bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Bronchial Epithelial Cell Transcriptome Changes in Response to Serum from Patients with Different Status of Inflammation
Authors: Sivaraman Kokilavani , Liu Bin , Martinez-Delgado Beatriz , Held Julia , Büttner Manuela , Illig Thomas , Volland Sonja , Gomez-Mariano Gema , Jedicke Nils , Yevsa Tetyana , Welte Tobias , DeLuca David S. , Wrenger Sabine , Olejnicka Beata , Janciauskiene Sabina 
Published: March 2024

Abstract
Purpose
To investigate the transcriptome of human bronchial epithelial cells (HBEC) in response to serum from patients with different degrees of inflammation.

Methods
Serum from 19 COVID-19 patients obtained from the Hannover Unified Biobank was used. At the time of sampling, 5 patients had a WHO Clinical Progression Scale (WHO-CPS) score of 9 (severe illness). The remaining 14 patients had a WHO-CPS of below 9 (range 1–7), and lower illness. Multiplex immunoassay was used to assess serum inflammatory markers. The culture medium of HBEC was supplemented with 2% of the patient’s serum, and the cells were cultured at 37 °C, 5% CO2 for 18 h. Subsequently, cellular RNA was used for RNA-Seq.

Results
Patients with scores below 9 had significantly lower albumin and serum levels of E-selectin, IL-8, and MCP-1 than patients with scores of 9. Principal component analysis based on 500 “core genes” of RNA-seq segregated cells into two subsets: exposed to serum from 4 (I) and 15 (II) patients. Cells from a subset (I) treated with serum from 4 patients with a score of 9 showed 5566 differentially expressed genes of which 2793 were up- and 2773 downregulated in comparison with cells of subset II treated with serum from 14 patients with scores between 1 and 7 and one with score = 9. In subset I cells, a higher expression of TLR4 and CXCL8 but a lower CDH1, ACE2, and HMOX1, and greater effects on genes involved in metabolic regulation, cytoskeletal organization, and kinase activity pathways were observed.

Conclusion
This simple model could be useful to characterize patient serum and epithelial cell properties.
A comprehensive analysis of CD47 expression in various histological subtypes of soft tissue sarcoma: exploring novel opportunities for macrophage-directed treatments
Authors: Benesova Iva , Capkova Linda , Ozaniak Andrej , Pacas Pavel , Kopeckova Katerina , Galova Dominika , Lischke Robert , Buchler Tomas , Ozaniak Strizova Zuzana 
Published: March 2024

Abstract
Purpose
The CD47 molecule, often referred to as the “do not eat me” signal, is frequently overexpressed in tumor cells. This signaling pathway limits phagocytosis by macrophages. Our objective was to determine CD47 abundance in various soft tissue sarcomas (STS) to investigate whether it could serve as a potential evasion mechanism for tumor cells. Additionally, we aimed to assess the prognostic value of CD47 expression by examining its association with different clinicopathological factors. This study aimed to elucidate the significance of CD47 in the context of emerging anti-tumor targeting approaches.

Methods
In this retrospective study, formalin-fixed paraffine-embedded (FFPE) tumor tissues of 55 treatment-naïve patients were evaluated by immunohistochemistry for the abundance of CD47 molecule on tumor cells. The categorization of CD47 positivity was as follows: 0 (no staining of tumor cells), 1 + (less than 1/3 of tumor area positive), 2 + (between 1/3 and 2/3 of tumor area positive), and 3 + (more than 2/3 of tumor area positive for CD47). Next, we compared CD47 abundance between different tumor grades (G1–3). We used Kaplan–Meier survival curves with log-rank test to analyze the differences in survival between patients with different CD47 expression. Moreover, we performed Cox proportional hazards regression model to evaluate the clinical significance of CD47.

Results
CD47 is widely prevalent across distinct STS subtypes. More than 80% of high grade undifferentiated pleiomorphic sarcoma (UPS), 70% of myxofibrosarcoma (MFS) and more than 60% of liposarcoma (LPS) samples displayed a pattern of moderate-to-diffuse positivity. This phenomenon remains consistent regardless of the tumor grade. However, there was a tendency for higher CD47 expression levels in the G3 group compared to the combined G1 + G2 groups when all LPS, MFS, and UPS were analyzed together. No significant associations were observed between CD47 abundance, death, and metastatic status. Additionally, high CD47 expression was associated with a statistically significant increase in progression-free survival in the studied cohort of patients.

Conclusion
This study highlights the potential of the CD47 molecule as a promising immunotherapeutic target in STS, particularly given its elevated expression levels in diverse sarcoma types. Our data showed a notable trend linking CD47 expression to tumor grade, while also suggesting an interesting correlation between enhanced abundance of CD47 expression and a reduced hazard risk of disease progression. Although these findings shed light on different roles of CD47 in STS, further research is crucial to assess its potential in clinical settings.
Androgen deprivation therapy-related fracture risk in prostate cancer: an insurance claims database study in Japan
Authors: Matsushima Hisashi , Taguchi Tetsuya , Kodama Sho , Okubo Naoki , Saito Kengo , Jabłońska Katarzyna , Fukumoto Seiji , Matsumoto Toshio 
Published: March 2024

Abstract
Introduction
Androgen deprivation therapy (ADT) is widely used for the treatment of prostate cancer. ADT is associated with reduced bone density leading to an increased risk of osteoporotic fracture. The objective of this retrospective cohort study was to quantify fracture risk in men treated with ADT for prostate cancer in real-world practice in Japan.

Materials and methods
Data were extracted from the Japanese Medical Data Vision (MDV) database. Men initiating ADT for treatment of prostate cancer between April 2010 and March 2021 were identified and matched to a cohort of prostate cancer patients not taking ADT using a propensity score. Fracture rates were estimated by a cumulative incidence function and compared between cohorts using a Cox cause-specific hazard model. Information was extracted on demographics, comorbidities and bone densitometry.

Results
30,561 men with PC starting ADT were matched to 30,561 men with prostate cancer not treated with ADT. Following ADT initiation, <5% of men underwent bone densitometry. Prescription of ADT was associated with an increased fracture risk compared to not taking ADT (adjusted hazard ratio: 1.63 [95% CI 1.52–1.75]).

Conclusion
ADT is associated with a 1.6-fold increase in the risk of osteoporotic fracture in men with prostate cancer. Densitometry in this population is infrequent and monitoring urgently needs to be improved in order to implement effective fracture prevention.
The Labyrinth of Corruption in the Construction Industry: A System Dynamics Model Based on 40 Years of Research
Authors: Zarghami Seyed Ashkan 
Published: March 2024

AbstractThe academic literature has viewed drivers of corruption in isolation and, consequently, failed to examine their synergistic effect. Such an isolated view provides incomplete information, leads to a misleading conclusion, and causes great difficulty in curbing corruption. This paper conducts a systematic literature review to identify the drivers of corruption in the construction industry. Subsequently, it develops a system dynamics (SD) model by conceptualizing corruption as a complex system of interacting drivers. Building on stakeholder and open systems theories, the proposed SD model shows how the complex reinforcing relationship between authoritative, organizational, cultural, and financial drivers of corruption further increases corrupt practices. The new model also provides lessons that can be helpful in the development of policy frameworks to control corruption in the construction industry. To achieve success in the fight against corruption, the findings of this research suggest that (1) corruption must be understood at both the organizational and state levels, (2) anticorruption practices must be informed by ethically grounded stakeholder management strategies, and (3) anticorruption reforms must go hand-in-hand with strategies to tackle the economic downturn.
The Effect of Reduction Pretreatments on the Size of Supported Pt and Pd Nanoparticles Prepared by Strong Electrostatic Adsorption
Authors: Patwary Md. Fakhruddin , Neito Manuel , Ojo Alaba , Regalbuto John R. 
Published: March 2024

AbstractSupported catalyst synthesis involves pretreatment (drying, reduction) of metal complexes to form metal nanoparticles. This study has been undertaken to explore the effect of reduction temperature, heating rate, and water partial pressure on final particle size of Pt and Pd supported on a total of four carbon and oxide supports. Supported nanoparticles were synthesized by strong electrostatic adsorption (SEA) and dry impregnation (DI); the former method was hypothesized to yield greater nanoparticle stability in thermochemical reducing environments stemming from the strong interaction of the precursor with the support during impregnation. Reduced samples were characterized by in-situ and ex-situ XRD and STEM. The DI-derived samples generally showed an expected increase of particle size with increased reduction temperature, and severe particle coalescence in humid hydrogen, while the SEA-derived samples did not sinter at the elevated reduction temperatures (up to 500 °C) and were remarkably stable in the humid reducing environment.
Graphical Abstract
Genome of Argania spinosa L.: insights into oil production and the tocopherol biosynthesis pathway
Authors: Rupp Oliver , Roessner Clemens , Lederer-Ponzer Naemi , Wollenweber Tassilo Erik , Becker Annette , Lamaoui Mouna 
Published: March 2024

AbstractArgan (Argania spinosa L.) is a highly valued tree for its multiple uses as food and feed and for being linked to a broad range of benefits of pharmaceutical and cosmetic relevance. This multipurpose resource is becoming increasingly overused, which may disrupt the whole ecosystem’s sustainability. Due to the high socio-economic status of this tree, research interventions are needed to reverse the forest regressive trend, restore the disturbed ecosystem, and conserve genetic diversity. However, research on argan is restricted by the lack of accessible information on the genetic and genomic bases of the species, specifically a functional annotated genome. Herein, we report the reference transcriptome aided annotation of the argan tree genome using de novo gene prediction programs aided by homology information from different plants. The results of the genome annotation using AUGUSTUS were subsequently improved by performing RNA sequencing. A total of 62,590 gene loci could be identified with 82,286 isoforms and a BUSCO completeness of 91.7%. To gain insight into the agronomically important compounds in argan oil, a comparative genome analysis and ortholog identification was performed, followed by phylogenetic tree construction of the main biosynthesis genes. Among those are fatty acids and tocopherols, the latter being the main factor behind the increasing demands for argan oil. Our analysis is the initial step to provide breeders, geneticists, and the industries with adequate genomic information, facilitate improvement of economically important traits and to selectively adapt the tree to the increasing impact of climate change.
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces
Authors: Hönig Sophia M. N. , Flachsenberg Florian , Ehrt Christiane , Neumann Alexander , Schmidt Robert , Lemmen Christian , Rarey Matthias 
Published: March 2024

Abstract
The growing size of make-on-demand chemical libraries is posing new challenges to cheminformatics. These ultra-large chemical libraries became too large for exhaustive enumeration. Using a combinatorial approach instead, the resource requirement scales approximately with the number of synthons instead of the number of molecules. This gives access to billions or trillions of compounds as so-called chemical spaces with moderate hardware and in a reasonable time frame. While extremely performant ligand-based 2D methods exist in this context, 3D methods still largely rely on exhaustive enumeration and therefore fail to apply. Here, we present SpaceGrow: a novel shape-based 3D approach for ligand-based virtual screening of billions of compounds within hours on a single CPU. Compared to a conventional superposition tool, SpaceGrow shows comparable pose reproduction capacity based on RMSD and superior ranking performance while being orders of magnitude faster. Result assessment of two differently sized subsets of the eXplore space reveals a higher probability of finding superior results in larger spaces highlighting the potential of searching in ultra-large spaces. Furthermore, the application of SpaceGrow in a drug discovery workflow was investigated in four examples involving G protein-coupled receptors (GPCRs) with the aim to identify compounds with similar binding capabilities and molecular novelty.

Graphical abstract
SpaceGrow descriptor comparison for an example cut in the molecule of interest. Scoring scheme is implied for one fragment of this cut.
Entropy Barrier Mitigation and Harnessing Localized Upcycled Graphene Nanoplatelets in Polypropylene/High-Density Polyethylene Nanoblends
Authors: Şahin Dündar Gülayşe , Saner Okan Burcu 
Published: March 2024

AbstractIn pursuit of a sustainable future, the focus on thermoplastic compounding emerges as a transformative avenue. Strategically blending and compounding thermoplastics unlock the potential for eco-friendly materials, addressing pressing environmental concerns. Polymer blending is a widely utilized technique that offers significant advantages in terms of cost-effectiveness and the development of materials with diverse properties. However, achieving compatibility between polymers remains a challenge due to their non-negligible entropy, particularly in the case of immiscible polymers like Polypropylene (PP) and High-Density Polyethylene (HDPE). The success of such systems heavily depends on optimizing factors such as additive selection, mixing methodology, composition, and processing conditions. Despite the extensive industrial usage of polymers like PP and HDPE, there is still limited understanding regarding the impact of blending these polymers, especially when graphene is introduced. This study addresses these challenges by overcoming the entropy barrier between PP and HDPE using a high shear rate thermo-kinetic mixer and employing upcycled graphene nanoplatelets (GNP) as a type of low-cost graphene material through interface engineering. The GNP content in the blends ranged from 0 to 1 wt%, and through meticulous selection of the polymer weight fraction and the use of minimal GNP content, GNP was strategically localized at the blend interface. This resulted in remarkable mechanical performance achieved through the optimized manufacturing technique. Incorporating 0.1 wt% GNP resulted in a significant 38% increase in tensile modulus, while flexural modulus and flexural strength saw respective increments of 39% and 22% compared to neat PP. Further enhancements were observed with higher GNP contents. This study illuminates the transformative potential of thermoplastic compounding as a key driver toward a sustainable future.
Graphical Abstract
Symbol detection based on a novel discrete harmony search algorithm in MIMO-FBMC/OQAM system
Authors: Şimşir Şakir 
Published: March 2024

AbstractDue to its high spectral efficiency and various other advantages, filter bank multicarrier/offset quadrate amplitude modulation (FBMC/OQAM) has long been considered as a candidate waveform for the fifth generation (5G) and beyond telecommunication technologies. On the other hand, it is possible to both increase the data rate and alleviate the channel fading effects by using the multiple-input multiple-output (MIMO) antenna structure in the FBMC/OQAM transceiver. However, since the symbol detection is an indispensable task to be fulfilled in wireless communication, it is crucial to employ an efficient symbol detector at the MIMO-FBMC/OQAM receiver. Maximum likelihood (ML) detector, which always finds the optimal symbols by trying all of the possible symbol combinations likely to be transmitted, is known for its extremely high computational complexity making it impractical to be used in any system. On the other hand, it is possible to both considerably reduce the ML complexity and achieve the near-ML performance by optimizing the symbol vectors instead of implementing an exhaustive search. Since searching for the optimal symbol combination in discrete space is a combinatorial optimization problem, we developed a novel discrete harmony search (disHS) algorithm to perform this operation. According to the simulation results, the newly developed disHS algorithm not only achieves near-ML performance with lower computational complexity, but also clearly leaves behind the other symbol detectors considered in this paper.
Existence results for singular strongly non-linear integro-differential BVPs on the half line
Authors: Anceschi Francesca 
Published: March 2024

AbstractThis work is devoted to the study of singular strongly non-linear integro-differential equations of the type $$\begin{aligned} (\Phi (k(t)v'(t)))'=f\left( t,\int _0^t v(s)\, \textrm{d}s,v(t),v'(t) \right) , \text{ a.e. } \text{ on } {\mathbb {R}}^{+}_0 := [0, + \infty [, \end{aligned}$$

(
Φ

(
k

(
t
)

v
′

(
t
)

)

)

′

=
f

t
,

∫
0
t

v

(
s
)

d
s
,
v

(
t
)

,

v
′

(
t
)

,

a.e.

on

R

0
+

:
=

[
0
,
+
∞
[

,

where f is a Carathéodory function, $$\Phi $$
Φ
is a strictly increasing homeomorphism, and k is a non-negative integrable function, which is allowed to vanish on a set of zero Lebesgue measure, such that $$1/k \in L^p_\textrm{loc}({\mathbb {R}}^{+}_0)$$

1
/
k
∈

L
loc
p

(

R

0
+

)

for a certain $$p>1$$

p
>
1

. By considering a suitable set of assumptions, including a Nagumo–Wintner growth condition, we prove existence and non-existence results for boundary value problems associated with the non-linear integro-differential equation of our interest in the sub-critical regime on the real half line.
Development and characterization of gelatin-based biodegradable films incorporated with pistachio shell hemicellulose
Authors: Harrazi Narjes , Özbek Hatice Neval , Yanık Derya Koçak , Zaghbib Imen , Göğüş Fahrettin 
Published: March 2024

AbstractThis study aimed to incorporate pistachio shell hemicellulose into a film of gelatin and glycerol for the production of biodegradable films. The gelatin and glycerol are chosen because of their functional properties, which make it extensively used in food industry. The film composition was defined after a statistical optimization by central composite face-centered design and response surface methodology. The hemicellulose/gelatin ratio of 35.93% and the glycerol ratio of 18.02% were the optimum conditions to obtain lower film water solubility, higher tensile strength, and elongation at break values. The physical, structural, mechanical, and barrier properties of the developed hemicellulose-gelatin film were analyzed and compared with those of the gelatin film. Tensile strength and film water solubility values were reduced significantly with hemicellulose incorporation from 20.41 to 16.64 MPa and 49.57 to 39.21%, respectively, while EB was enhanced by 4.34 times. In addition, hemicellulose incorporation enhanced the water vapor permeability and the film degradation in the soil. The films were also examined by Fourier transform infrared spectroscopy and differential scanning calorimetry. The novelty of this study is to use pistcahio shell hemicellulose in the production of an edible film for the first time.
Single center experience with ALPPS and timing with stage 2 in patients with fibrotic/cirrhotic liver
Authors: Hung Kuo-Chen , Wang Hao-Ping , Li Wei-Feng , Lin Yu-Cheng , Wang Chih-Chi 
Published: March 2024

AbstractAssociating liver partition and portal vein ligation for staged hepatectomy (ALPPS) is a novel procedure for major resection in patients with insufficient future liver remnant (FLR). Effective FLR augmentation is pivotal in the completion of ALPPS. Liver fibrosis/cirrhosis associated with chronic viral hepatitis impairs liver regeneration. To investigate the augmentation of FLR in associating ALPPS between patients with fibrotic/cirrhotic livers (FL) and non-fibrotic livers (NFL) and compare their short-term clinical outcomes and long-term survival. Patients were divided into two groups based on the Ishak modified staging: non-fibrotic liver group (NFL, stage 0) and fibrotic/cirrhotic liver group (FL, stage 1–5/6). Weekly liver regeneration in FLR, perioperative data, and survival outcomes were investigated. Twenty-seven patients with liver tumors underwent ALPPS (NFL, n = 7; FL, n = 20). NFL and FL patients had viral hepatitis (28.6% [n = 2] and 95% [n = 19]), absolute FLR volume increments of 134.90 ml and 161.85 ml (p = 0.825), and rates of hypertrophy were 16.46 ml/day and 13.66 ml/day (p = 0.507), respectively. In the FL group, baseline FLR volume was 360.13 ml, postoperatively it increased to a plateau (542.30 ml) in week 2 and declined (378.45 ml) in week 3. One patient (3.7%) with cirrhotic liver (stage 6) failed to proceed to ALPPS-II. The overall ALPPS-related major complication rate was 7.4%. ALPPS is feasible for fibrotic liver patients classified by Ishak modified stages ≤ 5. After ALPPS-I, 14 days for FLR augmentation seems an appropriate waiting time to reach a maximum FLR volume in these patients.
Analysis of the finasteride treatment and its withdrawal in the rat hypothalamus and hippocampus at whole-transcriptome level
Authors: Giatti S. , Cioffi L. , Diviccaro S. , Piazza R. , Melcangi R. C. 
Published: March 2024

Abstract
Purpose
As reported in patients treated for androgenetic alopecia with finasteride (i.e., a blocker of the enzyme 5 alpha-reductase) and in an animal model, side effects affecting sexual, psychiatric, neurological, and physical domains, may occur during the treatment and persist with drug suspension. The etiopathogenesis of these side effects has been poorly explored. Therefore, we performed a genome-wide analysis of finasteride effects in the brain of adult male rat.

Methods
Animals were treated (i.e., for 20 days) with finasteride (1mg/rat/day). 24 h after the last treatment and 1 month after drug suspension, RNA sequencing analysis was performed in hypothalamus and hippocampus. Data were analyzed by differential expression analysis and Gene-Set Enrichment Analyses (GSEA).

Results
Data obtained after finasteride treatment showed that 186 genes (i.e., 171 up- and 15 downregulated) and 19 (i.e., 17 up- and 2 downregulated) were differentially expressed in the hypothalamus and hippocampus, respectively. Differential expression analysis at the drug withdrawal failed to identify dysregulated genes. Several gene-sets were enriched in these brain areas at both time points.

Conclusion
Some of the genes reported to be differentially expressed (i.e., TTR, DIO2, CLDN1, CLDN2, SLC4A5, KCNE2, CROT, HCRT, MARCKSL1, VGF, IRF2BPL) and GSEA, suggest a potential link with specific side effects previously observed in patients and in the animal model, such as depression, anxiety, disturbance in memory and attention, and sleep disturbance. These data may provide an important background for future experiments aimed at confirming the pathological role of these genes.