bluuebunny/crossref_metadata_2025 huggingface dataset:
hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit
Authors: Wang Yupu , Salazar Rio J. , Simonetta Luciano T. , Sorrentino Violet , Gatton Terrence J. , Wu Bill , Vecsey Christopher G. , Carrillo Robert A.
Published: April 2024

Our nervous system contains billions of neurons that form precise connections with each other through interactions between cell surface proteins. In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth, and cell survival. However, the upstream regulatory mechanisms of Dprs and DIPs are not clear. On the other hand, while transcription factors have been implicated in target recognition, their downstream cell surface proteins remain mostly unknown. We conduct an F1 dominant modifier genetic screen to identify regulators of Dprs and DIPs. We identify huckebein (hkb), a transcription factor previously implicated in target recognition of the dorsal Is motor neuron. We show that hkb genetically interacts with DIP-α and loss of hkb leads to complete removal of DIP-α expression specifically in dorsal Is motor neurons. We then confirm that this specificity is through the dorsal Is motor neuron specific transcription factor, even-skipped (eve), which acts downstream of hkb. Analysis of the genetic interaction between hkb and eve reveals that they act in the same pathway to regulate dorsal Is motor neuron connectivity. Our study provides insight into the transcriptional regulation of DIP-α and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons.
Dynamic structure of E. coli cytoplasm: supramolecular complexes and cell aging impact spatial distribution and mobility of proteins
Authors: Linnik Dmitrii , Maslov Ivan , Punter Christiaan Michiel , Poolman Bert
Published: April 2024

Protein diffusion is a critical factor governing the functioning and organization of a cell’s cytoplasm. In this study, we investigate the influence of (poly)ribosome distribution, cell aging, protein aggregation, and biomolecular condensate formation on protein mobility within the E. coli cytoplasm. We employ nanoscale single-molecule displacement mapping (SMdM) to determine the spatial distribution of the proteins and to meticulously track their diffusion. We show that the distribution of polysomes does not impact the lateral diffusion coefficients of proteins. However, the degradation of mRNA induced by rifampicin treatment leads to an increase in protein mobility within the cytoplasm. Additionally, we establish a significant correlation between cell aging, the asymmetric localization of protein aggregates and reduced diffusion coefficients at the cell poles. Notably, we observe variations in the hindrance of diffusion at the poles and the central nucleoid region for small and large proteins, and we reveal differences between the old and new pole of the cell. Collectively, our research highlights cellular processes and mechanisms responsible for spatially organizing the bacterial cytoplasm into domains with different structural features and apparent viscosity.
Synthesis, characterisation, and catalytic application of a soluble molecular carrier of sodium hydride activated by a substituted 4-(dimethylamino)pyridine
Authors: Macdonald Peter A. , Kennedy Alan R. , Weetman Catherine E. , Robertson Stuart D. , Mulvey Robert E.
Published: April 2024

Recently main group compounds have stepped into the territory of precious transition metal compounds with respect to utility in the homogeneous catalysis of fundamentally important organic transformations. Inspired by the need to promote more sustainability in chemistry because of their greater abundance in nature, this change of direction is surprising since main group metals generally do not possess the same breadth of reactivity as precious transition metals. Here, we introduce the dihydropyridylsodium compound, Na-1,2-tBu-DH(DMAP), and its monomeric variant [Na-1,2-tBu-DH(DMAP)]·Me6TREN, and demonstrate their effectiveness in transfer hydrogenation catalysis of the representative alkene 1,1-diphenylethylene to the alkane 1,1-diphenylethane using 1,4-cyclohexadiene as hydrogen source [DMAP = 4-dimethylaminopyridine; Me6TREN = tris(N,N-dimethyl-2-aminoethyl)amine]. Sodium is appealing because of its high abundance in the earth’s crust and oceans, but organosodium compounds have been rarely used in homogeneous catalysis. The success of the dihydropyridylsodium compounds can be attributed to their high solubility and reactivity in organic solvents.
Shifting sediment depocenters track ice-margin retreat in Baffin Bay
Authors: Okuma Emmanuel , Titschack Jürgen , Weiser Jens , Normandeau Alexandre , Kienast Markus , Hebbeln Dierk
Published: April 2024

Reconstructing the depositional history of Baffin Bay allows insights into the deglacial retreat of the Laurentide, Innuitian, and Greenland ice sheets from their maximum extent during the Last Glacial Maximum. Here, we present radiocarbon-controlled sedimentation rates from Baffin Bay based on 79 sediment cores to assess spatio-temporal variabilities in sediment deposition since the Last Glacial Maximum. This comprehensive dataset reveals that until ~15,000 years ago the deep basin and slopes were the dominant active sediment depocenters along most margins of Baffin Bay, suggesting prolonged ice-margin stability near the shelf edge, much longer than previously suggested. Between 13,000-11,000 years ago, most depocenters shifted quickly from the slope to the inner shelf, evidencing a very rapid landward ice-sheet retreat. The sedimentation rate-based mean erosion rates (0.17 and 0.08 millimeters/year) derived from the West Greenland Shelf underscore the high erosion capacity of the western Greenland Ice Sheet draining into Baffin Bay.
Large area van der Waals MoS2–WS2 heterostructures for visible-light energy conversion
Authors: Gardella Matteo , Zambito Giorgio , Ferrando Giulio , Bisio Francesco , Giordano Maria Caterina , Buatier de Mongeot Francesco
Published: April 2024

Large area MoS2–WS2 van der Waals heterostructures have been fabricated using a physical deposition process. The type-II band alignment promotes electro-optical photoconversion and enhances organic pollutant photodissociation.
Designing excellent UV birefringent materials through the synergistic interaction of two highly distorted functional groups
Authors: Zhou Xiaoyan , Mao Xiang , Zhang Pu , Dong Xuehua , Huang Ling , Cao Liling , Gao Daojiang , Zou Guohong
Published: April 2024

Two outstanding UV birefringent materials SbTeO3Cl and SbTeO3Br with a honeycomb-like two-dimensional (2D) layer structure, have been successfully designed, demonstrating significant birefringence (0.281@546 nm and 0.227@546 nm, respectively).
Electrocatalytic conversion of ω-azido carboxylic acids to 1-pyrrolines via a combined process of oxidative decarboxylation and intramolecular Schmidt rearrangement
Authors: Yang Kai , Li Rui , Gu Peiming
Published: April 2024

An efficient electrochemical oxidation of ω-azido carboxylic acids followed by an intramolecular Schmidt reaction for synthesis of 1-pyrroline has been reported.
Synthesis and photocatalytic performance investigation of an NH4Cl-assisted two-step calcination method for modified g-C3N4
Authors: Zhang Xinyue , Yuan Lin , Zhang Yu , Shu Xinyu , Li Renjie , Deng Qunfen , Zhang Zilong , Yang Rui
Published: April 2024

Compared to the bulk CN and fragmented CN-2, the structure of 650-CN-2 exhibits a more porous nature and possesses a larger specific surface area. Hence, it exhibits a more suitable band gap structure and displays higher photocatalytic efficiency.
Specific Preoperative Factors Increase Manipulations under Anesthesia Following Primary TKA
Authors: Bautista Anson G. , Kolodychuk Nicholas L. , Frederick Jeremy S. , Held Michael B. , Cooper H John , Shah Roshan P. , Geller Jeffrey A.
Published: April 2024

Arthrofibrosis following primary total knee arthroplasty (TKA) can result in pain and limit postoperative range of motion (ROM), jeopardizing clinical outcomes and patient satisfaction. This study aims to identify preoperative risk factors associated with necessitating a manipulation under anesthesia (MUA) following primary TKA.

We retrospectively reviewed 950 cases of consecutive primary TKAs performed at one institution by three arthroplasty surgeons between May 2017 and May 2019. Recorded preoperative variables included smoking status, race, preoperative ROM, presence of effusion or positive anterior drawer, and medical comorbidities. Demographic characteristics were compared with Student's t-tests or chi-square tests as appropriate. For each preoperative factor, we obtained an odds ratio (OR) for MUA risk using multivariate logistic regression.

Twenty (2.3%) patients underwent MUA following their index primary TKA surgery. History of ipsilateral knee surgery (OR: 2.727, p = 0.047) and diagnosed hypertension (OR: 4.764, p = 0.016) were identified as risk factors associated with significantly increased risk of MUA. The greater the preoperative ROM, the higher likelihood needed of MUA (OR: 1.031, p = 0.034).

Patients who had diagnosed hypertension or a history of prior ipsilateral knee surgery were associated with increased risk of necessitating an MUA following primary TKA. Additionally, a greater total arc of motion preoperatively increased the odds of needing MUA.

Level III of evidence was present.
Relationship between Kinesiophobia and Dynamic Postural Stability after Anterior Cruciate Ligament Reconstruction: A Prospective Cohort Study
Authors: Knapik Derrick M. , Kamitani Aguri , Smith Matthew V. , Motley John , Haas Amanda K. , Matava Matthew J. , Wright Rick W. , Brophy Robert H.
Published: April 2024

Anterior cruciate ligament (ACL) injuries in young, active patients generally require ACL reconstruction (ACLR) to restore mechanical and postural stability. The fear of movement or reinjury (kinesiophobia) has become increasingly recognized in the post-ACLR population; however, the association between restoration of postural stability and kinesiophobia remains largely unknown. The purpose of this study was to investigate changes in mean Tampa Scale of Kinesiophobia-11 (TSK-11), dynamic motion analysis (DMA) scores, and time on the testing platform, as well as any correlation between TSK-11 and mean overall and individual translational and rotational DMA scores during the first 12 months following ACLR. Cohort study. Patients undergoing ACLR were prospectively enrolled and dynamic postural stability and kinesiophobia based on the TSK-11 were collected within 2 days prior to surgery and at 6 and 12 months following ACLR. Dynamic postural stability was quantified by calculating a DMA score, with score calculated in three translational (anterior/posterior [AP], up/down [UD], medial/lateral [ML]) and three rotational (left/right [LR], flexion/extension, and internal/external rotation) independent planes of motions. Correlations between DMA and TSK-11 scores at each time point were analyzed. A total of 25 patients meeting inclusion criteria were analyzed. Mean overall DMA and TSK-11 scores increased with each successive testing interval. At 6-month follow-up, a weakly positive association between TSK-11 and DMA scores was appreciated based on overall DMA, AP, UD, ML, and LR. At 12 months, a moderately positive correlation was appreciated between TSK-11 and the translational, but not rotational, planes of motion. Following ACLR, lower level of kinesiophobia were found to be moderately associated with improved dynamic stability, especially in the translation planes of motion.
Silver-Mediated Homocoupling of Arylboronic Acids
Authors: Ohtaka Atsushi , Sakaguchi Tomoya , Fukuoka Kyuta , Matsuki Takuya , Kawase Misa , Tazawa Aya , Uozumi Yasuhiro , Matsumura Yoshimasa , Shimomura Osamu
Published: April 2024

Here we describe a homocoupling reaction of arylboronic acid facilitated by silver carbonate, which proceeds smoothly in MeOH even at ambient temperature. The reaction exhibits broad functional group compatibility, affording a variety of symmetrical biaryls in satisfactory yields. Silver nanoparticles formed in situ serve as an accelerator in this process. Moreover, initial mechanistic investigations suggest that this transformation may occur via a radical mechanism.
Measuring Chinese mobility behaviour during COVID-19 using geotagged social media data
Authors: Zhu Kaixin , Cheng Zhifeng , Wang Jianghao
Published: April 2024

COVID-19 caused widespread disruption to normal lives and human activities. In China, the mobility behaviour response to the COVID-19 pandemic at the intra-city and population group levels is largely unknown, mainly due to a lack of individual-level publicly available mobility data. Using 210 million geotagged posts from 10 million social media users, the study quantified the changes in stay-at-home and outings across amenities and groups in China during the pandemic. The users were compared to national census data to examine their representativeness. To validate the results externally, the geotagged data was performed post-stratified correction and further comparison with commonly used data sources. The findings reveal that (i) there was between 16.8% and 57.7% decrease in visits to places of work, retail and recreation sites, parks, transit stations, grocery stores, and pharmacies within one month of the outbreak; (ii) those who are young, have a bachelor’s degree or higher, and are unmarried experienced a greater decline in outings; (iii) people preferred to visit nearby locations, resulting in a 4.3% increase in visits to retail and recreational sites within a 3-kilometer radius of their homes. The data and findings could gain insight into the asymmetric impact of the pandemic on public infrastructure use and socio-demographic groups, helping design targeted policies to promote outdoor activities, stimulate economic recovery, and alleviate social inequality in vulnerable groups.
Multiparameter flow cytometric detection and analysis of rare cells in in vivo models of cancer metastasis
Authors: Mallin Mikaela M , Rolle Louis T A , Pienta Kenneth J , Amend Sarah R
Published: April 2024

Rapid and reliable circulating tumor cell (CTC) and disseminated tumor cell (DTC) detection are critical for rigorous evaluation of in vivo metastasis models. Clinical data show that each step of the metastatic cascade presents increasing barriers to success, limiting the number of successful metastatic cells to fewer than 1 in 1,500,000,000. As such, it is critical for scientists to employ approaches that allow for the evaluation of metastatic competency at each step of the cascade. Here, we present a flow cytometry-based method that enables swift and simultaneous comparison of both CTCs and DTCs from single animals, enabling evaluation of multiple metastatic steps within a single model system. We present the necessary gating strategy and optimized sample preparation conditions necessary to capture CTCs and DTCs using this approach. We also provide proof-of-concept experiments emphasizing the appropriate limits of detection of these conditions. Most importantly, we successfully recover CTCs and DTCs from murine blood and bone marrow. In Supplemental materials, we expand the applicability of our method to lung tissue and exemplify a potential multi-plexing strategy to further characterize recovered CTCs and DTCs. This approach to multiparameter flow cytometric detection and analysis of rare cells in in vivo models of metastasis is reproducible, high throughput, broadly applicable, and highly adaptable to a wide range of scientific inquiries. Most notably, it simplifies the recovery and analysis of CTCs and DTCs from the same animal, allowing for a rapid first look at the comparative metastatic competency of various model systems throughout multiple steps of the metastatic cascade.
Post-hospitalization Short Versus Long Steroid Taper Strategies in Patients With Acute Severe Ulcerative Colitis: A Comparison of Clinical Outcomes
Authors: Alomari Mohammad , Chadalavada Pravallika , Afraz Sadaf , AlGhadir-AlKhalaileh Mu’ed , Suarez Zoilo K , Swartz Alec , Rashid Mamoon , Khazaaleh Shrouq , Cohen Benjamin L , Ur Rahman Asad , Alomari Mohammad
Published: April 2024

Background

Ulcerative colitis (UC) is a chronic inflammatory colon disease characterized by relapsing flares and remission episodes. However, the optimal steroid tapering strategy in patients hospitalized for acute severe UC (ASUC) remains relatively unknown. We aim to examine the clinical outcomes in patients hospitalized for ASUC regarding variable prednisone taper regimens upon discharge.

Methods

We retrospectively reviewed all adult patients admitted to our facility with ASUC between 2000 and 2022. Patients were divided into 2 groups based on the duration of steroid taper on discharge (< 6 and > 6 weeks). Patients who had colectomy at index admission were excluded from the analysis. The primary outcome was rehospitalization for ASUC within 6 months of index admission. Secondary outcomes included the need for colectomy, worsening endoscopic disease extent and/or severity during the follow-up period (6 months), and a composite outcome as a surrogate of worsening disease (defined as a combination of all products above). Two-sample t-tests and Pearson’s chi-square tests were used to compare the means of continuous and categorical variables, respectively. Multivariate logistic regression analysis was performed to identify independent predictors for rehospitalization with ASUC.

Results

A total of 215 patients (short steroid taper = 91 and long steroid taper = 124) were analyzed. A higher number of patients in the long steroid taper group had a longer disease duration since diagnosis and moderate-severe endoscopic disease activity (63.8 vs. 25.6 months, p < 0.0001, 46.8% vs. 23.1%, P = ≤ .05, respectively). Both groups had similar disease extent, prior biologic therapy, and the need for inpatient rescue therapy. At the 6-month follow-up, rates of rehospitalization with a flare of UC were comparable between the 2 groups (68.3% vs. 68.5%, P = .723). On univariate and multivariate logistic regression, escalation of steroid dose within four weeks of discharge (aOR 6.09, 95% CI: 1.82–20.3, P  = .003) was noted to be the only independent predictor for rehospitalization with ASUC.

Conclusions

This is the first study comparing clinical outcomes between post-discharge steroid tapering regimens in hospitalized patients for ASUC. Both examined steroid taper regimens upon discharge showed comparable clinical results. Hence, we suggest a short steroid taper as a standard post-hospitalization strategy in patients following ASUC encounters. It is likely to enhance patient tolerability and reduce steroid-related adverse effects without adversely affecting outcomes.
The frozen elephant trunk: seeking a more definitive treatment for acute type A aortic dissection
Authors: Papakonstantinou Nikolaos A , Martinez-Lopez Daniel , Chung Jennifer Chia-Ying
Published: April 2024

OBJECTIVES

Conventional treatment for type A aortic dissection includes replacement of the ascending aorta with an open distal anastomosis in the hemiarch position. The frozen elephant trunk (FET) is a hybrid technique that extends the repair to the descending thoracic aorta. The goal is to improve resolution of malperfusion syndrome and to induce positive aortic remodelling and reduce the need for reintervention on the downstream aorta. We aim to summarize the data on the short and long-term outcomes of this technique.

METHODS

A thorough search of the literature was conducted isolating all articles dealing with aortic remodelling after the use of FET in case of type A acute aortic dissection. Keywords ‘aortic dissection’, ‘frozen elephant trunk’, ‘aortic remodelling’ and ‘false lumen thrombosis’ were used. Data for type B and chronic aortic dissections were excluded.

RESULTS

FET use favourably influences aortic remodelling. The main advantages lie in the exclusion of distal entry tears in either the aortic arch or descending aorta thus restoring antegrade blood flow in the true lumen and inducing false lumen thrombosis. False lumen thrombosis is not only induced at the level of the stent deployment but also lower in the distal descending aorta. Moreover, it offers an adequate landing zone in the mid-descending aorta for second-stage endovascular or open surgical aortic repair, if needed.

CONCLUSIONS

FET can be advantageous in the treatment of acute type A aortic dissection dealing with extended aortic pathology.
Adaptive alien genes are maintained amid a vanishing introgression footprint in a sea squirt
Authors: Touchard Fanny , Cerqueira Frédérique , Bierne Nicolas , Viard Frédérique
Published: April 2024

Human transport of species across oceans disrupts natural dispersal barriers and facilitates hybridization between previously allopatric species. The recent introduction of the North Pacific sea squirt, Ciona robusta, into the native range of the North Atlantic sea squirt, Ciona intestinalis, is a good example of this outcome. Recent studies have revealed an adaptive introgression in a single chromosomal region from the introduced into the native species. Here, we monitored this adaptive introgression over time, examining both the frequency of adaptive alleles at the core and the hitchhiking footprint in the shoulders of the introgression island by studying a thousand Ciona spp. individuals collected in 22 ports of the contact zone, 14 of which were sampled 20 generations apart. For that purpose, we developed a KASP multiplex genotyping approach, which proved effective in identifying native, nonindigenous and hybrid individuals and in detecting introgressed haplotypes. We found no early generation hybrids in the entire sample, and field observations suggest a decline in the introduced species. At the core region of the introgression sweep, where the frequency of C. robusta alleles is the highest and local adaptation genes must be, we observed stable frequencies of adaptive alien alleles in both space and time. In contrast, we observed erosion of C. robusta ancestry tracts in flanking chromosomal shoulders on the edges of the core, consistent with the second phase of a local sweep and a purge of hitchhiked incompatible mutations. We hypothesize that adaptive introgression may have modified the competition relationships between the native and invasive species in human-altered environments.
Endoscopic retrograde appendicitis therapy: current and the future
Authors: Liu Dan , Zhang Jiyu , Liu Bingrong
Published: April 2024

This article presents an overview of endoscopic retrograde appendicitis therapy (ERAT), an innovative and minimally invasive treatment for appendicitis with an appendix-preserving manner. Since its initial application in 2009, ERAT has gained significant popularity in China, due to its rapid recovery and minimal risk of complications. The ERAT procedures comprise several steps, including appendiceal orifice access and intubation, appendiceal lumen imaging, decompression and irrigation, fecalith removal, and stenting. ERAT has been used in various forms of complicated appendicitis, such as in pregnant women and children, with continuous improvements in both technique and safety. It has the potential to become the preferred diagnostic and treatment method for appendicitis. Until 2023, over 10,000 ERAT procedures have been successfully conducted in China, and the technique has gained more attention worldwide. However, challenges remain, including training, standardization of ERAT practice, research and technology improvement, enhancing public awareness, and fostering international collaboration. In summary, ERAT can be the standard treatment for appendicitis treatment, which represents a paradigm shift in the conventional clinical practice.
Genetic susceptibility to chronic diseases leads to heart failure among Europeans: the influence of leukocyte telomere length
Authors: Wong Jason Y Y , Blechter Batel , Liu Zhonghua , Shi Jianxin , Roger Véronique L
Published: April 2024

Background

Genetic susceptibility to various chronic diseases has been shown to influence heart failure (HF) risk. However, the underlying biological pathways, particularly the role of leukocyte telomere length (LTL), are largely unknown. We investigated the impact of genetic susceptibility to chronic diseases and various traits on HF risk, and whether LTL mediates or modifies the pathways.

Methods

We conducted prospective cohort analyses on 404 883 European participants from the UK Biobank, including 9989 incident HF cases. Multivariable Cox regression was used to estimate associations between HF risk and 24 polygenic risk scores (PRSs) for various diseases or traits previously generated using a Bayesian approach. We assessed multiplicative interactions between the PRSs and LTL previously measured in the UK Biobank using quantitative PCR. Causal mediation analyses were conducted to estimate the proportion of the total effect of PRSs acting indirectly through LTL, an integrative marker of biological aging.

Results

We identified 9 PRSs associated with HF risk, including those for various cardiovascular diseases or traits, rheumatoid arthritis (P = 1.3E-04), and asthma (P = 1.8E-08). Additionally, longer LTL was strongly associated with decreased HF risk (P-trend = 1.7E-08). Notably, LTL strengthened the asthma-HF relationship significantly (P-interaction = 2.8E-03). However, LTL mediated only 1.13% (P < 0.001) of the total effect of the asthma PRS on HF risk.

Conclusions

Our findings shed light onto the shared genetic susceptibility between HF risk, asthma, rheumatoid arthritis, and other traits. Longer LTL strengthened the genetic effect of asthma in the pathway to HF. These results support consideration of LTL and PRSs in HF risk prediction.
Usefulness of final transection of the proximal pulmonary artery in robotic left upper lobectomy
Authors: Uchida Shinsuke , Matsunaga Takeshi , Tomita Hisashi , Fukui Mariko , Hattori Aritoshi , Takamochi Kazuya , Suzuki Kenji
Published: April 2024

OBJECTIVES

The pulmonary artery runs around the left upper bronchus, which poses the risk of blood vessel injury when cutting in the blind spot of the bronchus. During robotic surgery, the robotic arm holds the tissue under constant tension; therefore, even if the pulmonary artery is left for final transection, it is not injured by unexpected tension. In this study, we examined the usefulness of final transection of the proximal pulmonary artery in robotic left upper lobectomy.

METHODS

This retrospective single-institution study evaluated patients who had undergone robotic lung resection. Of the 453 robotic lung resections performed at our institution between 2017 and 2022, 49 patients who had undergone left upper lobectomy were evaluated. Patients who had undergone bronchial transection followed by pulmonary artery transection were assigned to the group, bronchus prior transection (BT group, n = 38), and those who had undergone pulmonary artery transection followed by bronchial transection were assigned to the group, pulmonary artery prior transection (AT group, n = 11). Patient characteristics and perioperative outcomes were compared between the groups.

RESULTS

The groups did not differ significantly in age, sex, smoking history, tumour size, complication rates or 30-day mortality. The BT group inclined to shorter operative times and lesser blood loss. No active intraoperative bleeding occurred in the BT group. However, the AT group had 2 cases of intraoperative pulmonary artery bleeding, one of which required urgent conversion to thoracotomy.

CONCLUSIONS

Final transection of the proximal pulmonary artery is a novel and effective surgical technique for robotic left upper lobectomy.
A joint configuration method for multiple flexible resources in low carbon distribution networks based on massive scene dimensionality reduction
Authors: Zheng Zhen , Zhang Guanhua , Wang Duhong , Mou Kai , He Zhizhuo , Xing Haijun
Published: April 2024

Due to the extensive access of renewable sources in distribution networks, this research proposes a joint configuration method for multiple flexible resources in low carbon distribution networks based on massive scene dimensionality reduction to maximize the access capacity of renewable sources. The dimensionality reduction clustering is carried out on the wind-light-load mass high-dimensional scenes by the principal component Gaussian mixture clustering algorithm, and the typical scene set of wind-power-loads is obtained. Hereafter, a joint configuration model for multiple flexible resources of distribution network for massive scenarios is constructed, and using the second-order cone relaxation technique to convert the non-convex constraints in the model to convex processing. Last, a Portugal 54 distribution system is employed to verify the proposed method.
Scientific Advice and the COVID-19 Pandemic: Revisiting the Asian Disease Problem
Authors: Neumann Robert , Brust Oliver , Kadel Jasmin , von Hermanni Hagen , Menold Natalja
Published: April 2024

The coronavirus disease 2019 pandemic has underscored the importance of scientific knowledge and highlighted the challenge for politicians: They had to rely on expert advice and still had to make decisions under uncertainty due to the lack of long-term health data. This article investigates how expert judgments and expert advice affect the choices between programs that are proposed to combat the outbreak of a viral disease by means of a between-subjects design embedded in a survey. We use the classic Asian disease experiment and extend earlier applications by varying the professional background of the experts (virologists vs. social scientists) within the experimental set-up. We use data from a university wide web-survey to show the persistence of framing effects and that the disciplinary background of the expert is not related to individual decision-making under risk.
Contestation in a World of Liberal Orders
Authors: Goddard Stacie E , Krebs Ronald R , Kreuder-Sonnen Christian , Rittberger Berthold
Published: April 2024

It is widely acknowledged that the core institutions of the Liberal International Order (LIO) have in recent years been subject to increasingly intense contestation. There is less agreement on the sources of this contestation. This introductory paper to the special forum on “contestation in a world of liberal orders” makes two main contributions. First, the paper develops a theory of endogenous order contestation. It conceptualizes the LIO as a system of different types of suborders, which vary in the extent to which they reflect and promote liberal values and in the extent to which they are legally institutionalized. The paper explains how these different suborders generate their own types of order contestation. More liberally embedded and institutionalized suborders endogenously generate more intense and order-challenging contestation, while less liberal and less institutionalized orders are amenable to more modest and order-consistent contestation. Second, this paper identifies the specific endogenous mechanisms through which contestation shifts from order-consistent to order-challenging in especially these more liberally embedded and institutionalized suborders. It argues that not only liberal resistance to reform gives rise to order-challenging contestation, but even liberal accommodation and responsiveness can ultimately paralyze and ossify LIO institutions, which in turn lose legitimacy, frustrate would-be reformers, and drive them to order-challenging contestation. The different contributions to this special issue examine our core propositions across a range of economic, security, and social–political LIO suborders.
Jump Clustering, Information Flows, and Stock Price Efficiency
Authors: Chen Jian
Published: April 2024

We study the clustering behavior of stock return jumps modeled by a self/cross-exciting process embedded in a stochastic volatility model. Based on the model estimates, we propose a novel measurement of stock price efficiency characterized by the extent of jump clustering that stock returns exhibit. This measurement demonstrates the capability of capturing the speed at which stock prices assimilate new information, especially at the firm-specific level. Furthermore, we assess the predictability of self-exciting (clustered) jumps in stock returns. We employ a particle filter to sample latent states in the out-of-sample period and perform one-step-ahead probabilistic forecasting on upcoming jumps. We introduce a new statistic derived from predicted probabilities of positive and negative jumps, which has been shown to be effective in return predictions.
Addressing social needs in oncology care: another research-to-practice gap
Authors: Haines Emily , Shelton Rachel C , Foley Kristie , Beidas Rinad S , Dressler Emily V , Kittel Carol A , Chaiyachati Krisda H , Fayanju Oluwadamilola M , Birken Sarah A , Blumenthal Daniel , Rendle Katharine A
Published: April 2024

Social determinants of health and unmet social needs are directly related to cancer outcomes, from diagnosis to survivorship. If identified, unmet social needs can be addressed in oncology care by changing care plans in collaboration with patients’ preferences and accounting for clinical practice guidelines (eg, reducing the frequency of appointments, switching treatment modalities) and connecting patients to resources within healthcare organizations (eg, social work support, patient navigation) and with community organizations (eg, food banks, housing assistance programs). Screening for social needs is the first step to identifying those who need additional support and is increasingly recognized as a necessary component of high-quality cancer care delivery. Despite evidence about the relationship between social needs and cancer outcomes and the abundance of screening tools, the implementation of social needs screening remains a challenge, and little is known regarding the adoption, reach, and sustainability of social needs screening in routine clinical practice. We present data on the adoption and implementation of social needs screening at two large academic cancer centers and discuss three challenges associated with implementing evidence-based social needs screening in clinical practice: (1) identifying an optimal approach for administering social needs screening in oncology care, (2) adequately addressing identified unmet needs with resources and support, and (3) coordinating social needs screening between oncology and primary care.
Explaining the spatial segregation of ethnic groups in an early industrial city: the case of Vyborg
Authors: Härkönen Antti
Published: April 2024

An early industrial town’s spatial segregation is studied using empirical data concerning the Russian population of the town of Vyborg. Several hypotheses for explaining segregation are considered using spatial analysis. The spatial data are derived from historical maps and demographic data from various tax records. Socioeconomic segregation is studied as a possible cause of ethnic segregation. The main drivers of spatial segregation were the explicit policies of segregation enforced by both the Russian military administration and the town’s civilian administration. While the effects of segregation gradually diminished due to social diffusion, the impact of policy decisions driving segregation in the 18th and early 19th centuries was still visible in the population’s later 19th-century segregation. Yet neither the different preferences of Russians and others nor the income differences between areas explains the distribution of Russians. Segregation based on the membership of a guild was insignificant, with a few exceptions. Other factors such as discrimination, prejudice, and differences in housing market information probably contributed to segregation, but they cannot be studied with the data used.
Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing
Authors: Leduque Basile , Edera Alejandro , Vitte Clémentine , Quadrana Leandro
Published: April 2024

Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.
iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning
Authors: Yu Haopeng , Li Fan , Yang Bibo , Qi Yiman , Guneri Dilek , Chen Wenqian , Waller Zoë A E , Li Ke , Ding Yiliang
Published: April 2024

DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce ‘iM-Seeker’, an innovative computational platform designed for the prediction and evaluation of i-motifs. iM-Seeker exhibits the capability to identify potential i-motifs within DNA segments or entire genomes, calculating stability scores for each predicted i-motif based on parameters such as the cytosine tracts number, loop lengths, and sequence composition. Furthermore, the webserver leverages automated machine learning (AutoML) to effortlessly fine-tune the optimal i-motif scoring model, incorporating user-supplied experimental data and customised features. As an advanced, versatile approach, ‘iM-Seeker’ promises to advance genomic research, highlighting the potential of i-motifs in cell biology and therapeutic applications. The webserver is freely available at https://im-seeker.org.
A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs
Authors: Eijlers Peter , Al-Khafaji Mohammed , Soto-Martin Eva , Fasimoye Rotimi , Stead David , Wenzel Marius , Müller Berndt , Pettitt Jonathan
Published: April 2024

Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5′ ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5′ ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
The effects of different feeding strategies providing different levels of vitamin A on animal performance, carcass traits, and the conversion rate of subcutaneous fat color in cull-cows
Authors: Parkinson J T , Cochran H J , Kieffer J D , Relling A E , Boyles S L , Kopec R E , Garcia L G
Published: April 2024

Cull cows represent a significant percentage of revenue received from the U.S. beef industry; however, cull cows are heavily price discounted at time of slaughter. This experiment’s objective is to evaluate different feeding strategies and their effects on body condition score, subcutaneous fat color, and carcass yield and quality traits in cull cows. The central hypothesis is feeding a high-energy diet, with low levels of vitamin A, for 56 d will improve animal performance, carcass yield, and quality traits in addition to capturing the point (rate) of the conversion of yellow to white subcutaneous fat. In the present experiment 98 Angus crossbreed cows were utilized. Cows were fed either low vitamin A (LVA) diet consisting of whole shelled corn, soybean hulls, soybean meal, and a mineral-vitamin supplement or high vitamin A (HVA) diet, formulated using whole shelled corn, fescue hay, dry distiller grains with soluble, and a mineral-vitamin supplement for 56 d. During the 56 d feeding period, body weights and condition scores, and subcutaneous adipose samples were collected every 14 d. On day 56, cattle were slaughtered; 48 h postmortem carcass characteristics and objective color scores (subcutaneous adipose tissue) were recorded and a sample of the longissimus dorsi lumborum was collected. Subcutaneous adipose tissue samples were utilized to record subjective color scores and then ground to be analyzed for β-carotene concentration. The longissimus dorsi lumborum samples (2.54 cm slices) were removed for Warner-Bratzler shear force (WBSF) and pH testing. Data were analyzed using the MIXED procedure of SAS. Feeding cull cows LVA resulted in differences in subcutaneous carcass fat color (P = 0.01) as well as b* values (P < 0.01) on day 56 compared with HVA. Subjective fat color scores were not different (P > 0.10) on day 0 or 14 but were different (P ≤ 0.05) on days 28, 42, and 56. Additionally, 9-cis-β-carotene concentration on day 56 were different (P = 0.05) between treatments. A trend was noticed for all-trans-β-carotene concentration (P = 0.10) on day 56 as well. Cull cow body weights were greater (P ≤ 0.04) when fed the LVA diet starting on days 14, 28, and 42; and a trend was noticed on day 56 (P = 0.09). Overall, cows fed the LVA treatment for 56 d exhibited decreased adipose yellowness and β-carotene concentrations as well as increased live weights.
Treatment and Outcome of Supracondylar Humeral Fractures in Children Over 10 Years of Age at the Time of Injury: A Review of 60 Cases
Authors: Li YiQiang , Wei Sheng , Canavese Federico , Liu YuanZhong , Li JingChun , Liu YanHan , Xu HongWen
Published: April 2024

Objectives:

To assess the treatment and outcomes of supracondylar humeral fractures (SHFs) in children older than 10 years of age at the time of injury.

Methods:

The study analyzed clinical data from 60 patients who sustained SHF, all over the age of 10 years, were analyzed. The patients included 49 males and 11 females with a mean age of 10.9 ± 0.9 years (range, 10 to 14.5). All patients underwent surgical treatment under general anesthesia. Closed reduction (CR) and percutaneous fixation were the primary treatment, with open reduction and internal fixation being employed only in cases CR was unsuccessful. The study assessed the healing of fractures by measuring the radiographic angles, including the carrying angle (RCA), Baumann’s angle (BA), and metaphyseal–diaphyseal angle (MDA) on anteroposterior radiographs of the elbow joint. In addition, the study evaluated whether the anterior humeral line (AHL) appropriately passed through the middle third of the capitellum. The final follow-up visit used the Mayo Elbow Performance Index score (MEPI) and Flynn’s criteria to analyze the recovery of elbow function.

Results:

There were 15 (25%) SHF type II, 17 (28.3%) type III and 28 (46.7%) type IV. Of the 60 patients, 56 (93.3%) underwent successful CR, whereas 4 (6.7%) required open reduction and internal fixation because of an unsuccessful CR. The final follow-up showed the average BA as 72° ± 5.3°, the average MDA as 88.3° ± 2.8°, and the average RCA as 9.6° ± 3.9°. The AHL bisected accurately the capitellum in 59 cases (98.3%). The average range of elbow flexion-extension was 146.6° ± 8.6°, whereas the average MEPI score was 99.9 ± 0.6; 98.3% (n=59) were rated as excellent and 1.7% (n=1) were rated as good. According to Flynn’s criteria, 86.7% had an excellent outcome (n=52), 10% had a good outcome (n=6), and 3.3% had a poor outcome (n=2). Only 1 patient (1.7%) experienced redisplacement. Eight cases of nerve injury were reported, with 7 involving the radial nerve and 1 involving the ulnar nerve; all resolved spontaneously.

Conclusions:

CR and percutaneous fixation have been shown to be effective in treating SHF in 93.3% of children aged 10 years old and older at the time of injury, with favorable radiographic and functional outcomes and a low risk of secondary displacement. Open reduction should only be considered when CR is ineffective.
In silicodesign of stable single-domain antibodies with high affinity
Authors: Zhang Zhongyao , van der Kant Rob , Marković Iva , Vizarraga David , Garcia Teresa , Maragkou Katerina , Delgado Blanco Javier , Cianferoni Damiano , Orlando Gabriele , Cia Gabriel , Geukens Nick , Carolis Carlo , Volkov Alexander N. , Savvides Savvas N. , Dewilde Maarten , Schymkowitz Joost , Serrano Pubul Luis , Rousseau Frederic
Published: April 2024

Antibody-based therapeutics have become indispensable in modern medicine, but traditional methods of antibody discovery often present with limitations in developability, cross-reactivity, and ethical concerns. While deep learning and generative approaches have shown promise in the design of high affinity protein binders,de novoantibody design remains challenging. Here, we present EvolveX, a structure-based computational pipeline for designing antibody fragments. EvolveX utilizes ModelX and empirical force field FoldX to optimize complementarity- determining regions (CDRs) and TANGO for aggregation analysis. We demonstrate the ability of EvolveX to redesign a single-domain VHH antibody fragment targeting mouse Vsig4 to address two challenges: enhancing stability and affinity for the original target and redesigning it for high affinity to the human ortholog. The redesigned variants of VHH fragments specific to mouse Vsig4 showed improved physicochemical properties, while retaining binding affinities comparable to the original version. Notably, EvolveX improved the binding affinity of VHHs to human Vsig4 by over 1000-fold, transforming low-affinity binders into nanomolar-affinity molecules. Structural analyses by X-ray crystallography and NMR confirmed the accuracy of the designs, which display optimized interactions with the antigen. NGS and re-modelling analysis further demonstrated the efficiency of FoldX-based design pipeline. Collectively, our study highlights EvolveX’s potential to overcome current limitations in antibody design, offering a powerful tool for the development of next-generation therapeutics with enhanced specificity, stability, and efficacy.