bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ernst Denert Software Engineering Award 2022
Authors: Bodden Eric , Felderer Michael , Hasselbring Wilhelm , Herber Paula , Koziolek Heiko , Lilienthal Carola , Matthes Florian , Prechelt Lutz , Rumpe Bernhard , Schaefer Ina 
Published: March 2024

AbstractThe Ernst Denert Award is already existing since 1992, which does not only honor the award winners but also the software engineering field in total. Software engineering is a vivid and intensively extending field that regularly spawns new subfields such as automotive software engineering, research software engineering, or quantum software engineering, covering specific needs but also generalizing solutions, methods, and techniques when they become applicable. This is the introductory chapter of the book on the Ernst Denert Software Engineering Award 2022. It provides an overview of the five nominated PhD theses.
The origin of Calabi-Yau crystals in BPS states counting
Authors: Bao Jiakang , Seong Rak-Kyeong , Yamazaki Masahito 
Published: March 2024

Abstract
We study the counting problem of BPS D-branes wrapping holomorphic cycles of a general toric Calabi-Yau manifold. We evaluate the Jeffrey-Kirwan residues for the flavoured Witten index for the supersymmetric quiver quantum mechanics on the worldvolume of the D-branes, and find that BPS degeneracies are described by a statistical mechanical model of crystal melting. For Calabi-Yau threefolds, we reproduce the crystal melting models long known in the literature. For Calabi-Yau fourfolds, however, we find that the crystal does not contain the full information for the BPS degeneracy and we need to explicitly evaluate non-trivial weights assigned to the crystal configurations. Our discussions treat Calabi-Yau threefolds and fourfolds on equal footing, and include discussions on elliptic and rational generalizations of the BPS states counting, connections to the mathematical definition of generalized Donaldson-Thomas invariants, examples of wall crossings, and of trialities in quiver gauge theories.
Deep learning bulk spacetime from boundary optical conductivity
Authors: Ahn Byoungjoon , Jeong Hyun-Sik , Kim Keun-Young , Yun Kwan 
Published: March 2024

Abstract
We employ a deep learning method to deduce the bulk spacetime from boundary optical conductivity. We apply the neural ordinary differential equation technique, tailored for continuous functions such as the metric, to the typical class of holographic condensed matter models featuring broken translations: linear-axion models. We successfully extract the bulk metric from the boundary holographic optical conductivity. Furthermore, as an example for real material, we use experimental optical conductivity of UPd2Al3, a representative of heavy fermion metals in strongly correlated electron systems, and construct the corresponding bulk metric. To our knowledge, our work is the first illustration of deep learning bulk spacetime from boundary holographic or experimental conductivity data.
Polarized fragmenting jet functions in inclusive and exclusive jet production
Authors: Kang Zhong-Bo , Xing Hongxi , Zhao Fanyi , Zhou Yiyu 
Published: March 2024

Abstract
In this work, we present a complete theoretical framework for analyzing the distribution of polarized hadrons within jets, with and without measuring the transverse momentum relative to the standard jet axis. Using soft-collinear effective theory (SCET), we derive the factorization and provide the theoretical calculation of both semi-inclusive and exclusive fragmenting jet functions (FJFs) under longitudinal and transverse polarization. With the polarized FJFs, one gains access to a variety of new observables that can be used for extracting both collinear and transverse momentum dependent parton distribution functions (PDFs) and fragmentation functions (FFs). As examples, we provide numerical results for the spin asymmetry $$ {A}_{TU,T}^{\cos \left({\phi}_S-{\hat{\phi}}_{S_h}\right)} $$

A

TU
,
T

cos

ϕ
S

−

ϕ
̂

S
h

from polarized semi-inclusive hadron-in-jet production in polarized pp collisions at RHIC kinematics, where a transversely polarized quark would lead to the transverse spin of the final-state hadron inside the jet and is thus sensitive to the transversity fragmentation functions. Similarly, another spin asymmetry, $$ {A}_{TU,L}^{\cos \left({\phi}_q-{\phi}_S\right)} $$

A

TU
,
L

cos

ϕ
q

−

ϕ
S

from polarized exclusive hadron-in-jet production in polarized ep collisions at EIC kinematics would allow us to access the helicity fragmentation functions. These observables demonstrate promising potential in investigating transverse momentum dependent PDFs and FFs and are worthwhile for further measurements.
Amplitude basis for conformal correlators
Authors: Lee Hayden , Wang Xinkang 
Published: March 2024

Abstract
We present a classification of conformally-invariant three-point tensor structures in d dimensions that parallels the classification of three-particle scattering amplitudes in d + 1 dimensions. Using a set of canonically-normalized weight-shifting operators, we construct a basis of three-point structures involving conserved currents or stress tensors and non-conserved spinning operators, directly from their amplitude counterparts. As an application, we also examine the conformal block expansion of the four-point functions of external currents and stress tensors in this amplitude basis. Our results can be useful for conformal bootstrap applications involving spinning correlators as well as Witten diagram computations in anti-de Sitter space.
Ideal Structure of Nica-Toeplitz Algebras
Authors: Bilich Boris 
Published: March 2024

AbstractWe study the gauge-invariant ideal structure of the Nica-Toeplitz algebra $$\mathcal {N}\mathcal {T}(X)$$

N
T
(
X
)

of a product system (A, X) over $$\mathbb {N}^n$$

N

n

. We obtain a clear description of X-invariant ideals in A, that is, restrictions of gauge-invariant ideals in $$\mathcal {N\hspace{-1.111pt}T}(X)$$

N

T

(
X
)

to A. The main result is a classification of gauge-invariant ideals in $$\mathcal {N\hspace{-1.111pt}T}(X)$$

N

T

(
X
)

for a proper product system in terms of families of ideals in A. We also apply our results to higher-rank graphs.
Traumatic rhabdomyolysis: rare but morbid, potentially lethal, and inconsistently monitored
Authors: Giles Thomas , King Kate , Meakes Simone , Weaver Natasha , Balogh Zsolt J. 
Published: March 2024

Abstract
Purpose
Although traumatic rhabdomyolysis (TR) is shown to be associated with acute kidney injury (AKI), there are no large prospective epidemiological studies, interventional trials, official guidelines outlining the appropriate investigation, monitoring, and treatment on this poorly understood condition. We aimed to establish the contemporary epidemiology and describe current practices for TR to power future higher quality studies. We hypothesised that investigation and monitoring occur in an ad hoc fashion.

Material and methods
We conducted a 1-year retrospective cohort study of all patients > 16 years of age, with an ISS > 12 and, admitted to a level 1 trauma centre. Demographics, initial vital signs, admission laboratory values, and daily creatinine kinase (CK) values were collected. The primary outcome was TR (defined by CK > 5000 IU), secondary outcomes included AKI (KDIGO criteria), mortality, multiple organ failure, length of stay, and need for renal replacement therapy (RRT).

Results
586 patients met inclusion criteria and 15 patients (2.56%) developed TR. CK testing occurred in 78 (13.1%) patients with 29 (37.7%) of these having values followed until downtrending. AKI occurred in 63 (10.8%) patients within the entire study population. Among those with TR, nine (60%) patients developed AKI. Patients with TR had higher ISS (median 29 vs 18) and mortality (26.7% vs 8.9%).

Discussion
Whilst TR appears rare without liberal screening, it is strongly associated with AKI. Given the poor outcomes, standardised monitoring, and liberal testing of CK could be justified in trauma patients with higher injury severity. This epidemiological data can help to define study populations and power future multicentre prospective studies on this infrequent yet morbid condition.
Fighting pathogenic yeasts with plant defensins and anti-fungal proteins from fungi
Authors: Manzanares Paloma , Giner-Llorca Moisés , Marcos Jose F. , Garrigues Sandra 
Published: March 2024

Abstract
Fungal infections represent a significant health risk worldwide. Opportunistic infections caused by yeasts, particularly by Candida spp. and their virulent emerging isolates, have become a major threat to humans, with an increase in fatal cases of infections attributed to the lack of effective anti-yeast therapies and the emergence of fungal resistance to the currently applied drugs. In this regard, the need for novel anti-fungal agents with modes of action different from those currently available is undeniable. Anti-microbial peptides (AMPs) are promising candidates for the development of novel anti-fungal biomolecules to be applied in clinic. A class of AMPs that is of particular interest is the small cysteine-rich proteins (CRPs). Among CRPs, plant defensins and anti-fungal proteins (AFPs) of fungal origin constitute two of the largest and most promising groups of CRPs showing anti-fungal properties, including activity against multi-resistant pathogenic yeasts. In this review, we update and compare the sequence, structure, and properties of plant defensins and AFPs with anti-yeast activity, along with their in vitro and in vivo potency. We focus on the current knowledge about their mechanism of action that may lead the way to new anti-fungals, as well as on the developments for their effective biotechnological production.

Key points
• Plant defensins and fungal AFPs are alternative anti-yeast agents
• Their multi-faceted mode of action makes occurrence of resistance rather improbable
• Safe and cost-effective biofactories remain crucial for clinical application
Macrophage mannose receptor CD206 targeting of fluoride-18 labeled mannosylated dextran: A validation study in mice
Authors: Andriana Putri , Fair-Mäkelä Ruth , Liljenbäck Heidi , Kärnä Salli , Iqbal Imran , Makrypidi Konstantina , Rajander Johan , Pirmettis Ioannis , Li Xiang-Guo , Jalkanen Sirpa , Saraste Antti , Salmi Marko , Roivainen Anne 
Published: March 2024

Abstract
Purpose
Aluminum fluoride-18-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid-conjugated mannosylated dextran derivative (Al[18F]F-NOTA-D10CM) is a new tracer for PET imaging. We report here on in vitro and in vivo validation of the tracer’s ability to target the macrophage mannose receptor CD206.

Methods
First, the uptake of intravenously (i.v.) administered Al[18F]F-NOTA-D10CM was compared between wild-type (WT) and CD206−/− knockout (KO) mice. C57BL/6N mice were injected with complete Freund’s adjuvant (CFA) in the left hind leg and the uptake of Al[18F]F-NOTA-D10CM after i.v. or intradermal (i.d.) injection was studied at 5 and 14 days after CFA induction of inflammation. Healthy C57BL/6N mice were studied as controls. Mice underwent PET/CT on consecutive days with [18F]FDG, i.v. Al[18F]F-NOTA-D10CM, and i.d. Al[18F]F-NOTA-D10CM. After the last imaging, Al[18F]F-NOTA-D10CM was i.v. injected for an ex vivo biodistribution study and autoradiography of inflamed tissues. Blood plasma samples were analyzed using high-performance liquid chromatography. To evaluate the specificity of Al[18F]F-NOTA-D10CM binding, an in vitro competitive displacement study was performed on inflamed tissue sections using autoradiography. CD206 expression was assessed by immunohistochemical staining.

Results
Compared with WT mice, the uptake of Al[18F]F-NOTA-D10CM was significantly lower in several CD206−/− KO mice tissues, including liver (SUV 8.21 ± 2.51 vs. 1.06 ± 0.16, P < 0.001) and bone marrow (SUV 1.63 ± 0.37 vs. 0.22 ± 0.05, P < 0.0001). The uptake of i.v. injected Al[18F]F-NOTA-D10CM was significantly higher in inflamed ankle joint (SUV 0.48 ± 0.13 vs. 0.18 ± 0.05, P < 0.0001) and inflamed foot pad skin (SUV 0.41 ± 0.10 vs. 0.04 ± 0.01, P < 0.0001) than in the corresponding tissues in healthy mice. The i.d.-injected Al[18F]F-NOTA-D10CM revealed differences between CFA-induced lymph node activation and lymph nodes in healthy mice. Ex vivo γ-counting, autoradiography, and immunohistochemistry supported the results, and a decrease of ~ 80% in the binding of Al[18F]F-NOTA-D10CM in the displacement study with excess NOTA-D10CM confirmed that tracer binding was specific. At 60 min after i.v. injection, an average 96.70% of plasma radioactivity was derived from intact Al[18F]F-NOTA-D10CM, indicating good in vivo stability. The uptake of Al[18F]F-NOTA-D10CM into inflamed tissues was positively associated with the area percentage of CD206-positive staining.

Conclusion
The uptake of mannosylated dextran derivative Al[18F]F-NOTA-D10CM correlated with CD206 expression and the tracer appears promising for inflammation imaging.

Graphical abstract
Vacuum-assisted mini-percutaneous nephrolithotomy is associated with lower rates of infectious complications compared to vacuum-cleaner procedure in patients at high risk for infections: a single-center experience
Authors: Marmiroli Andrea , Nizzardo Marco , Zanetti Stefano Paolo , Lucignani Gianpaolo , Turetti Matteo , Silvani Carlo , Gadda Franco , Longo Fabrizio , De Lorenzis Elisa , Albo Giancarlo , Salonia Andrea , Montanari Emanuele , Boeri Luca 
Published: March 2024

Abstract
Purpose
To evaluate the impact of vacuum-assisted mini-percutaneous nephrolithotomy (vamPCNL) vs. vacuum-cleaner mPCNL (vcmPCNL) on the rate of postoperative infectious complications in a cohort of patients with high risk factors for infections.

Methods
We retrospectively analysed data from 145 patients who underwent mPCNL between 01/2016 and 12/2022. Patient’s demographics, stones characteristics and operative data were collected. vamPCNL and vcmPCNL were performed based on the surgeon’s preference. High-risk patients were defied as having ≥ 2 predisposing factors for infections such as a history of previous urinary tract infections, positive urine culture before surgery, stone diameter ≥ 3 cm, diabetes mellitus and hydronephrosis. Complications were graded according to modified Clavien classification. Descriptive statistics and logistic regression models were used to identify factors associated with postoperative infectious complications.

Results
vamPCNL and vcmPCNL were performed in 94 (64.8%) and 51 (35.2%) cases, respectively. After surgery, infectious complications occurred in 43 (29.7%) participants. Patients who developed infectious complications had larger stone volume (p = 0.02) and higher rate of multiple stones (p = 0.01) than those who did not. Infectious complications occurred more frequently after vcmPCNL than vamPCNL (55.9% vs. 44.1%. p = 0.01) in high-risk patients. Longer operative time (p < 0.01) and length of stay (p < 0.01) were observed in cases with infectious complications. At multivariable logistic regression analysis, longer operative time (OR 1.1, p = 0.02) and vcmPCNL (OR 3.1, p = 0.03) procedures were independently associated with the risk of infectious complications post mPCNL, after accounting for stone volume.

Conclusion
One out of three high-risk patients showed infectious complications after mPCNL. vamPCL and shorter operative time were independent protective factors for infections after surgery.
An interior penalty coupling strategy for isogeometric non-conformal Kirchhoff–Love shell patches
Authors: Guarino Giuliano , Antolin Pablo , Milazzo Alberto , Buffa Annalisa 
Published: March 2024

AbstractThis work focuses on the coupling of trimmed shell patches using Isogeometric Analysis, based on higher continuity splines that seamlessly meet the $$C^1$$

C
1

requirement of Kirchhoff–Love-based discretizations. Weak enforcement of coupling conditions is achieved through the symmetric interior penalty method, where the fluxes are computed using their correct variationally consistent expression that was only recently proposed and is unprecedentedly adopted herein in the context of coupling conditions. The constitutive relationship accounts for generically laminated materials, although the proposed tests are conducted under the assumption of uniform thickness and lamination sequence. Numerical experiments assess the method for an isotropic and a laminated plate, as well as an isotropic hyperbolic paraboloid shell from the new shell obstacle course. The boundary conditions and domain force are chosen to reproduce manufactured analytical solutions, which are taken as reference to compute rigorous convergence curves in the $$L^2$$

L
2

, $$H^1$$

H
1

, and $$H^2$$

H
2

norms, that closely approach optimal ones predicted by theory. Additionally, we conduct a final test on a complex structure comprising five intersecting laminated cylindrical shells, whose geometry is directly imported from a STEP file. The results exhibit excellent agreement with those obtained through commercial software, showcasing the method’s potential for real-world industrial applications.
Mid- and long-term results of open repair for chronic type B aortic dissection in endovascular era
Authors: Takazawa Akitoshi , Asakura Toshihisa , Kinoshita Osamu , Nakajima Hiroyuki , Yoshitake Akihiro 
Published: March 2024

AbstractMedical management is the standard treatment of chronic type B aortic dissection (CTBAD). However, the roles of open surgical repair (OSR) and thoracic endovascular repair (TEVAR) in patients with CTBAD remain controversial. Thus, this study aimed to assess and compare the mid- and long-term clinical outcomes of OSR via left thoracotomy with that of TEVAR for CTBAD. The data of 85 consecutive patients who underwent surgery for CTBAD from April 2007 to May 2021 were retrospectively reviewed. The patients were divided into two groups: Group G, which included patients who underwent OSR, and Group E, which included patients who underwent TEVAR. Groups G and E comprised 33 and 52 patients, respectively. Preoperative and postoperative computed tomography (CT) studies were retrospectively analyzed for the maximum diameter. The mean duration of the follow-up period was 5.8 years. Operative mortality did not occur. There was no difference in complications, such as stroke (G: 2 vs. E: 0, p = 0.30), paraplegia (G: 1 vs. E: 1, p = 0.66), and respiratory failure (G: 2, vs. E: 0, p = 0.30). The difference in preoperative factors was observed, including the intervals between onset and operation (G; 4.9 years vs. E; 1.9 years, p < 0.01), maximum diameter in preoperative CT (G; 59.0 mm vs. E; 50.5 mm, p < 0.001), and maximum false lumen diameter (G; 35.5 mm vs. E; 29.0 mm, p < 0.01). There was no significant difference in the mid- and long-term survival rates (p = 0.49), aorta-related deaths (p = 0.33), and thoracic re-intervention rates (p = 0.34). Postoperative adverse events occurred in Group E: four cases of retrospective type A aortic dissection, two cases of aorto-bronchial fistula, and one case of aorto-esophagus fistula. Aorta-related death and re-intervention rates crossed over in both groups after seven years postoperatively. Although endovascular repair of CTBAD is less invasive, the rate of freedom from re-intervention was unsatisfactory. Some fatal complications were observed in the endovascular group, and the mid- and long-term outcomes were reversed compared with those in the OSR group. Although OSR is an invasive procedure, it could be performed safely without perioperative complications. OSR has more feasible mid- and long-term outcomes.
Metabolic changes contribute to maladaptive right ventricular hypertrophy in pulmonary hypertension beyond pressure overload: an integrative imaging and omics investigation
Authors: García-Lunar Inés , Jorge Inmaculada , Sáiz Jorge , Solanes Núria , Dantas Ana Paula , Rodríguez-Arias Juan José , Ascaso María , Galán-Arriola Carlos , Jiménez Francisco Rafael , Sandoval Elena , Nuche Jorge , Moran-Garrido Maria , Camafeita Emilio , Rigol Montserrat , Sánchez-Gonzalez Javier , Fuster Valentín , Vázquez Jesús , Barbas Coral , Ibáñez Borja , Pereda Daniel , García-Álvarez Ana 
Published: March 2024

AbstractRight ventricular (RV) failure remains the strongest determinant of survival in pulmonary hypertension (PH). We aimed to identify relevant mechanisms, beyond pressure overload, associated with maladaptive RV hypertrophy in PH. To separate the effect of pressure overload from other potential mechanisms, we developed in pigs two experimental models of PH (M1, by pulmonary vein banding and M2, by aorto-pulmonary shunting) and compared them with a model of pure pressure overload (M3, pulmonary artery banding) and a sham-operated group. Animals were assessed at 1 and 8 months by right heart catheterization, cardiac magnetic resonance and blood sampling, and myocardial tissue was analyzed. Plasma unbiased proteomic and metabolomic data were compared among groups and integrated by an interaction network analysis. A total of 33 pigs completed follow-up (M1, n = 8; M2, n = 6; M3, n = 10; and M0, n = 9). M1 and M2 animals developed PH and reduced RV systolic function, whereas animals in M3 showed increased RV systolic pressure but maintained normal function. Significant plasma arginine and histidine deficiency and complement system activation were observed in both PH models (M1&M2), with additional alterations to taurine and purine pathways in M2. Changes in lipid metabolism were very remarkable, particularly the elevation of free fatty acids in M2. In the integrative analysis, arginine–histidine–purines deficiency, complement activation, and fatty acid accumulation were significantly associated with maladaptive RV hypertrophy. Our study integrating imaging and omics in large-animal experimental models demonstrates that, beyond pressure overload, metabolic alterations play a relevant role in RV dysfunction in PH.