bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive analysis of liquid–liquid phase separation propensities of HSV‐1 proteins and their interaction with host factors
Authors: Subedi Sushma , Nag Niharika , Shukla Harish , Padhi Aditya K. , Tripathi Timir
Published: October 2023

In recent years, it has been shown that the liquid–liquid phase separation (LLPS) of virus proteins plays a crucial role in their life cycle. It promotes the formation of viral replication organelles, concentrating viral components for efficient replication and facilitates the assembly of viral particles. LLPS has emerged as a crucial process in the replication and assembly of herpes simplex virus‐1 (HSV‐1). Recent studies have identified several HSV‐1 proteins involved in LLPS, including the myristylated tegument protein UL11 and infected cell protein 4; however, a complete proteome‐level understanding of the LLPS‐prone HSV‐1 proteins is not available. We provide a comprehensive analysis of the HSV‐1 proteome and explore the potential of its proteins to undergo LLPS. By integrating sequence analysis, prediction algorithms and an array of tools and servers, we identified 10 HSV‐1 proteins that exhibit high LLPS potential. By analysing the amino acid sequences of the LLPS‐prone proteins, we identified specific sequence motifs and enriched amino acid residues commonly found in LLPS‐prone regions. Our findings reveal a diverse range of LLPS‐prone proteins within the HSV‐1, which are involved in critical viral processes such as replication, transcriptional regulation and assembly of viral particles. This suggests that LLPS might play a crucial role in facilitating the formation of specialized viral replication compartments and the assembly of HSV‐1 virion. The identification of LLPS‐prone proteins in HSV‐1 opens up new avenues for understanding the molecular mechanisms underlying viral pathogenesis. Our work provides valuable insights into the LLPS landscape of HSV‐1, highlighting potential targets for further experimental validation and enhancing our understanding of viral replication and pathogenesis.
Perceived barriers, recommendations, and resources for multistate licensure in the United States: A mixed‐methods study of laboratory genetic counselors
Authors: Mackall Mia S. , Tschirgi Matthew L.
Published: October 2023

With genetic counselor licensure now available in 32 states, the number of laboratory genetic counselors (LGCs) who are required to be licensed in multiple states has risen substantially. Although previous studies have documented the complexity of the multistate licensing (MSL) process, there has been little research on the experiences of LGCs applying for and maintaining licensure. The purpose of this study was to identify perceived barriers, recommendations, and resources for LGCs pursuing MSL. A 15‐item mixed‐methods, anonymous questionnaire was used to survey genetic counselors currently or formerly employed by genetic testing laboratories. Responses were analyzed with a combination of descriptive statistics and inductive thematic analysis. Of the 150 eligible participants who completed the survey, the majority worked at a commercial, non‐academic laboratory (84%, n = 126), had 1–4 years of laboratory genetic counseling experience (54%, n = 81), held non‐patient‐facing roles (65%, n = 97), and were required by their employer to hold licensure in at least one state (73%, n = 110). Most participants (86%, n = 129) felt there were barriers to MSL for LGCs, with three emergent themes: (1) resource burden, (2) complexity, and (3) legislative ambiguity. Participants described the current MSL process as tedious, cumbersome, confusing, overwhelming, and redundant. Several shared that the current licensing system undermines the intent to improve the status of the profession and actually negatively impacts patient care. Recommendations to improve MSL included overall process enhancements, like transitioning to online systems and a single central information repository for licensees, increased professional advocacy, and investing in collaborative pathways to licensure such as interstate compacts. Participants found national genetic counseling organizations, state‐based genetic counseling organizations, and genetic counseling colleagues to be the most helpful resources for understanding licensure law and where to apply for licensure.
Traits and Behavior Theory of Leadership: Critique from Undistributed Middle
Authors: Jalšenjak Borna , Richards Randy L.
Published: October 2023

Traits and/or behavior theory of leadership has a long tradition but the popular understanding of it may lead to fallacious positions. The current paper provides a critique, stemming from logic, of a reductionist approach to leadership in popular sources. The reductionist approach is manifested in propositions such as “possession of trait and/or behavior X makes one a leader.” First, the logical fallacy of the undistributed middle is explained. Second, the paper presents the appearance of the fallacy of the undistributed middle in leadership training and popular leadership materials. The paper demonstrates that popular unchecked traits and/or behavioral understandings of leadership generate misleading and logically flawed statements about leadership. The understanding of leadership built on such statements both originates and increases the ambiguity of the term leader and it likely results in ineffective training programs and actual performance on the job.
Designing Clinical MRI for Enhanced Workflow and Value
Authors: Lin Dana J. , Doshi Ankur M. , Fritz Jan , Recht Michael P.
Published: October 2023

MRI is an expensive and traditionally time‐intensive modality in imaging. With the paradigm shift toward value‐based healthcare, radiology departments must examine the entire MRI process cycle to identify opportunities to optimize efficiency and enhance value for patients. Digital tools such as “frictionless scheduling” prioritize patient preference and convenience, thereby delivering patient‐centered care. Recent advances in conventional and deep learning‐based accelerated image reconstruction methods have reduced image acquisition time to such a degree that so‐called nongradient time now constitutes a major percentage of total room time. For this reason, architectural design strategies that reconfigure patient preparation processes and decrease the turnaround time between scans can substantially impact overall throughput while also improving patient comfort and privacy. Real‐time informatics tools that provide an enterprise‐wide overview of MRI workflow and Picture Archiving and Communication System (PACS)‐integrated instant messaging can complement these efforts by offering transparent, situational data and facilitating communication between radiology team members. Finally, long‐term investment in training, recruiting, and retaining a highly skilled technologist workforce is essential for building a pipeline and team of technologists committed to excellence. Here, we highlight various opportunities for optimizing MRI workflow and enhancing value by offering many of our own on‐the‐ground experiences and conclude by anticipating some of the future directions for process improvement and innovation in clinical MR imaging.

Evidence Level

N/A

Technical Efficacy

Stage 1
Tunable Localization of Higher‐Order Bound States in Non‐Hermitian Optical Waveguide Lattices
Authors: Kang Juan , Zhang Qinglong , Wei Ruishan , Qiu Jianrong , Yang Zhongmin , Dong Guoping
Published: October 2023

Higher‐order corner‐bound states in a 2D structure have been found to possess robust and exotic properties beyond the “ordinary” topological edge states, giving rise to a promising applicative potential. For example, the topological nanocavity designed based on the corner states exhibits much better performance than that of the conventional photonic crystal cavity. However, the corner states in the finite Hermitian system are usually coupled with each other, which results in the weakening of their localization. As such, the contradiction between the performance and footprint of topological devices is vexing. Here, it shows that introducing non‐Hermiticity in the higher‐order topological insulators is an effective strategy to enhance the localization of corner states in finite systems. By designing and analyzing the 2D finite Su‐Schriffer‐Heeger optical lattices with two types of non‐Hermitian configuration, the localization degree of higher‐order corner states is found to depend on the gain/loss strength. This is experimentally demonstrated by observing the distribution of corner states in the femtosecond‐laser‐writing loss‐controlled waveguide arrays. This scheme tuning localization of higher‐order corner‐bound states by non‐Hermiticity may offer a new avenue to design robust and compact devices, such as topological nano‐lasers with an ultra‐low threshold.
Core Cross‐Linking Enhances the Anti‐Inflammatory Performance of Oxidation‐Sensitive Polymeric Micelles
Authors: d'Arcy Richard , Tirelli Nicola
Published: October 2023

Nanomaterials able to scavenge biologically relevant oxidants (reactive oxygen species, ROS) can directly act as anti‐inflammatory agents. Here, micelles made of amphiphilic poly(ethylene glycol)(PEG)‐polysulfide block copolymers are focused on; the polysulfide blocks are responsible of ROS‐scavenging and are composed of propylene sulfide and ethylene sulfide units in ratios of 20:0, 15:5, 10:10. These polymers can be intramicellarly cross‐linked through thermal thiol‐yne reaction of terminal alkynes (trithiol cross‐linker). Self‐assembled and cross‐linked micelles are virtually identical in size and scavenging kinetics, but greatly differ in stability against dilution (critical aggregation concentration (CAC) respectively of ≈0.1 and <0.01 mg mL−1) and in the final state after oxidation (soluble polymers vs cross‐linked nanoparticles). Most importantly, self‐assembled micelles have significant toxicity and damage cell membranes already at 0.5 mg mL−1, which seriously hampers their anti‐inflammatory activity. On the contrary, cross‐linked micelles do not appreciably harm cells at least up to 1 mg mL−1, and effectively inhibit the production of inflammatory cytokines in activated macrophages. In this study, a detailed interpretation of the morphological evolution of the two types of micelles during oxidation is provided and it is proved that core cross‐linking significantly widens the therapeutic window.
American lobster and Jonah crab populations inside and outside the Northeast Canyons and Seamounts Marine National Monument, USA
Authors: Arnott Stephen A. , Long Michael P. , Ellertson Aubrey , Bethoney N. David
Published: October 2023

Objective

There is international pressure to increase the worldwide expanse of marine protected areas (MPAs). However, MPAs often lack preexisting long-term biological baselines, which are essential for assessing MPA effects and for refining the conservation and socioeconomic benefits they confer to society. Our study addresses this issue by establishing demographic baselines for two commercially important species prior to a proposed fishing ban inside the Northeast Canyons and Seamounts Marine National Monument, a recently established MPA on the continental shelf break approximately 200 km southeast of Cape Cod, Massachusetts.

Methods

Samples were obtained by the Commercial Fisheries Research Foundation's American Lobster and Jonah Crab Research Fleet, which is an industry-based, fishery-dependent data collection program. Specially trained participants recorded year-round biological data from their 2013 to 2021 commercial catches of American lobster Homarus americanus and Jonah crab Cancer borealis. Samples were taken from an area inside the MPA and from two areas outside the MPA, spanning 130 km to the east and west.

Result

American lobster sizes and sex ratios varied between areas, and their sizes, sex ratios, and proportion of ovigerous females differed between submarine canyons within areas. American lobster sizes, sex ratio, proportion of ovigerous females, and prevalence of shell disease were also affected by season and/or depth. Jonah crab parameters did not vary between areas, but sex ratio varied with season and depth, and the proportion of ovigerous females varied with depth.

Conclusion

These demographic baselines are the only data available, at a sufficient spatial and temporal resolution, for evaluating the effects of a proposed fishing ban in the MPA, and they fill important data gaps for stock assessments. To evaluate possible future population changes, it will be necessary to continue collecting data from inside and outside the MPA using comparable methods, and to account for the preexisting sources of variation that we have identified.
Circumventricular organ‐hypothalamic circuit endoplasmic reticulum stress drives hepatic steatosis during obesity
Authors: Kim Han Rae , Young Colin N.
Published: October 2023

Objective

Nonalcoholic fatty liver disease (NAFLD), characterized by excess liver triglyceride accumulation (hepatic steatosis), leads to an increased risk for cardiometabolic diseases and obesity‐related mortality. Emerging evidence points to endoplasmic reticulum (ER) stress in the central nervous system as critical in NAFLD pathogenesis. Here, we tested the contribution of ER stress in a circumventricular organ‐hypothalamic circuit in NAFLD development during obesity.

Methods

C57BL/6J male mice were fed a high‐fat diet (HFD) or normal chow. A combination of histological, viral tracing, intersectional viral targeting, and in vivo integrative physiological approaches were used to examine the role of ER stress in subfornical organ to hypothalamic paraventricular nucleus projecting neurons (SFO➔PVN) in NAFLD during diet‐induced obesity.

Results

Immunohistochemical analysis revealed marked unfolded protein response activation in the SFO, particularly in excitatory SFO➔PVN neurons of HFD‐fed animals. Moreover, intersectional viral inhibition of ER stress in SFO➔PVN neurons resulted in a reduction in hepatomegaly, hepatic steatosis, and a blunted increase in body weight gain during diet‐induced obesity, independent of changes in food intake, substrate partitioning, energy expenditure, and ambulatory activity.

Conclusions

These results indicate that ER stress in an SFO➔PVN neural circuit contributes to hepatic steatosis during obesity.
Ultraprocessed, hyper‐palatable, and high energy density foods: Prevalence and distinction across 30 years in the United States
Authors: Sutton Cassandra A. , Stratton Matthew , L'Insalata Alexa M. , Fazzino Tera L.
Published: October 2023

Objective

Ultraprocessed foods (UPF), hyper‐palatable foods (HPF), and high energy density (HED) foods may contribute to obesity risk. All have distinct definitions; however, it is unknown the degree to which they may identify overlapping or distinct foods. This study examined the availability of UPF, HPF, and HED foods in the US food system from 1988 to 2018 and the degree of distinction across definitions.

Methods

Four data sets representing the US food system (1988, 2001, 2006, 2018) from the US Department of Agriculture were analyzed. UPF were identified based on the extent of industrialized processing. HPF were identified using the standardized definition that specifies palatability‐inducing nutrient combinations. HED was characterized as >2.0 kcal/g.

Results

Across years, 58% to 65% of foods were classified as UPF, 55% to 69% as HPF, and 37% to 47% as HED. Prevalence of UPF, HPF, and HED foods was higher in 2018 versus 1988 (p values < 0.001); HPF evidenced the largest increase (14%) and UPF evidenced the smallest (4%) over time. There was moderate to high overlap in foods (40%–70%) across definitions.

Conclusions

Together, UPF, HPF, and HED foods comprise most foods in the US food supply. Changes in availability varied across definitions, with substantial increases in HPF and HED and relative stability of UPF.
Numerical detection of synchronization phenomena in quasi‐periodic solutions
Authors: Seifert Alexander , Baeuerle Simon , Hetzler Hartmut
Published: October 2023

In science and technology, dynamical systems can show so‐called quasi‐periodic solutions. These solutions are composed of two or more base frequencies. The solution in the time domain can be represented by an invariant manifold. To parametrize the invariant manifold, we choose the hyper‐time parametrization. If quasi‐periodic solutions branches are continued by means of a path continuation, the phenomenon of synchronization may occur. This is important, because the hyper‐time parametrization is only valid, as long as the number of base frequencies remains unchanged. Therefore, it is essential to detect a parametrization to a synchronization point. Synchronization can happen in different types. We address the mechanism of suppression, where one base frequency becomes suppressed until its amplitude vanishes. This corresponds to the quasi‐periodic solution ending in a Neimark–Sacker bifurcation. We present a method to derive a scalar measure from the quasi‐periodic solution in the hyper‐time parametrization, to detect an approach to a Neimark–Sacker bifurcation while continuing the solution branch.
Targeting the fibroblast growth factor pathway in molecular subtypes of castration‐resistant prostate cancer
Authors: Labrecque Mark P. , Brown Lisha G. , Coleman Ilsa M. , Nguyen Holly M. , Dalrymple Susan , Brennen W. Nathaniel , Isaacs John T. , Li Dapei , Lakely Bryce , DeLucia Diana C. , Lee John K. , Schweizer Michael T. , Lin Daniel W. , Corey Eva , Nelson Peter S. , Morrissey Colm
Published: October 2023

Background

Androgen receptor (AR) pathway inhibition remains the cornerstone for prostate cancer therapies. However, castration‐resistant prostate cancer (CRPC) tumors can resist AR signaling inhibitors through AR amplification and AR splice variants in AR‐positive CRPC (ARPC), and conversion to AR‐null phenotypes, such as double‐negative prostate cancer (DNPC) and small cell or neuroendocrine prostate cancer (SCNPC). We have shown previously that DNPC can bypass AR‐dependence through fibroblast growth factor receptor (FGFR) signaling. However, the role of the FGFR pathway in other CRPC phenotypes has not been elucidated.

Methods

RNA‐Seq analysis was conducted on patient metastases, LuCaP patient‐derived xenograft (PDX) models, and CRPC cell lines. Cell lines (C4‐2B, VCaP, and 22Rv1) and ex vivo LuCaP PDX tumor cells were treated with enzalutamide (ENZA) and FGFR inhibitors (FGFRi) alone or in combination and sensitivity was determined using cell viability assays. In vivo efficacy of FGFRi in ARPC, DNPC, and SCNPC were evaluated using PDX models.

Results

RNA‐Seq analysis of FGFR signaling in metastatic specimens, LuCaP PDX models, and CRPC cell lines revealed significant FGF pathway activation in AR‐low PC (ARLPC), DNPC, and SCNPC tumors. In vitro/ex vivo analysis of erdafitinib and CH5183284 demonstrated robust and moderate growth suppression of ARPC, respectively. In vivo studies using four ARPC PDX models showed that combination ENZA and CH5183284 significantly suppressed tumor growth. Additional in vivo studies using four ARPC PDX models revealed that erdafitinib monotherapy was as effective as ENZA in suppressing tumor growth, and there was limited combination benefit. Furthermore, two of three DNPC models and two of four SCNPC models responded to CH5183284 monotherapy, suggesting FGFRi responses were model dependent. RNA‐Seq and gene set enrichment analysis of end‐of‐study ARPC tumors treated with FGFRi displayed decreased expression of E2F and MYC target genes and suppressed G2M checkpoint genes, whereas end‐of‐study SCNPC tumors had heterogeneous transcriptional responses.

Conclusions

Although FGFRi treatments suppressed tumor growth across CRPC phenotypes, our analyses did not identify a single pathway or biomarker that would identify tumor response to FGFRi. This is very likely due to the array of FGFR1–4 expression and tumor phenotypes present in CRPC. Nevertheless, our data nominate the FGFR pathway as a clinically actionable target that promotes tumor growth in diverse phenotypes of treatment‐refractory metastatic CRPC.
Novel sliding‐mode control for a class of second‐order systems with mismatched disturbances
Authors: Fu Baozeng , Che Weiwei , Liu Yongchao , Wang Qingzhi , Yu Haisheng
Published: October 2023

This article investigates a novel sliding‐mode control (SMC) approach for a class of second‐order nonlinear systems subject to mismatched disturbances. To solve this problem, a novel sliding surface is designed based on the disturbance estimation of the nonlinear disturbance observer (DOB). By designing a novel time‐varying switching gain, a DOB‐based improved SMC law is constructed to compensate the influence of mismatched disturbances on the system output and make the system output converge asymptotically to zero. The novel SMC scheme owns two advantages. One is that the switching gain is an exponential decay function varying synchronously with the disturbance estimation error, which substantially alleviates the chattering problem. The other one is that a new function is defined as the switching gain coefficient based on the disturbance estimation, which helps the proposed approach to maintain the nominal control performance of the system, that is, the novel SMC law degrades to the baseline SMC law in the absence of disturbances. A numerical simulation example verifies the effectiveness and superiority of the developed approach by comparisons.
Design and implementation of resource‐aware robust event‐based integral sliding mode controller for a networked wheeled mobile robot
Authors: Nath Krishanu , Bera Manas Kumar
Published: October 2023

This work discusses the design and implementation of a robust control strategy based on integral sliding mode (ISM) for tracking a reference trajectory by a nonholonomic wheeled mobile robot (WMR). A state feedback control law using dynamic feedback linearization is adopted to design the controller for the unperturbed dynamics of the WMR. To nullify the effects of perturbations in the WMR and to retain the performance of the nominal controller, the ISM control scheme is introduced, which uses discontinuous control to guarantee the robustness of the closed‐loop system. To relax the frequent use of the communication network due to the continuous exchange of the sensor measurements, the control law is redesigned using event‐based sampled data information. The control signal is updated in an aperiodic manner by designing a novel triggering rule where the triggering occurs only when either of the two sampling errors violates a predefined threshold condition. This design approach gives a balanced solution for a networked WMR regarding network usage and control performance. Finally, a simulation study with comparative analysis and hardware‐in‐loop testing of the proposed controller is performed on a mobile robot system to establish the feasibility of the theoretical results.
Bone‐Targeted Biomimetic Nanogels Re‐Establish Osteoblast/Osteoclast Balance to Treat Postmenopausal Osteoporosis
Authors: Cui Yongzhi , Lv Bin , Li Zhongying , Ma Chunming , Gui Zhengwei , Geng Yongtao , Liu Guohui , Sang Linchao , Xu Chen , Min Qi , Kong Li , Zhang Zhiping , Liu Yang , Qi Xiangbei , Fu Dehao
Published: October 2023

Insufficient bone formation and excessive bone resorption caused by estrogen deficiency are the major factors resulting in the incidence of postmenopausal osteoporosis (PMOP). The existing drugs usually fail to re‐establish the osteoblast/osteoclast balance from both sides and generate side‐effects owing to the lack of bone‐targeting ability. Here, engineered cell‐membrane‐coated nanogels PNG@mR&C capable of scavenging receptor activator of nuclear factor‐κB ligand (RANKL) and responsively releasing therapeutic PTH 1–34 in the bone microenvironment are prepared from RANK and CXCR4 overexpressed bone mesenchymal stem cell (BMSC) membrane‐coated chitosan biopolymers. The CXCR4 on the coated‐membranes confer bone‐targeting ability, and abundant RANK effectively absorb RANKL to inhibit osteoclastogenesis. Meanwhile, the release of PTH 1–34 triggered by osteoclast‐mediated acid microenvironment promote osteogenesis. In addition, the dose and frequency are greatly reduced due to the smart release property, prolonged circulation time, and bone‐specific accumulation. Thus, PNG@mR&C exhibits satisfactory therapeutic effects in the ovariectomized (OVX) mouse model. This study provides a new paradigm re‐establishing the bone metabolic homeostasis from multitargets and shows great promise for the treatment of PMOP.
Implications of structural design on the effectiveness of active vibration control of floor structures
Authors: Hudson E J. , Reynolds P.
Published: October 2023

Active vibration control has shown great potential for reducing the response of floor structures and has the potential to realise significant material savings in slender designs through incorporation from the conceptual stage. However, different structural designs result in different modal properties, and these can significantly affect the effectiveness of an active vibration control implementation.

This paper investigates the implications of these different structural designs. Two floor structures with known vibration serviceability issues are considered; both of these are fairly typical designs. Active control is then simulated on each floor in order to improve the response of the structure.

A multipedestrian walking force model is developed and used to generate the response of each structure. This loading model is calibrated and verified using experimentally acquired data on the structures considered.

It was found that the effectiveness of the control was localised to each structural panel, and therefore the structural design that yielded larger panels required fewer actuators to reduce the response over the entire structure. Copyright © 2013 John Wiley & Sons, Ltd.
Assessing urban transformational strategies through innovative farming practices in the Johannesburg city center
Authors: Ngie Adeline , Sithole Nobukhosi
Published: October 2023

The Johannesburg metropolitan city, which is the largest city in South Africa, like others in most emerging or developing economies, is plagued by numerous challenges among which is food insecurity. The numerous skyscrapers to maximize land space over the years without adequate maintenance pose as deteriorated sites. Technological advancement has then improved these sites and provided not only regenerated buildings and spaces but also solutions to food insecurity for the inhabitants through transformational strategies from the local government. These strategies have promoted urban agriculture and introduced innovative farming measures such as rooftop gardening and hydroponic farming. These measures have been geared toward attaining sustainable environmental goals for land and water optimization within limited land spaces in the inner‐city center. This study assessed the state of these measures toward attaining the environmental goals by engaging stakeholders where open‐ended interviews were used to obtain experiences. Results showed that transformational strategies have not only improved household food security and created income‐generating opportunities but also regenerated the infrastructure of the city center. However, numerous challenges are threatening the complete realization, which are soil and water flow availability to the rooftop gardens. The situation is better with hydroponics though with its own hurdles, including the need for consistent energy supplies, input costs, and technological challenges. Overall, hydroponics presents a more promising solution to attaining land and water resource use efficiency goals with proper governance and policy support.
Comparisons of Absolute Gravimeters as a Key Component of the International Terrestrial Gravity Reference Frame (ITGRF) Shown on the Example of the WET-CAG2021 at Wettzell, Germany
Authors: Wziontek Hartmut , Falk Reinhard , Pálinkáš Vojtech , Engfeldt Andreas , Glässel Julian , Hellerschmied Andreas , Iacovone Domenico , Kostelecky Jakub , Reich Marvin , Timmen Ludger , Ullrich Christian , Valluzzi Alessandro , Zehetmaier Barbara
Published: October 2023

Comparisons of absolute gravimeters are essential to guarantee their traceability to the International System of Units (SI) and their compatibility and will be a key component of the upcoming International Terrestrial Gravity Reference Frame (ITGRF) of IAG.

The results of the regional comparison of absolute gravimeters WET-CAG2021 hosted at the Geodetic Observatory Wettzell, Germany, in autumn 2021 are presented. Seven FG5/X absolute gravimeters and—for the first time—two commercial AQG absolute quantum gravimeters took part. Temporal gravity variations during the comparison period of 12 weeks were monitored with the superconducting gravimeter GWR OSG-030. The equivalence of each absolute gravimeter is evaluated against a common reference level derived from the measurements during this comparison period. Although the comparison is outside the scope of CIPM MRA it is linked to the EURAMET.M.G-K3 2018 at the same site and the CM.G-K2.2017 in Beijing, China, which ensures the traceability.
The Software Heritage Open Science Ecosystem
Authors: Cosmo Roberto Di , Zacchiroli Stefano
Published: October 2023

Software Heritage is the largest public archive of software source code and associated development history, as captured by modern version control systems. As of July 2023, it has archived more than 16 billion unique source code files coming from more than 250 million collaborative development projects. In this chapter, we describe the Software Heritage ecosystem, focusing on research and open science use cases.

On the one hand, Software Heritage supports empirical research on software by materializing in a single Merkle direct acyclic graph the development history of public code. This giant graph of source code artifacts (files, directories, and commits) can be used –and has been used– to study repository forks, open source contributors, vulnerability propagation, software provenance tracking, source code indexing, and more.

On the other hand, Software Heritage ensures availability and guarantees integrity of the source code of software artifacts used in any field that relies on software to conduct experiments, contributing to making research reproducible. The source code used in scientific experiments can be archived –e.g., via integration with open-access repositories – referenced using persistent identifiers that allow downstream integrity checks and linked to/from other scholarly digital artifacts.
Neff constraints on light mediators coupled to neutrinos: the dilution-resistant effect
Authors: Li Shao-Ping , Xu Xun-Jie
Published: October 2023

Abstract

We investigate the impact of new light particles, carrying significant energy in the early universe after neutrino decoupling, on the cosmological effective relativistic neutrino species, Neff. If the light particles are produced from decoupled neutrinos, Neff is predominantly modified through the dilution-resistant effect. This effect arises because the energy stored in the mass of new particles is less diluted than the photon and neutrino energy as the universe expands. Our study comprehensively explores this effect, deriving Neff constraints on the couplings of light mediators with neutrinos, encompassing both scalar and vector mediators. We find that the dilution-resistant effect can increase Neff by 0.118 and 0.242 for scalar and vector mediators, respectively. These values can be readily reached by forthcoming CMB experiments. Upon reaching these levels, future Neff constraints on the couplings will be improved by many orders of magnitude.
The cosmological constant is probably still zero
Authors: Liu Yang , Padilla Antonio , Pedro Francisco G.
Published: October 2023

Abstract

We consider a wide class of four-dimensional effective field theories in which gravity is coupled to multiple four-forms and their dual scalar fields, with membrane sources charged under the corresponding three-form potentials. Four-form flux, quantised in units of the membrane charges, generically generates a landscape of vacua with a range of values for the cosmological constant that is scanned through membrane nucleation. We list various ways in which the landscape can be made sufficiently dense to be compatible with observations of the current vacuum without running into the empty universe problem. Further, we establish the general criteria required to ensure the absolute stability of the Minkowski vacuum under membrane nucleation and the longevity of those vacua that are parametrically close by. This selects the current vacuum on probabilistic grounds and can even be applied in the classic model of Bousso and Polchinski, albeit with some mild violation of the membrane weak gravity conjecture. We present other models where the membrane weak gravity conjecture is not violated but where the same probabilistic methods can be used to tackle the cosmological constant problem.
Behavioral responses of free-flying Drosophila melanogaster to shiny, reflecting surfaces
Authors: Mathejczyk Thomas F. , Babo Édouard J. , Schönlein Erik , Grinda Nikolai V. , Greiner Andreas , Okrožnik Nina , Belušič Gregor , Wernet Mathias F.
Published: October 2023

Active locomotion plays an important role in the life of many animals, permitting them to explore the environment, find vital resources, and escape predators. Most insect species rely on a combination of visual cues such as celestial bodies, landmarks, or linearly polarized light to navigate or orient themselves in their surroundings. In nature, linearly polarized light can arise either from atmospheric scattering or from reflections off shiny non-metallic surfaces like water. Multiple reports have described different behavioral responses of various insects to such shiny surfaces. Our goal was to test whether free-flying Drosophila melanogaster, a molecular genetic model organism and behavioral generalist, also manifests specific behavioral responses when confronted with such polarized reflections. Fruit flies were placed in a custom-built arena with controlled environmental parameters (temperature, humidity, and light intensity). Flight detections and landings were quantified for three different stimuli: a diffusely reflecting matt plate, a small patch of shiny acetate film, and real water. We compared hydrated and dehydrated fly populations, since the state of hydration may change the motivation of flies to seek or avoid water. Our analysis reveals for the first time that flying fruit flies indeed use vision to avoid flying over shiny surfaces.
Surgical treatment and overall survival in patients with right-sided obstructing colon cancer—a nationwide retrospective cohort study
Authors: Boeding Jeske R. E. , Elferink Marloes A. G. , Tanis Pieter J. , de Wilt Johannes H. W. , Gobardhan Paul D. , Verhoef Cornelis , Schreinemakers Jennifer M. J.
Published: October 2023

Purpose

The aim of this study was to compare baseline characteristics, 90-day mortality and overall survival (OS) between patients with obstructing and non-obstructing right-sided colon cancer at a national level.

Methods

All patients who underwent resection for right-sided colon cancer between January 2015 and December 2016 were selected from the Netherlands Cancer Registry and stratified for obstruction. Primary outcome was 5-year OS after excluding 90-day mortality as assessed by the Kaplan-Meier and multivariable Cox regression analysis.

Results

A total of 525 patients (7%) with obstructing and 6891 patients (93%) with non-obstructing right-sided colon cancer were included. Patients with right-sided obstructing colon cancer (OCC) were older and had more often transverse tumour location, and the pathological T and N stage was more advanced than in those without obstruction (p < 0.001). The 90-day mortality in patients with right-sided OCC was higher compared to that in patients with non-obstructing colon cancer: 10% versus 3%, respectively (p < 0.001). The 5-year OS of those surviving 90 days postoperatively was 42% in patients with OCC versus 73% in patients with non-obstructing colon cancer, respectively (p < 0.001). Worse 5-year OS was found in patients with right-sided OCC for all stages. Obstruction was an independent risk factor for decreased OS in right-sided colon cancer (HR 1.79, 95% CI 1.57–2.03).

Conclusion

In addition to increased risk of postoperative mortality, a stage-independent worse 5-year OS after excluding 90-day mortality was found in patients with right-sided OCC compared to patients without obstruction.
Mitophagy for cardioprotection
Authors: Titus Allen Sam , Sung Eun-Ah , Zablocki Daniela , Sadoshima Junichi
Published: October 2023

Mitochondrial function is maintained by several strictly coordinated mechanisms, collectively termed mitochondrial quality control mechanisms, including fusion and fission, degradation, and biogenesis. As the primary source of energy in cardiomyocytes, mitochondria are the central organelle for maintaining cardiac function. Since adult cardiomyocytes in humans rarely divide, the number of dysfunctional mitochondria cannot easily be diluted through cell division. Thus, efficient degradation of dysfunctional mitochondria is crucial to maintaining cellular function. Mitophagy, a mitochondria specific form of autophagy, is a major mechanism by which damaged or unnecessary mitochondria are targeted and eliminated. Mitophagy is active in cardiomyocytes at baseline and in response to stress, and plays an essential role in maintaining the quality of mitochondria in cardiomyocytes. Mitophagy is mediated through multiple mechanisms in the heart, and each of these mechanisms can partially compensate for the loss of another mechanism. However, insufficient levels of mitophagy eventually lead to mitochondrial dysfunction and the development of heart failure. In this review, we discuss the molecular mechanisms of mitophagy in the heart and the role of mitophagy in cardiac pathophysiology, with the focus on recent findings in the field.
On Triple Lines and Cubic Curves: The Orchard Problem Revisited
Authors: Elekes György , Szabó Endre
Published: October 2023

Planar point sets with many triple lines (which contain at least three distinct points of the set) have been studied for 180 years, started with Jackson and followed by Sylvester. Green and Tao (Discret Comput Geom 50(2):409–468, 2013) have shown that the maximum possible number of triple lines for an n-element set is $$\lfloor n\hspace{0.33325pt}(n - 3)/6\rfloor + 1$$

⌊
n

(
n
-
3
)
/
6
⌋
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. Here we address the related problem of describing the structure of the asymptotically near-optimal configurations, i.e., of those for which the number of straight lines which go through three or more points has a quadratic (i.e., best possible) order of magnitude. We pose the problem whether such point sets must always be related to cubic curves. To support this conjecture we settle various special cases; some of them are also related to the four-in-a-line problem of Erdős.
Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading
Authors: Cornalba Federico , Disselkamp Constantin , Scassola Davide , Helf Christopher
Published: October 2023

We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.
Praxistaugliches Sprachentwicklungsscreening (SPES) für 2- und 3-jährige Kinder
Authors: Holzinger Daniel , Bergmann Hannah , Habermaier Laura , Fellinger Johannes
Published: October 2023

Sprachliche Entwicklungsverläufe stehen in deutlichem Zusammenhang mit der Entwicklung von sozialen Kompetenzen, Beziehungen mit Gleichaltrigen, psychischer Gesundheit, schulischem Lernen und beruflichen Chancen. Eine frühe Erkennung von erhöhtem Risiko für Sprachentwicklungsprobleme erlaubt eine gezielte weitere Abklärung und eine abgestufte Intervention. Die Umsetzung von Sprachförderstrategien in der Familie ist effektiv, in weiterer Folge kann sprachtherapeutische Unterstützung erforderlich sein. In Oberösterreich wurden in langjähriger Forschungsarbeit in der direkten Anwendung in kinderärztlichen Praxen zwei treffsichere und praxistaugliche Sprachscreenings entwickelt, die nun für den Einsatz für 2‑ und 3‑jährige Kinder zur Verfügung stehen. Adaptierungen im Sinne einer Tablet-basierten und somit papierfreien Umsetzung sind in Erprobung. Zudem wird aktuell ein Online-Elterntraining zur frühen Sprachförderung evaluiert.
Metal–Organic Frameworks: Challenges Addressed via Magnetic Resonance Spectroscopy
Authors: Funke Lena Marie , Lund Alicia , Zhuang Hao , Reimer Jeffrey A.
Published: October 2023

Magnetic resonance spectroscopies occupy a premier position within the chemical sciences by revealing structure and dynamics in molecules and solids associated with photosynthesis, enzymology, Alzheimer proteins, pharmaceuticals, catalysts, polymers, and electronic materials. Here, we review the recent literature contributions of NMR and EPR spectroscopy towards the study of metal–organic frameworks from 2017 to mid-2022. We organize the review around what we perceive to be the intellectual challenges in MOF research: structure, dynamics, synthesis, properties, and function.
A side-by-side comparison of the new VITEK MS PRIME and the MALDI Biotyper sirius in the clinical microbiology laboratory
Authors: Thelen Philipp , Graeber Sandra , Schmidt Erika , Hamprecht Axel
Published: October 2023

Purpose

This study aims to evaluate the performance of two latest generation matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems in routine laboratory settings, focusing on turnaround time (TAT), time to results (TTR), hands-on time, and identification rate.

Methods

We conducted a time and motion study on three workflow scenarios to simulate different laboratory settings. Overall, 618 bacterial isolates from a tertiary hospital’s laboratory were processed using the VITEK MS PRIME (bioMérieux) and the MALDI Biotyper sirius (Bruker Daltonics) and their corresponding databases VITEK IVD Database 3.2 and MBT reference library 12.

Results

The target preparation process showed no significant difference in TAT, but the Biotyper workflow had a shorter hands-on time by 3 to 6 min. In the measurement process, TTR was three to five times shorter for the Biotyper sirius while hands-on time was significantly shorter for VITEK MS PRIME (approximately 1.5 min per target). The identification rate without retesting was 97.9% for VITEK MS PRIME and 98.9% for Biotyper sirius. Both systems achieved 100% agreement at genus and 96.2% at species level.

Conclusion

Both systems exhibited excellent identification rates for routine bacterial isolates. Due to its high speed, the Biotyper sirius is suited for laboratories with high sample throughput and a workflow designed for processing larger batches. The VITEK MS PRIME, with its “load and go” system accommodating up to 16 targets, reduces hands-on time, making it a reasonable choice for laboratories with fewer identifications overall but a higher number of targets and a workflow designed for parallel processing on different workstations.
Calibrated imputation for multivariate categorical data
Authors: de Waal Ton , Daalmans Jacco
Published: October 2023

Non-response is a major problem for anyone collecting and processing data. A commonly used technique to deal with missing data is imputation, where missing values are estimated and filled in into the dataset. Imputation can become challenging if the variable to be imputed has to comply with a known total. Even more challenging is the case where several variables in the same dataset need to be imputed and, in addition to known totals, logical restrictions between variables have to be satisfied. In our paper, we develop an approach for a broad class of imputation methods for multivariate categorical data such that previously published totals are preserved while logical restrictions on the data are satisfied. The developed approach can be used in combination with any imputation model that estimates imputation probabilities, i.e. the probability that imputation of a certain category for a variable in a certain unit leads to the correct value for this variable and unit.
Dispersal in Kentish Plovers (Charadrius alexandrinus): adult females perform furthest movements
Authors: Cimiotti Dominic V. , Eberhart-Hertel Luke , Audevard Aurélien , Garcias Salas Pere Joan , Gelinaud Guillaume , Günther Klaus , Rocha Afonso , Schulz Rainer , van der Winden Jan , Schmaljohann Heiko , Küpper Clemens
Published: October 2023

Dispersal is an important behavioral process that plays a significant role in, among others, speciation, population viability, and individual fitness. Despite progress in avian dispersal research, there are still many knowledge gaps. For example, it is of interest to study how dispersal propensity relates to age- and/or sex-specific patterns. Here, we investigated the role of sex and life stage on natal (i.e., movement from birth site to first breeding site) and breeding dispersal (i.e., movement between sequential breeding sites) in the Kentish Plover (Charadrius alexandrinus) for dispersal events of more than 10 km. This small and inconspicuous wader is characterized by flexible mating behavior that includes monogamy, and serial polygynandry. Using a continent-wide dataset of ringing and re-encounter data throughout the species’ range in Europe, we found that adult females generally dispersed further than adult males between seasons, but we detected no sex difference in natal dispersal distances and no general difference between natal and breeding dispersal distances. Furthermore, females were the main group exhibiting ‘long-distance’ breeding dispersal, which we defined as dispersal greater than ≥ 108 km, i.e., the upper 10% percentile of our dataset. The data set included dispersal of two females that first bred in the Mediterranean before being detected breeding at the North Sea in the subsequent year, having dispersed 1290 and 1704 km, respectively. These observations represent the longest breeding dispersal observed within the genus Charadrius. Our long-distance dispersal records are consistent with low genetic differentiation between mainland populations shown in previous work. The dispersal of the Kentish Plover is likely linked to its breeding behavior: polyandrous females exhibit extensive mate searching and habitat prospecting. We recommend that the dispersal traits of Kentish Plover be incorporated into the species’ conservation and management planning to more accurately inform models of population connectivity and metapopulation dynamics.