that can induce observable signals. Here we propose a new approach to this problem by separating the calculation of constraints and projected sensitivities into model-independent and model-dependent parts. The former rely on extensive Monte Carlo simulations of ALP production and decays, as well as estimates of the detection efficiencies based on simplified detector geometries. Once these simulations have been performed and tabulated, the latter parts only require simple analytical rescalings that can be performed using the public code ALPINIST released together with this work. We illustrate this approach by considering several ALP models with couplings to Standard Model gauge bosons. For the case of ALPs coupled to gluons we show that the sensitivity of proton beam dump experiments can be extended significantly by considering hadronic ALP decays into three-body final states.
Ghrelin rapidly elevates protein synthesis in vitro by employing the rpS6K-eEF2K-eEF2 signalling axis
Authors: Zhdanov Alexander V. , Golubeva Anna V. , Yordanova Martina M. , Andreev Dmitry E. , Ventura-Silva Ana Paula , Schellekens Harriet , Baranov Pavel V. , Cryan John F. , Papkovsky Dmitri B.
Published: July 2022

Activated ghrelin receptor GHS-R1α triggers cell signalling pathways that modulate energy homeostasis and biosynthetic processes. However, the effects of ghrelin on mRNA translation are unknown. Using various reporter assays, here we demonstrate a rapid elevation of protein synthesis in cells within 15–30 min upon stimulation of GHS-R1α by ghrelin. We further show that ghrelin-induced activation of translation is mediated, at least in part, through the de-phosphorylation (de-suppression) of elongation factor 2 (eEF2). The levels of eEF2 phosphorylation at Thr56 decrease due to the reduced activity of eEF2 kinase, which is inhibited via Ser366 phosphorylation by rpS6 kinases. Being stress-susceptible, the ghrelin-mediated decrease in eEF2 phosphorylation can be abolished by glucose deprivation and mitochondrial uncoupling. We believe that the observed burst of translation benefits rapid restocking of neuropeptides, which are released upon GHS-R1α activation, and represents the most time- and energy-efficient way of prompt recharging the orexigenic neuronal circuitry.
Managing argon interference during measurements of 18O/16O ratios in O2 by continuous-flow isotope ratio mass spectrometry
Authors: Bopp Charlotte E. , Bolotin Jakov , Pati Sarah G. , Hofstetter Thomas B.
Published: July 2022

Monitoring changes in stable oxygen isotope ratios in molecular oxygen allows for studying many fundamental processes in bio(geo)chemistry and environmental sciences. While the measurement of $$^{18}$$

18

O/$$^{16}$$

16

O ratios of $$\mathrm {O}_{2}$$

O
2

in gaseous samples can be carried out conveniently and from extracting moderately small aqueous samples for analyses by continuous-flow isotope ratio mass spectrometry (CF-IRMS), oxygen isotope signatures, $$\updelta ^{18}$$

δ
18

O, could be overestimated by more than 6$$\permille$$
‱
because of interferences from argon in air. Here, we systematically evaluated the extent of such Ar interferences on $$^{18}$$

18

O/$$^{16}$$

16

O ratios of $$\mathrm {O}_{2}$$

O
2

for measurements by gas chromatography/IRMS and GasBench/IRMS and propose simple instrumental modifications for improved Ar and $$\mathrm {O}_{2}$$

O
2

separation as well as post-measurement correction procedures for obtaining accurate $$\updelta ^{18}$$

δ
18

O. We subsequently evaluated the consequences of Ar interferences for the quantification of O isotope fractionation in terms of isotope enrichment factors, $$\upepsilon _{\mathrm {O}}$$

ϵ
O

, and $$^{18}$$

18

O kinetic isotope effects ($$^{18}$$

18

O KIEs) in samples where $$\mathrm {O}_{2}$$

O
2

is consumed and Ar:$$\mathrm {O}_{2}$$

O
2

ratios increase steadily and substantially over the course of a reaction. We show that the extent of O isotope fractionation is overestimated only slightly and that this effect is typically smaller than uncertainties originating from the precision of $$\updelta ^{18}$$

δ
18

O measurements and experimental variability. Ar interferences can become more relevant and bias $$\upepsilon _{\mathrm {O}}$$

ϵ
O

values by more than $$2\permille$$

2
‱

in aqueous samples where fractional $$\mathrm {O}_{2}$$

O
2

conversion exceeds 90%. Practically, however, such samples would typically contain less than 25 $$\upmu$$
μ
M of $$\mathrm {O}_{2}$$

O
2

at ambient temperature, an amount that is close to the method detection limit of $$^{18}$$

18

O/$$^{16}$$

16

O ratio measurement by CF-IRMS.

Graphical abstract
Strategies to manage auxiliary pain medications in chronic pain trials: a topical review
Authors: Hasvik Eivind , Gran Jon Michael , Haugen Anne Julsrud , Grøvle Lars
Published: July 2022

Chronic pain trials commonly allow auxiliary pain medications such as rescue and concomitant analgesics in addition to the randomized treatment. Changes in auxiliary pain medications after randomization represent intercurrent events that may affect either the interpretation or the existence of the measurements associated with the clinical question of interest, complicating the assessment of treatment efficacy. In chronic pain trials, pain intensity typically varies and patients may take the auxiliary medications 1 day but not the next or increase and decrease the dosages temporarily while continuing their randomized study medication. This distinctive feature of auxiliary pain medications as an intercurrent event has received little attention in the literature. Further clarifications on how to manage these issues are therefore pressing. Here we provide perspectives on issues related to auxiliary pain medication-related intercurrent events in randomized controlled chronic pain trials considering the strategies suggested in the E9(R1) addendum to the ICH guideline on statistical principles for clinical trials.
Feasibility and Safety of Oral Nutritional Supplementation with High‐Density Liquid Diet After Total Gastrectomy for Gastric Cancer
Authors: Yamada Takanobu , Hayashi Tsutomu , Fujikawa Hirohito , Kumazu Yuta , Nagasawa Shinsuke , Nakazono Masato , Kano Kazuki , Hara Kentaro , Watanabe Hayato , Komori Keisuke , Shimoda Yota , Takahashi Kosuke , Ogata Takashi , Oshima Takashi , Yoshikawa Takaki
Published: July 2022

Introduction

Patients requiring total gastrectomy for gastric cancer experience a decrease in food intake leading to severe body weight loss after surgery. This loss may be prevented using a high‐density liquid diet of high caloric content and minimal volume. This phase II study evaluated the feasibility and safety of a high‐density liquid diet (UpLead®; Terumo Corporation, Tokyo, Japan) after total gastrectomy.

Methods

UpLead® (1 pack, 100 mL, 400 kcal/day) was administered after surgery for 28 days. The primary endpoint was the % relative dose intensity of 28 days of UpLead intake®. The secondary endpoint was % body weight loss at 1 and 3 months after surgery. The sample size was 35 considering expected and threshold values of 80 and 60%, respectively, with a one‐sided alpha error of 10% and statistical power of 80%.

Results

Among 35 patients enrolled before surgery between April 2018 and December 2019, 29 patients who could initiate UpLead® after surgery were analyzed. Seven patients had interrupted UpLead® intake due to taste intolerance (n = 6) and due to a duodenal stump fistula (n = 1). The remaining 22 patients completed 28 days of UpLead® intake, including temporary interruption, with no associated adverse events. The median relative dose intensity was 25.8% (95% confidence interval: 20.6–42.0%). The median body weight loss at 1 and 3 months after surgery was 7.2% (range: 3.2–13.9%) and 13.1% (range: 2.5–20.4%), respectively.

Conclusions

Oral nutritional supplementation with a high‐density liquid diet (UpLead®) was safely administered but was not feasible after total gastrectomy for gastric cancer.

Clinical trial registration number UMIN000032291.
Counting and optimising maximum phylogenetic diversity sets
Authors: Manson Kerry , Semple Charles , Steel Mike
Published: July 2022

In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary ‘Tree of Life’. This approach recognises that extinction not only removes species but also the branches of the tree on which unique features shared by the extinct species arose. In this paper, we investigate three questions that are relevant to PD. The first asks how many sets of species of given size k preserve the maximum possible amount of PD in a given tree. The number of such maximum PD sets can be very large, even for moderate-sized phylogenies. We provide a combinatorial characterisation of maximum PD sets, focusing on the setting where the branch lengths are ultrametric (e.g. proportional to time). This leads to a polynomial-time algorithm for calculating the number of maximum PD sets of size k by applying a generating function; we also investigate the types of tree shapes that harbour the most (or fewest) maximum PD sets of size k. Our second question concerns optimising a linear function on the species (regarded as leaves of the phylogenetic tree) across all the maximum PD sets of a given size. Using the characterisation result from the first question, we show how this optimisation problem can be solved in polynomial time, even though the number of maximum PD sets can grow exponentially. Our third question considers a dual problem: If k species were to become extinct, then what is the largest possible loss of PD in the resulting tree? For this question, we describe a polynomial-time solution based on dynamical programming.
Neuropathologic scales of cerebrovascular disease associated with diffusion changes on MRI
Authors: Nguyen Aivi T. , Kouri Naomi , Labuzan Sydney A. , Przybelski Scott A. , Lesnick Timothy G. , Raghavan Sheelakumari , Reid Robert I. , Reichard R. Ross , Knopman David S. , Petersen Ronald C. , Jack Clifford R. , Mielke Michelle M. , Dickson Dennis W. , Graff-Radford Jonathan , Murray Melissa E. , Vemuri Prashanthi
Published: July 2022

Summarizing the multiplicity and heterogeneity of cerebrovascular disease (CVD) features into a single measure has been difficult in both neuropathology and imaging studies. The objective of this work was to evaluate the association between neuroimaging surrogates of CVD and two available neuropathologic CVD scales in those with both antemortem imaging CVD measures and postmortem CVD evaluation. Individuals in the Mayo Clinic Study of Aging with MRI scans within 5 years of death (N = 51) were included. Antemortem CVD measures were computed from diffusion MRI (dMRI), FLAIR, and T2* GRE imaging modalities and compared with postmortem neuropathologic findings using Kalaria and Strozyk Scales. Of all the neuroimaging measures, both regional and global dMRI measures were associated with Kalaria and Strozyk Scales (p < 0.05) and modestly correlated with global cognitive performance. The major conclusions from this study were: (i) microstructural white matter injury measurements using dMRI may be meaningful surrogates of neuropathologic CVD scales, because they aid in capturing diffuse (and early) changes to white matter and secondary neurodegeneration due to lesions; (ii) vacuolation in the corpus callosum may be associated with white matter changes measured on antemortem dMRI imaging; (iii) Alzheimer’s disease neuropathologic change did not associate with neuropathologic CVD scales; and (iv) future work should be focused on developing better quantitative measures utilizing dMRI to optimally assess CVD-related neuropathologic changes.
Progressive loss of hearing and balance in superficial siderosis due to occult spinal dural defects
Authors: Halmagyi G. Michael , Parker Geoffrey D. , Chen Luke , Welgampola Miriam S. , Watson John D. G. , Barnett Michael H. , Todd Michael J. , El-Wahsh Shadi , Rose Victoria , Stoodley Marcus A. , Brennan Jeffrey W.
Published: July 2022

Purpose

Superficial siderosis, a progressive, debilitating, neurological disease, often presents with bilateral impairment of auditory and vestibular function. We highlight that superficial siderosis is often due to a repairable spinal dural defect of the type that can also cause spontaneous intracranial hypotension.

Methods

Retrospective chart review of five patients presenting with moderate to severe, progressive bilateral sensorineural hearing loss as well as vestibular loss. All patients had developed superficial siderosis from spinal dural defects: three after trauma, one after spinal surgery and one from a thoracic discogenic microspur.

Results

The diagnosis was made late in all five patients; despite surgical repair in four, hearing and vestibular loss failed to improve.

Conclusions

In patients presenting with progressive bilateral sensorineural hearing loss, superficial siderosis should be considered as a possible cause. If these patients also have bilateral vestibular loss, cerebellar impairment and anosmia, then the diagnosis is likely and the inevitable disease progress might be halted by finding and repairing the spinal dural defect.
Real-world treatment of German patients with recurrent and advanced endometrial cancer with a post-platinum treatment: a retrospective claims data analysis
Authors: Mevius Antje , Karl Florian , Wacker Margarethe , Welte Robert , Krenzer Stefanie , Link Theresa , Maywald Ulf , Wilke Thomas
Published: July 2022

Purpose

Endometrial cancer (EC) is the sixth most common malignancy among females worldwide. Due to limited therapeutic options, treatment of advanced or recurrent disease is associated with poor outcomes. The aim of this study was to describe the real-world treatment of patients with advanced or recurrent EC who received a systemic treatment following platinum-based chemotherapy.

Methods

This retrospective cohort study was based on anonymized German claims data covering the period between January 1, 2010, and June 30, 2020. Patients with EC who started an anticancer treatment following platinum-based chemotherapy were observed for a minimum follow-up of 12 months. Available claims data were used to describe patient characteristics, subsequent treatment lines, healthcare resource utilization, and overall survival (OS) of patients.

Results

Out of 713 patients with advanced or recurrent EC and who had received a platinum-based treatment, 201 (mean age: 68.9 years) with a post-platinum-based treatment were identified and observed. The median OS in this population was 335.0 days. Of the 201 patients, 79 patients (39.3%) received a second line of treatment (LOT), and 21 patients (10.4%) had 3 or more treatment lines. In the LOTs following platinum-based chemotherapy, more than 70 different treatment regimens were observed. The hospitalization rate was generally high, with 5.2 hospitalizations per patient-year in the follow-up period.

Conclusion

The wide variety of therapeutic regimens applied in patients in Germany who progressed after platinum-based therapy confirms the lack of therapeutic strategy for these patients, and the poor prognosis highlights the urgent need for new treatment strategies.
Machine learning-driven credit risk: a systemic review
Authors: Shi Si , Tse Rita , Luo Wuman , D’Addona Stefano , Pau Giovanni
Published: July 2022

Credit risk assessment is at the core of modern economies. Traditionally, it is measured by statistical methods and manual auditing. Recent advances in financial artificial intelligence stemmed from a new wave of machine learning (ML)-driven credit risk models that gained tremendous attention from both industry and academia. In this paper, we systematically review a series of major research contributions (76 papers) over the past eight years using statistical, machine learning and deep learning techniques to address the problems of credit risk. Specifically, we propose a novel classification methodology for ML-driven credit risk algorithms and their performance ranking using public datasets. We further discuss the challenges including data imbalance, dataset inconsistency, model transparency, and inadequate utilization of deep learning models. The results of our review show that: 1) most deep learning models outperform classic machine learning and statistical algorithms in credit risk estimation, and 2) ensemble methods provide higher accuracy compared with single models. Finally, we present summary tables in terms of datasets and proposed models.
Synthesis and characterization of cobalt SCS pincer complexes
Authors: Pecak Jan , Käfer Matthias , Fleissner Sarah , Artner Werner , Kirchner Karl
Published: July 2022

The synthesis and characterization of two Co(II) complexes stabilized by a tridentate SCS pincer ligand are described. Paramagnetic [Co(κ3-SCSCH2-Et)2] and [Co(κ3-SCSCH2-tBu)(κ2-SCSCH2-tBu)] were obtained via transmetalation protocol from CoBr2 and S(C-Br)SCH2-R (R = Et, tBu). Oxidation of the latter with [Cp2Fe]PF6 affords the diamagnetic 18 VE complex [Co(κ3-SCSCH2-tBu)2]PF6. X-ray structures and DFT calculations are presented.

Graphical abstract
Well-developed spatial reversal learning abilities in harbor seals (Phoca vitulina)
Authors: Niesterok Benedikt , Martin Shanie , Hildebrand Lisa , Dehnhardt Guido , Hanke Frederike D.
Published: July 2022

In this study, behavioral plasticity in harbor seals was investigated in spatial reversal learning tasks of varying complexities. We started with a classic spatial reversal learning experiment with no more than one reversal per day. The seals quickly learned the task and showed progressive improvement over reversals, one seal even reaching one-trial performance. In a second approach, one seal could complete multiple reversals occurring within a session. Again, a number of reversals were finished with only one error occurring at the beginning of a session as in experiment 1 which provides evidence that the seal adopted a strategy. In a final approach, reversals within a session were marked by an external cue. This way, an errorless performance of the experimental animal was achieved in up to three consecutive reversals. In conclusion, harbor seals master spatial, in contrast to visual, reversal learning experiments with ease. The underlying behavioral flexibility can help to optimize behaviors in fluctuating or changing environments.
Platial mobility: expanding place and mobility in GIS via platio-temporal representations and the mobilities paradigm
Authors: Chishtie Farrukh , Bulbul Rizwan , Babukova Panka , Scholz Johannes
Published: July 2022

While platial representations are being developed for sedentary entities, a parallel and useful endeavor would be to consider time in so-called “platio-temporal” representations that would also expand notions of mobility in GIScience, that are solely dependent on Euclidean space and time. Besides enhancing such aspects of place and mobility via spatio-temporal, we also include human aspects of these representations via considerations of the sociological notions of mobility via the mobilities paradigm that can systematically introduce representation of both platial information along with mobilities associated with ‘moving places.’ We condense these aspects into ‘platial mobility,’ a novel conceptual framework, as an integration in GIScience and the mobilities paradigm in sociology, that denotes movement of places in our platio-temporal and sociology-based representations. As illustrative cases for further study using platial mobility as a framework, we explore its benefits and methodological aspects toward developing better understanding for disaster management, disaster risk reduction and pandemics. We then discuss some of the illustrative use cases to clarify the concept of platial mobility and its application prospects in the areas of disaster management, disaster risk reduction and pandemics. These use cases, which include flood events and the ongoing COVID-19 pandemic, have led to displaced and restricted communities having to change practices and places, which would be particularly amenable to the conceptual framework developed in our work.
New MRD codes from linear cutting blocking sets
Authors: Bartoli Daniele , Marino Giuseppe , Neri Alessandro
Published: July 2022

Minimal rank-metric codes or, equivalently, linear cutting blocking sets are characterized in terms of the second generalized rank weight, via their connection with evasiveness properties of the associated q-system. Using this result, we provide the first construction of a family of $$\mathbb F_{q^m}$$

F

q
m

-linear MRD codes of length 2m that are not obtained as a direct sum of two smaller MRD codes. In addition, such a family has better parameters, since its codes possess generalized rank weights strictly larger than those of the previously known MRD codes. This shows that not all the MRD codes have the same generalized rank weights, in contrast to what happens in the Hamming metric setting.
Analysis of the relationship between the amplitude of aortic wall motion and heart function
Authors: Tashiro Hideki , Koyanagi Samon , Honda Akihiro , Nonaka Toshikatu , Ohkubo Youhei , Naganuma Chisana , Fukui Daisuke , Ichimura Kenichi , Sakai Terufumi
Published: July 2022

Purpose

Because the posterior wall of the aorta and left atrium are interlocked, the amplitude of motion of the aortic wall (AMAW) may reflect cardiac and vessel functions. This study examined the relationship between cardiac and vessel functions and AMAW.

Methods

Patients with cardiovascular diseases or patients undergoing health examinations who visited a participating hospital and underwent echocardiography and brachial–ankle pulse-wave velocity (baPWV) examinations were registered. The correlations between echocardiographic indices, ankle–brachial index, and baPWV and AMAW on M-mode echocardiography were analyzed.

Results

Overall, 184 patients were enrolled. Heart rate (r =  − 0.1587), ejection fraction (EF; r = 0.3240), wall thickness (r =  − 0.1598), peak early diastolic mitral annular velocity (E) to peak early diastolic mitral annular velocity ratio (e’; r =  − 0.2463), and baPWV (r =  − 0.1928) significantly correlated with AMAW. In the stratified multiple regression analysis, E/e’ (standardized partial regression coefficients =  − 0.1863) and mean baPWV (standardized partial regression coefficients =  − 0.1917) in patients with an EF of ≥ 60% (n = 114) significantly correlated with AMAW. In patients with an EF of < 60% (n = 70), E/e’ (standardized partial regression coefficients =  − 0.2443) significantly correlated with AMAW.

Conclusion

Because E/e’ correlated with AMAW in patients with an EF of < 60% or ≥ 60%, AMAW might be an indicator of left atrial pressure elevation. Moreover, because AMAW correlated with baPWV in patients with an EF of ≥ 60%, changes in the restricted left atrial volume might influence diastolic dysfunction. AMAW may be related to cardiac and vessel functions.
Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions
Authors: Bedics Anna , Táncsics András , Tóth Erika , Banerjee Sinchan , Harkai Péter , Kovács Balázs , Bóka Károly , Kriszt Balázs
Published: July 2022

In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C16:0 and summed feature 3 (C16:1ω7c/iso-C15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7T and closest relatives were below the threshold values for species demarcation. The genome of strain B7T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7T (= LMG 32,345T = NCAIM B.02664T).
Seasonal dynamics of tick burden and associated Borrelia burgdorferi s.l. and Borrelia miyamotoi infections in rodents in a Dutch forest ecosystem
Authors: van Duijvendijk Gilian , Krijger Inge , van Schaijk Marloes , Fonville Manoj , Gort Gerrit , Sprong Hein , Takken Willem
Published: July 2022

Ixodes ricinus ticks transmit Borrelia burgdorferi sensu lato (s.l.) as well as Borrelia miyamotoi. Larvae become infected when feeding on infected rodents, with horizontal transmission of B. burgdorferi and horizontal and vertical transmission of B. miyamotoi. We studied seasonal dynamics of infection rates of I. ricinus and their rodent hosts, and hence transmission risk of these two distinctly different Borrelia species. Rodents were live-trapped and inspected for ticks from May to November in 2013 and 2014 in a forest in The Netherlands. Trapped rodents were temporarily housed in the laboratory and detached ticks were collected. Borrelia infections were determined from the trapped rodents and collected ticks. Borrelia burgdorferi s.l. and B. miyamotoi were found in ticks as well as in rodents. Rodent density was higher in 2014, whereas tick burden as well as the Borrelia infection rates in rodents were higher in 2013. The density of B. miyamotoi-infected nymphs did not differ between the years. Tick burdens were higher on Apodemus sylvaticus than on Myodes glareolus, and higher on males than on females. Borrelia-infection rate of rodents varied strongly seasonally, peaking in summer. As the larval tick burden also peaked in summer, the generation of infected nymphs was highest in summer. We conclude that the heterogeneity of environmental and host-specific factors affects the seasonal transmission of Borrelia spp., and that these effects act more strongly on horizontally transmitted B. burgdorferi spp. than on the vertically transmitted B. miyamotoi.
Where to search: the use of opportunistic data for the detection of an invasive forest pest
Authors: de Groot Maarten , Ogris Nikica , van der Meij Mark , Pocock Michael J. O.
Published: July 2022

Early detection is important for the management of invasive alien species. In the last decade citizen science has become an important source of such data. Here, we used opportunistic records from the “LIFE ARTEMIS” citizen science project, in which people submitted records from places where they observed tree pests, to understand the distribution of a rapidly-spreading forest pest: the oak lace bug (Corythucha arcuata) in Slovenia. These citizen science records were not distributed randomly. We constructed a species distribution model for C. arcuata that accounted for the biased distribution of citizen science by using the records of other tree pests and diseases from the same project as pseudo-absences (so-called constrained pseudo-absences), and compared this to a model with pseudo-absences selected randomly from across Slovenia. We found that the constrained pseudo-absence model showed that C. arcuata was more likely to be found in east, in places with more oak trees and at lower elevations, and also closer to highways and railways, indicating introduction and dispersal by accidental human transport. The outputs from the model with random pseudo-absences were broadly similar, although estimates from this model tended to be higher and less precise, and some factors that were significant (proximity to minor roads and human settlements) were artefacts of recorder bias, showing the importance of taking the distribution of recording into account wherever possible. The finding that C. arcuata is more likely to be found near highways allows us to design advice for where future citizen science should be directed for efficient early detection.
Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples
Authors: Meulenbroek Paul , Hein Thomas , Friedrich Thomas , Valentini Alice , Erős Tibor , Schabuss Michael , Zornig Horst , Lenhardt Mirjana , Pekarik Ladislav , Jean Pauline , Dejean Tony , Pont Didier
Published: July 2022

Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods failed in the past, thereby hampering reliable assessments, a prerequisite for conservation. Here, we describe the development and application of an environmental DNA (eDNA) metabarcoding approach for detecting rare sturgeons in large rivers. Exemplarily, we developed a reference database for five native Danube sturgeons (Acipenser stellatus, Acipenser gueldenstaedtii, Acipenser ruthenus, Acipenser nudiventris, and Huso huso) and two non-native species (Acipenser baerii and Acipenser transmontanus), assessed these ex situ, and used eDNA as a detection tool along the entire length of the Danube (Europe, ~ 2850 km) and major tributaries. In ex situ analyses, all assays yielded positive amplifications for the assessed sturgeon species. In the Danube, the presence of A. ruthenus was confirmed at 14 of 29 sites (48.3%), and in 2 of 18 tributary sites (11.1%), providing the first comprehensive large-scale biogeographical snapshot of this species. Relative number of reads assigned to A. ruthenus varied between 0 and 2.5%, with sites registering positive detections being clustered in 3 sections of the Danube. Our findings enabled us to confirm the advantages of eDNA monitoring over traditional sampling methods for comprehensive whole-river snapshot studies of sturgeons conducted on a large geographical scale, and therefore we consider it to be a promising approach for application in conservation measures, fisheries management, scientific studies, and adaptive management plans for sturgeons on a global scale.
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation
Authors: Sima Ana Claudia , Mendes de Farias Tarcisio , Anisimova Maria , Dessimoz Christophe , Robinson-Rechavi Marc , Zbinden Erich , Stockinger Kurt
Published: July 2022

The problem of natural language processing over structured data has become a growing research field, both within the relational database and the Semantic Web community, with significant efforts involved in question answering over knowledge graphs (KGQA). However, many of these approaches are either specifically targeted at open-domain question answering using DBpedia, or require large training datasets to translate a natural language question to SPARQL in order to query the knowledge graph. Hence, these approaches often cannot be applied directly to complex scientific datasets where no prior training data is available. In this paper, we focus on the challenges of natural language processing over knowledge graphs of scientific datasets. In particular, we introduce Bio-SODA, a natural language processing engine that does not require training data in the form of question-answer pairs for generating SPARQL queries. Bio-SODA uses a generic graph-based approach for translating user questions to a ranked list of SPARQL candidate queries. Furthermore, Bio-SODA uses a novel ranking algorithm that includes node centrality as a measure of relevance for selecting the best SPARQL candidate query. Our experiments with real-world datasets across several scientific domains, including the official bioinformatics Question Answering over Linked Data (QALD) challenge, as well as the CORDIS dataset of European projects, show that Bio-SODA outperforms publicly available KGQA systems by an F1-score of least 20% and by an even higher factor on more complex bioinformatics datasets. Finally, we introduce Bio-SODA UX, a graphical user interface designed to assist users in the exploration of large knowledge graphs and in dynamically disambiguating natural language questions that target the data available in these graphs.
A universal method to compare parts from STEP files
Authors: Ojal Nishant , Giera Brian , Devlugt Kyle T. , Jaycox Adam W. , Blum Alexander
Published: July 2022

Model Based Definition (MBD) captures the complete specification of a part in digital form and leverages (at least) the universal “Standard for the Exchange of Product” (STEP) file format. MBD has revolutionized manufacturing due to time and cost savings associated with containing all engineering data within a single digital source. This work presents a novel method to transform digital definitions in any given STEP file into a tensor-like structure that is unique for each part and can be used to regenerate the original STEP file completely. Resulting STEP tensors are amenable to part comparison based on various part specifications in a general and straightforward manner. Here, part similarity is evaluated among sets of parts according to specific geometry, material composition, and design intent. Importantly, specification similarity can be quantified using only the tensors’ structure. As such, this approach is not limited to families of geometric shapes, part types, or fabrication methods; nor does it require any prior knowledge about the parts being compared.