bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display
Authors: Hosseini Arman , Kumar Sachin , Hedin Kyle , Raeeszadeh‐Sarmazdeh Maryam 
Published: October 2023

AbstractOverexpression of specific matrix metalloproteinases (MMPs) has a key role in development of several diseases, such as cancer, neurological disorders, and cardiovascular diseases due to their critical role in degradation and remodeling of the extracellular matrix (ECM). Tissue inhibitors of metalloproteinases (TIMPs), a family of four in humans, are endogenous inhibitors of MMPs. TIMPs have a high level of sequence and structure homology, with a broad range of binding and inhibition to the family of MMPs. It is important to identify the key motifs of TIMPs responsible for inhibition of MMPs to develop efficient therapeutics targeting specific MMPs. We used DNA shuffling between the human TIMP family to generate a minimal TIMP hybrid library in yeast to identify the dominant minimal MMP inhibitory regions. The minimal TIMP variants screened toward MMP‐3 and MMP‐9 using fluorescent‐activated cell sorting (FACS). Interestingly, several minimal TIMP variants selected after screening toward MMP‐3cd or MMP‐9cd, with lengths as short as 20 amino acids, maintained or improved binding to MMP‐3 and MMP‐9. The TIMP‐MMP binding dissociation constant (KD), in the nM range, and MMP inhibition constants (Ki), in the pM range, of these minimal TIMP variants were similar to the N‐terminal domain of TIMP‐1 on the yeast surface and in solution indicating the potency of these minimal variants as MMP inhibitors. We further used molecular modeling simulation, and molecular docking of the minimal TIMP variants in complex with MMP‐3cd to understand the binding and inhibition mechanism of these variants.
Water level prediction using deep learning models: A case study of the Kien Giang River, Quang Binh Province
Authors: Hieu Trieu T. , Chieu Ta Q. , Quang Dinh N. , Hieu Nguyen D. 
Published: October 2023

AbstractTime‐series water level prediction during natural disasters, for example, typhoons and storms, is crucial for both flood control and prevention. Utilizing data‐driven models that harness deep learning (DL) techniques has emerged as an attractive and effective approach to water level prediction. This paper proposed an innovative data‐driven methodology using DL network architectures of Gated Recurrent Unit (GRU), Long Short‐Term Memory (LSTM), and Bidirectional Long‐Short Term Memory (Bi‐LSTM) to predict the water level at the Le Thuy station in the Kien Giang River. These models were implemented and validated based on hourly rainfall and water level observations at meteo‐hydrological stations. Three combinations of input variables with different time leads and time lags were established to evaluate the forecast capability of three proposed models by using five metrics, that is, R2, MAE, RMSE, Max Error Value, and Max Error Time. The results revealed that the LSTM model outperformed the Bi‐LSTM and GRU models, when water level and rainfall observations for one‐time lag at three stations were used to predict the water level at the Le Thuy station with 1‐h time lead, with the five metrics registering at 0.999; 3.6 cm; 2.6 cm; 12.9 cm; and −1 h, respectively.
Soil protein: A key indicator of soil health and nitrogen management
Authors: Naasko Katherine , Martin Tvisha , Mammana Christian , Murray Jacob , Mann Meredith , Sprunger Christine 
Published: October 2023

AbstractMonitoring soil nitrogen (N) dynamics in agroecosystems is foundational to soil health management and is critical for maximizing crop productivity in contrasting management systems. The newly established soil health indicator, autoclaved‐citrate extractable (ACE) protein, measures an organically bound pool of N. However, the relationship between ACE protein and other N‐related soil health indicators is poorly understood. In this study, ACE protein is investigated in relation to other soil N measures at four timepoints across a single growing season along a 33‐year‐old replicated eight‐system management intensity gradient located in southwest Michigan, USA. On average, polyculture perennial systems that promote soil health had two to four times higher (2–12 g kg−1 higher) ACE protein concentrations compared to annual cropping and monoculture perennial systems. In addition, ACE protein fluctuated less than total soil N, NH4+‐N, and NO3−‐N across the growing season, which shows the potential for ACE protein to serve as a reliable indicator of soil health and soil organic N status. Furthermore, ACE protein was positively correlated with total soil N and NH4+‐N and negatively correlated with NO3−‐N at individual sampling timepoints across the management intensity gradient. In addition, ACE protein, measured toward the end of the growing season, showed a consistent and positive trend with yield across different systems. This study highlights the potential for ACE protein as an indicator of sustainable management practices, SOM cycling, and soil health and calls for more studies investigating its relationship with crop productivity.
Intrahepatic splenosis as a differential diagnosis for hepatic neoplasia in a dog
Authors: Moser Jasmine , Bacon Nick , Guilherme Sergio 
Published: October 2023

AbstractIntrahepatic splenosis is the heterotopic autotransplantation of splenic tissue secondary to splenic trauma or splenectomy. A 12‐year‐old Cairn terrier was referred due to lethargy, collapse and abdominal discomfort. Abdominal ultrasound and a computed tomography scan (CT) revealed an intrahepatic mass in the left medial liver lobe. The dog underwent surgery for liver lobectomy, and subsequent histopathology revealed intrahepatic splenosis. The dog had undergone splenectomy 3 years previously due to splenic rupture following an abdominal trauma.
Clinical characteristics of sudden hearing loss during pregnancy
Authors: Wu Xiao‐Nan , Wang Hong‐Yang , Zhang Xiao‐Long , Chen Guo‐Hui , Guan Jing , Gao Yun , Wang Da‐Yong , Wang Qiu‐Ju 
Published: October 2023

AbstractObjectiveThe objective of this study was to explore the clinical characteristics and management of sudden hearing loss (HL) during pregnancy, thus better guiding the clinical practice.MethodsThe clinical and follow‐up data of 17 patients (17 ears) with sudden HL during pregnancy were analyzed retrospectively (the observe group). Twelve nonpregnant female patients (12 ears) with sudden HL of similar clinical characteristics were selected as the control group. The prognosis of the two groups was compared. All the patients were followed up after delivery, and two of them were readmitted to the hospital 1–2 months after delivery.ResultsThe observe group had better improvement in hearing and a higher response rate compared to the control group. The pure tone hearing and speech recognition rate of patients could still be improved after the readmitted treatment, and the hearing could partially recover spontaneously during follow‐up. The laboratory indicators that affect the inflammatory response and coagulation pathway were significantly different between the two groups.ConclusionsThe hearing condition of sudden HL during pregnancy is severe, and the prognosis of these patients is better than nonpregnant patients of similar clinical characteristics. Postpartum treatment is still effective, and some patients showed self‐healing with time during follow‐up. The inflammatory response and coagulation function may affect the hearing of patients through a metabolic pathway.
A theorem of Gordan and Noether via Gorenstein rings
Authors: Bricalli Davide , Favale Filippo Francesco , Pirola Gian Pietro 
Published: October 2023

AbstractGordan and Noether proved in their fundamental theorem that an hypersurface $$X=V(F)\subseteq {{\mathbb {P}}}^n$$

X
=
V

(
F
)

⊆

P

n

with $$n\le 3$$

n
≤
3

is a cone if and only if F has vanishing hessian (i.e. the determinant of the Hessian matrix). They also showed that the statement is false if $$n\ge 4$$

n
≥
4

, by giving some counterexamples. Since their proof, several others have been proposed in the literature. In this paper we give a new one by using a different perspective which involves the study of standard Artinian Gorenstein $${{\mathbb {K}}}$$
K
-algebras and the Lefschetz properties. As a further application of our setting, we prove that a standard Artinian Gorenstein algebra $$R={{\mathbb {K}}}[x_0,\dots ,x_4]/J$$

R
=
K
[

x
0

,
⋯
,

x
4

]
/
J

with J generated by a regular sequence of quadrics has the strong Lefschetz property. In particular, this holds for Jacobian rings associated to smooth cubic threefolds.
The INCH-trial: a multicenter randomized controlled trial comparing short- and long-term outcomes of open and laparoscopic surgery for incisional hernia repair
Authors: van Veenendaal Nadine , Poelman Marijn , Apers Jan , Cense Huib , Schreurs Hermien , Sonneveld Eric , van der Velde Susanne , Bonjer Jaap 
Published: October 2023

Abstract
Background
Laparoscopic incisional hernia repair is increasingly performed worldwide and expected to be superior to conventional open repair regarding hospital stay and quality of life (QoL). The INCisional Hernia-Trial was designed to test this hypothesis.

Methods
A multicenter parallel randomized controlled open-label trial with a superiority design was conducted in six hospitals in the Netherlands. Patients with primary or recurrent incisional hernias were randomized by computer-guided block-randomization to undergo either conventional open or laparoscopic repair. Primary endpoint was postoperative length of hospital stay in days. Secondary endpoints included QoL, complications, and recurrences. Patients were followed up for at least 5 years.

Results
Hundred-and-two patients were recruited and randomized. In total, 88 patients underwent surgery and were included in the intention-to-treat analysis (44 in the open group, 44 in the laparoscopic group). Mean age was 59.5 years, gender division was equal, and BMI was 28.8 kg/m. The trial was concluded early for futility after an unplanned interim analysis, which showed that the hypothesis needed to be rejected. There was no difference in primary outcome: length of hospital stay was 3 (range 1–36) days in the open group and 3 (range 1–12) days in the laparoscopic group (p = 0.481). There were no significant between-group differences in QoL questionnaires on the short and long term. Satisfaction was impaired in the open group. Overall recurrence rate was 19%, of which 16% in the open and 23% in the laparoscopic group (p = 0.25) at a mean follow-up of 6.6 years.

Conclusions
In a randomized controlled trial, short- and long-term outcomes after laparoscopic incisional hernia repair were not superior to open surgery. The persisting high recurrence rates, reduced QoL, and suboptimal satisfaction warrant the need for patient’s expectation management in the preoperative process and individualized surgical management.

Trial registration
Netherlands Trial Register NTR2808.
The role of laboratory investigations in the classification of tremors
Authors: Angelini Luca , Terranova Roberta , Lazzeri Giulia , van den Berg Kevin R E , Dirkx Michiel F , Paparella Giulia 
Published: October 2023

Abstract
Introduction
Tremor is the most common movement disorder. Although clinical examination plays a significant role in evaluating patients with tremor, laboratory tests are useful to classify tremors according to the recent two-axis approach proposed by the International Parkinson and Movement Disorders Society.

Methods
In the present review, we will discuss the usefulness and applicability of the various diagnostic methods in classifying and diagnosing tremors. We will evaluate a number of techniques, including laboratory and genetic tests, neurophysiology, and neuroimaging. The role of newly introduced innovative tremor assessment methods will also be discussed.

Results
Neurophysiology plays a crucial role in tremor definition and classification, and it can be useful for the identification of specific tremor syndromes. Laboratory and genetic tests and neuroimaging may be of paramount importance in identifying specific etiologies. Highly promising innovative technologies are being developed for both clinical and research purposes.

Conclusions
Overall, laboratory investigations may support clinicians in the diagnostic process of tremor. Also, combining data from different techniques can help improve understanding of the pathophysiological bases underlying tremors and guide therapeutic management.
Myocardial fibrosis associates with lupus anticoagulant in patients with systemic lupus erythematosus
Authors: Myhr Katrine A. , Zinglersen Amanda H. , Pecini Redi , Jacobsen Søren 
Published: October 2023

AbstractSystemic lupus erythematosus (SLE) is a chronic autoimmune disease that carries increased risk of cardiovascular disease; however, the underlying pathophysiological mechanisms remain poorly understood. We aimed to investigate the prevalence and degree of myocardial fibrosis in SLE patients and associated disease characteristics. Forty-nine SLE patients (89% female, mean age 52 ± 13 years, median disease duration 19 (11–25) years) and 79 sex-and age-matched healthy controls were included. CMR with T1 mapping was performed on SLE patients and healthy controls. Fifty-one SLE patients received gadolinium contrast for the evaluation of late gadolinium enhancement (LGE) and extra cellular volume (ECV). Multiple linear regression analyses were performed to investigate the association between markers of myocardial fibrosis on CMR (LGE, T1, ECV) and SLE-related variables [clinical disease activity, lupus nephritis, chronic kidney disease, anti-cardiolipin and/or anti-beta-2 glycoprotein I antibodies, and lupus anticoagulant (LAC)] with adjustment for traditional risk factors. T1 values were elevated in SLE patients compared to healthy controls (1031 ± 36 ms vs. 1019 ± 25 ms, p = 0.01). LGE was present in 20% of SLE patients who received gadolinium contrast. On multivariable analysis, LAC was associated with LGE in SLE patients (β = 3.87, p = 0.02). Neither T1 nor ECV associated with SLE disease characteristics; however, there was a trend towards an association between LAC and T1 (β = 16.9, p = 0.08). SLE patients displayed signs of myocardial fibrosis on CMR that were associated with the presence of LAC. These findings support the pathophysiological understanding of LAC as a mediator of microvascular and subsequent myocardial dysfunction.
Graphical abstract
Solving travelling thief problems using coordination based methods
Authors: Namazi Majid , Newton M. A. Hakim , Sanderson Conrad , Sattar Abdul 
Published: October 2023

AbstractA travelling thief problem (TTP) is a proxy to real-life problems such as postal collection. TTP comprises an entanglement of a travelling salesman problem (TSP) and a knapsack problem (KP) since items of KP are scattered over cities of TSP, and a thief has to visit cities to collect items. In TTP, city selection and item selection decisions need close coordination since the thief’s travelling speed depends on the knapsack’s weight and the order of visiting cities affects the order of item collection. Existing TTP solvers deal with city selection and item selection separately, keeping decisions for one type unchanged while dealing with the other type. This separation essentially means very poor coordination between two types of decision. In this paper, we first show that a simple local search based coordination approach does not work in TTP. Then, to address the aforementioned problems, we propose a human designed coordination heuristic that makes changes to collection plans during exploration of cyclic tours. We further propose another human designed coordination heuristic that explicitly exploits the cyclic tours in item selections during collection plan exploration. Lastly, we propose a machine learning based coordination heuristic that captures characteristics of the two human designed coordination heuristics. Our proposed coordination based approaches help our TTP solver significantly outperform existing state-of-the-art TTP solvers on a set of benchmark problems. Our solver is named Cooperation Coordination (CoCo) and its source code is available fromhttps://github.com/majid75/CoCo.
A novel impact model for the rocking motion of masonry arches
Authors: Bisegna Paolo , Coccia Simona , Como Mario , Nodargi Nicola A. 
Published: October 2023

AbstractThe in-plane rocking motion of a masonry arch subjected to ground acceleration is investigated, focusing on the impacts at stereotomy sections, which may occur during the motion. It is assumed that the arch arrives at the impact moving along a prescribed four-hinge mechanism and that, after the impact, it continues its motion along a new four-hinge mechanism to be determined. The novel concept of impulse line, which is analogous to the thrust line computed during the smooth motion, is introduced to describe the impulsive stress state arising within the arch at the impact. That is the basis for extending the Housner impact model, initially proposed for the rocking motion of a free-standing column, to the more complicated case of a masonry arch behaving as a single-degree-of-freedom system. The mechanism after the impact is determined by minimizing the kinetic energy loss of the arch at impact, i.e. by maximizing its restitution coefficient, over the set of compatible mechanisms that fulfill a suitable formulation of the virtual work principle. The descending impulse line is proven to be equilibrated, kinematically admissible (i.e., not resisting the opening of the hinges after the impact), and statically admissible (i.e., corresponding to a compressive impulsive stress state). Numerical results are presented, discussing the restitution coefficient of discrete and continuous circular arches with parameterized geometry, for which the four-hinge mechanism before the impact is assumed to follow from an equivalent static analysis.
Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system
Authors: Soldati Giulia , Turrina Stefania , Treccani Mirko , Saccardo Chiara , Ausania Francesco , De Leo Domenico 
Published: October 2023

Abstract
Background
Massively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses.

Methods and results
DNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened.

Conclusions
Although the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.
Congruence between vascular plants and bryophytes in response to ecological conditions in sustainably managed temperate forests (taxonomic- and trait-based levels)
Authors: Kutnar Lado , Kermavnar Janez , Sabovljević Marko S. 
Published: October 2023

AbstractVascular plant species (VP) and bryophytes (B) constitute a significant portion of forest biodiversity and respond to both management intensity and natural disturbances within forests. In this study, we investigated the cross-taxa congruence between understorey VP and B at both diversity and composition levels across a wide range of sustainably managed forests in Slovenia. The taxonomic and functional characteristics of the selected plant groups were studied, with a particular emphasis on ground-dwelling species. We employed a trait-based approach to examine the functional characteristics. On average, the species richness of B in sustainably managed temperate forests increased with the corresponding number of VP. Furthermore, a moderate positive correlation in species composition between the studied groups of ground-dwelling organisms was also observed. The ground-dwelling VP and B were congruent in terms of trait-based composition, which was influenced by soil reaction and nutrients and light availability, while trait-based diversity was only slightly similar in response to moisture. A negative correlation between the composition of stress-tolerant VP and B hemeroby was found, indicating forest environments with a low level of disturbance. This is likely due to the sustainable management of Slovenian forests, where climate change and natural disturbances have intensified in recent years. A cross-taxon comparison of the two groups at four different levels, namely taxonomic-based diversity and composition and trait-based diversity and composition, revealed varying degrees of congruence. It is therefore important to monitor the status and temporal trends of both groups from different aspects to draw reliable conclusions.
Evaluation of extraction and entrapment efficiency of black seed oil-containing emulsion as a delivery system for thymoquinone
Authors: Ardhi Aulia , Schreiner Matthias 
Published: October 2023

AbstractBlack seed oil (BSO) or Nigella sativa contains numerous bioactive components, in which thymoquinone (TQ) becomes a functional key compound and serves as an analytical marker. With its non-polar characteristic, lipid-based delivery systems can be a solution to improve the solubility of BSO. Thus, it is necessary to have a valid basis for TQ quantification, especially in the emulsion as the delivery system of BSO. This study aimed to validate a Gas Chromatography-Flame Ionization Detector (GC-FID) method for quantifying TQ, and subsequently employ the method to evaluate TQ extraction from BSO and BSO-containing emulsion and determine the entrapment efficiency of the emulsion. The method indicated a linearity between 10 and 1280 µg/ml with detection and quantification limits of 13,59 and 41,19 µg/ml, respectively. The extraction of TQ with the sample:methanol ratio of 1:9 and 30-min centrifugation yielded the maximum TQ recovery from BSO and BSO-containing emulsion. The entrapment efficiency in emulsion reached 64,83% obtained with the density-changing centrifugation method. Overall, this validated GC-FID method demonstrated that the selected condition in the methanol extraction could effectively separate TQ from both BSO and its emulsion matrices and support the determination of the entrapment efficiency of the BSO-containing emulsion.
Conditional tail moment and reinsurance premium estimation under random right censoring
Authors: Goegebeur Yuri , Guillou Armelle , Qin Jing 
Published: October 2023

AbstractWe propose an estimator of the conditional tail moment (CTM) when the data are subject to random censorship. The variable of main interest and the censoring variable both follow a Pareto-type distribution. We establish the asymptotic properties of our estimator and discuss bias-reduction. Then, the CTM is used to estimate, in case of censorship, the premium principle for excess-of-loss reinsurance. The finite sample properties of the proposed estimators are investigated with a simulation study and we illustrate their practical applicability on a dataset of motor third party liability insurance.