bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of Frustrated Nonsequential Double Ionization Channels With the Carrier-Envelope Phase of Elliptically Polarized Laser Pulses
Authors: Xu Tong-Tong , Zhang Lian-Lian , Gong Wei-Jiang
Published: January 2024

Using a classical approach, we theoretically investigate the frustrated double ionization (FDI) of Ar atoms under elliptically polarized (EP) laser fields. The FDI yield is calculated as a function of laser intensity with different carrier-envelope phases (CEPs), and, similar to the carrier-envelope phase (CEP) dependence of nonsequential double ionization (NSDI), several knee-shaped structures appear. Moreover, both recollision and direct ionization trajectories are observed in FDI events for the “knee” structure regime. The footprints of which channel leads to FDI are encoded in the photoelectron momentum distributions. FDI events related to recollision excitation with subsequent ionization channels and recollision impact ionization channels can be controlled by CEP in EP laser fields.
Prospects for the Belle II Experiment to Further Elucidate the KM Mechanism and Beyond
Authors: Taniguchi Nanae
Published: January 2024

We present prospects for the Belle II experiment to further elucidate the KM mechanism and beyond. Recent measurements of the CKM parameter, and the radiative and electroweak penguin decays are also reported.
Beyond pGALS: the need for a multifaceted musculoskeletal decision-making tool (‘pGALSplus’) in community-based clinical practice
Authors: Mercer Vicky , Smith Nicola , Jandial Sharmila , Guglieri Michela , Jones Simon A , Foster Helen E
Published: January 2024

Musculoskeletal (MSK) problems in children are common, and health-care professionals must identify those requiring onward referral. Paediatric gait, arms, legs and spine (pGALS) is an MSK assessment to discern abnormal joints. We aimed to identify MSK assessments to add to pGALS (pGALSplus) to facilitate decision-making in the context of exemplar conditions representing a spectrum of MSK presentations, namely JIA, mucopolysaccharidoses, muscular dystrophy and developmental co-ordination disorder. A literature review identified 35 relevant articles that focused on clinical assessments [including questionnaire(s), physical examination and functional tests] used by health-care professionals in the context of the exemplar conditions. We provide a description of these assessments and the rationale regarding how they, or components of such tools, might be useful within pGALSplus. This process provides a foundation for further work to develop and validate pGALSplus.
Trend Factor in China: The Role of Large Individual Trading
Authors: Liu Yang , Zhou Guofu , Zhu Yingzi
Published: January 2024

We propose a novel trend factor for the Chinese stock market that incorporates both price and volume information to capture dominant individual trading, momentum, and liquidity. We find that volume plays a more significant role in the trend factor for China than for the United States, reflecting the greater retail participation in China. By incorporating this trend factor into the 3-factor model of Liu et al. (2019), we propose a 4-factor model that explains a wide range of stylized facts and 60 representative anomalies. Our study highlights the important role of individual trading in asset pricing, especially in China. (JEL G12, G14, G15)
The association between timing of dietary macronutrient and sodium consumption and sleep duration and quality
Authors: Baidoo Velarie Yaa Ansu , Alexandria Shaina J , Zee Phyllis C , Knutson Kristen L
Published: January 2024

Study Objective

The objective of this study was to examine the association between the timing of dietary macronutrients and sodium intake and sleep quantity and quality.

Methods

This was a cross-sectional study that included 34 adults between 21 and 50 years of age. The main outcome measures were objective sleep measures assessed from three nights of wrist actigraphy including sleep duration, fragmentation, and wake after sleep onset (WASO), and one night of polysomnography (PSG), including rapid eye movement (REM) sleep, non-REM stage 2 (N2), stage 3 (N3), and WASO. Multiple linear regression models and linear mixed models were used to estimate the associations between sleep measures and dietary measures (carbohydrates, fats, saturated fats, proteins, and sodium). Dietary timing was examined in two ways: (1) the average amount of each nutrient consumed within 3 hours of sleep start, and (2) the interval between the final intake of each nutrient and sleep.

Results

Average fat intake within 3 hours of sleep was associated with greater WASO from PSG (β = 4.48, p = 0.01). No other associations were found between the macronutrients or sodium intake (p > 0.05) within 3 hours of sleep and the sleep parameters from PSG or actigraphy. Similarly, no associations were found between any of the PSG or actigraphy sleep measures and the interval between final nutrient intakes and sleep with sleep duration.

Conclusions

The study suggests that greater fat but not carbohydrate, protein, saturated fat, or sodium intake close to sleep may be associated with greater sleep disruption; however, no other associations were observed.
Neoadjuvant and adjuvant therapy for biliary tract cancer: Advances and limitations
Authors: Wilbur H. Catherine , Soares Heloisa P. , Azad Nilofer S.
Published: January 2024

Biliary tract cancers (BTC) are a rare and aggressive consortium of malignancies, consisting of intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma, and gallbladder carcinoma. While most patients present with metastatic disease, a minority of patients with BTC are eligible for curative surgical resection at the time of presentation. However, these patients have poor 5-year overall survival rates and high rates of recurrence, necessitating the improvement of the neoadjuvant and adjuvant treatment of BTC. In this review, we assess the neoadjuvant and adjuvant clinical trials for the treatment of BTC and discuss the challenges and limitations of clinical trials, as well as future directions for the treatment of BTC.
Somatization Mediates the Relationship Between Childhood Trauma and Pain Ratings in Patients with Irritable Bowel Syndrome
Authors: Schubach Abigail , Quigley Brian M. , Lackner Jeffrey M. , Gudleski Gregory D.
Published: January 2024

Goals:

To identify potential mechanisms by which childhood trauma may lead to the adult development of abdominal symptoms in patients with irritable bowel syndrome (IBS).

Background:

Patients with IBS frequently report a history of childhood trauma. The pathophysiology by which abdominal pain arises in patients with IBS is multidimensional, consisting of both peripheral factors, such as altered motility, inflammation, and bacterial overgrowth, as well as central factors, such as psychological distress and neuro-hormonal dysregulation.

Study:

Adult psychological factors (anxiety, depression, and somatization) were examined to determine if they mediate the relationship between retrospective reports of childhood trauma and current adult IBS abdominal symptoms in a study of 436 patients (M age=41.6, 79% F) meeting Rome III diagnosis criteria. Childhood trauma was measured using retrospective questions assessing physical and sexual abuse. Psychological factors in adulthood were measured with the subscales of the Brief Symptom Inventory-18. Outcome variables included adult IBS symptoms of abdominal pain, bloating, and satisfaction with bowel habits from the IBS Symptoms Severity Scale.

Results:

Results indicated that somatization mediated the relationship between childhood abuse and abdominal pain and bloating but not bowel satisfaction.

Conclusions:

This study provides insight into the multifactorial nature of IBS-associated abdominal pain in patients with a history of childhood trauma, elucidating the need for a trauma-informed treatment approach for patients with histories of abuse.
PHACE syndrome: a case report and a comprehensive review
Authors: William Munna , Bhusal Amrit , Umar Syed Muhammad , Jamal Ayesha , Anjum Abdul Sattar , Habib Mudasira
Published: January 2024

Introduction and importance:

PHACE syndrome is a rare neurocutaneous disorder characterized by large segmental hemangiomas on the face and is associated with multiple developmental defects. PHACE stands for posterior fossa malformations, hemangiomas, arterial abnormalities, cardiac defects, and eye anomalies, with the most common manifestation being hemangioma in the cervico-facial region in early childhood.

Case presentation:

The authors report a case of a 15-year-female with complaints of facial hemangioma which on multisystemic imaging showed features of central nervous system (CNS) anomalies that led to the diagnosis of PHACE syndrome. The patient was started on propanolol which decreased the size of hemangioma in follow-up visits.

Clinical discussion:

The hemangioma in the frontotemporal and frontonasal area of the face are associated more with CNS and cardiovascular anomalies needing a detailed multisystem approach. CNS anomalies include posterior cerebral fossa enlargement, cystic dilation of the fourth ventricle, arachnoid cyst, and cerebellar hypoplasia which were present in our case. Propanolol is considered the first-line drug for facial hemangioma with reported evidence of remarkable improvement and good tolerance. However, regular follow-up of the patient is needed to rule out any recurrence.

Conclusion:

PHACE syndrome, although being a rare occurrence, must be kept as a differential diagnosis in infants and children with facial hemangioma. Imaging modalities like MRI/magnetic resonance arteriography must be used to rule out possible associations related to PHACE syndrome and focus on early treatment to prevent possible complications.
The Orthopaedic NP Workforce
Authors: Pelletier Brittany , Hoyt Alex
Published: January 2024

Although a growing number of nurse practitioners (NPs) are practicing in orthopaedics, little is known about the workforce. The aim of this study was to estimate the size of the orthopaedic NP workforce, compare it with the workforce of primary care NPs, and investigate the interaction effect specialty NP practice and physician relationships have on NP role perception. We selected licensed, practicing orthopaedic and primary care NPs from the 2018 National Sample Survey of Registered Nurses and compared demographics, education, experience, functional autonomy, and job outcomes. Nationally, 2,796 NPs described their specialty as orthopaedics. Compared with primary care NPs, they spent 27% more time on care coordination, were half as likely to have their own patient panel, and were most likely to say that their NP education was fully utilized when in a collaborative relationship with physicians. Differences between orthopaedic and primary care NPs may call for reform of Consensus Model that currently places specialty practice outside its regulatory network.
Telemedicine and Cancer Care
Authors: Doshi Sahil D. , Bange Erin M. , Daly Bobby , Kuperman Gilad , Panageas Katherine S. , Morris Michael J.
Published: January 2024

Telemedicine holds the potential to transform cancer care delivery and optimize value, access, and quality of care. A transformed regulatory environment coupled with the need to continue medical care despite operational limitations led to the rapid expansion of telemedicine in cancer care during the COVID-19 pandemic. Its utilization has since varied, and it has faced significant challenges. In this review, we will explore the state of telemedicine in cancer care delivery, the challenges it faces, and strategies to enhance its successful implementation.
Supportive Care for Cancer Patients Via Telehealth
Authors: Soumerai Tara E. , Mulvey Therese M. , Jackson Vicki A. , Lennes Inga T.
Published: January 2024

Delivering oncologic care via telemedicine has presented a unique set of benefits and challenges. Discussions of sensitive topics between patients and providers can be difficult on a virtual platform. Although it was imperative to utilize telemedicine to keep cancer patients safe during the height of the pandemic, its continued use in the postvaccination era has provided important conveniences to both providers and patients. In the case of breaking bad news and end-of-life discussions, however, in-person care has remained the overwhelming preference of both groups. If face-to-face consultation is not possible or feasible in these situations, virtual visits are a viable option to connect oncologists with their patients.
Distinguishing fibromyalgia syndrome from small fiber neuropathy: a clinical guide
Authors: Jänsch Sarah , Evdokimov Dimitar , Egenolf Nadine , Meyer zu Altenschildesche Caren , Kreß Luisa , Üçeyler Nurcan
Published: January 2024

Introduction:

Fibromyalgia syndrome (FMS) and small fiber neuropathy (SFN) are distinct pain conditions that share commonalities and may be challenging as for differential diagnosis.

Objective:

To comprehensively investigate clinical characteristics of women with FMS and SFN to determine clinically applicable parameters for differentiation.

Methods:

We retrospectively analyzed medical records of 158 women with FMS and 53 with SFN focusing on pain-specific medical and family history, accompanying symptoms, additional diseases, and treatment. We investigated data obtained using standardized pain, depression, and anxiety questionnaires. We further analyzed test results and findings obtained in standardized small fiber tests.

Results:

FMS patients were on average ten years younger at symptom onset, described higher pain intensities requiring frequent change of pharmaceutics, and reported generalized pain compared to SFN. Pain in FMS was accompanied by irritable bowel or sleep disturbances, and in SFN by paresthesias, numbness, and impaired glucose metabolism (P < 0.01 each). Family history was informative for chronic pain and affective disorders in FMS (P < 0.001) and for neurological disorders in SFN patients (P < 0.001). Small fiber pathology in terms of skin denervation and/or thermal sensory threshold elevation was present in 110/158 (69.7 %) FMS patients and 39/53 (73.6 %) SFN patients. FMS patients mainly showed proximally reduced skin innervation and higher corneal nerve branch densities (p<0.001) whereas SFN patients were characterized by reduced cold detection and prolonged electrical A-delta conduction latencies (P < 0.05).

Conclusions:

Our data show that FMS and SFN differ substantially. Detailed pain, drug and family history, investigating blood glucose metabolism, and applying differential small fiber tests may help to improve diagnostic differentiation and targeted therapy.
Vanderbilt Mini-PROM–Breast for Breast Reconstruction: A Short-Form, Patient-Reported Outcomes Measure
Authors: Park Benjamin C. , Drolet Brian C. , Perdikis Galen
Published: January 2024

Background:

Breast reconstruction procedures are among the most commonly performed plastic surgery operations. Although there are well-validated patient-reported outcomes measures (PROMs) for breast reconstruction, there are several patient-, provider-, and service-level barriers to their implementation in routine clinical settings. Therefore, we developed a short-form PROM to evaluate breast reconstruction outcomes.

Methods:

Using a mixed-methods approach, the Vanderbilt Mini-PROM–Breast (VMP-B) was constructed and validated to assess patient-reported outcomes from breast reconstruction. Classic test theory methods were used to evaluate acceptability, reliability, and validity. External validation was subsequently performed using the BREAST-Q as a reference standard.

Results:

The VMP-B is a 16-item instrument composed of three domains: quality of life, body image, and breast satisfaction. Psychometric properties including acceptability, reliability, and validity exceeded reference criteria. When tested with 104 patients, the authors found significant benefits of breast reconstruction on quality of life, body image, and breast satisfaction. These results were associated with sizeable effect sizes (g) (g = 0.421, g = 0.520, and g = 1.25) demonstrative of clinically meaningful results. When tested concurrently in 70 patients, the VMP-B and the BREAST-Q showed similar results, exhibiting excellent convergent validity.

Conclusions:

The VMP-B is a validated short-form PROM that reliably assesses breast reconstruction outcomes. As a short form, the VMP-B decreases both patient and provider burden, which allows for routine, point-of-care collection of breast reconstruction outcomes.
Novel Noninvasive Hybrid Flap Preconditioning Surpasses Surgical Delay in the Murine Model
Authors: Du Xingyi , Liu Wenyue , Xu Boyang , Luan Jie , Liu Chunjun
Published: January 2024

Background:

Ischemic necrosis in the distal portion of a flap is a challenging complication in plastic surgery. The authors hypothesized that a novel hybrid flap preconditioning (HFP) device combining foam-mediated external suction and nonsurgical delay can promote skin flap survival better than surgical delay.

Method:

Twenty-eight mice were divided into 4 groups: a control group, in which a 4 × 1.5–cm dorsal flap was made with no preconditioning; a surgical delay group, in which surgical delay occurred 7 days before flap elevation; a foam-mediated external suction (FMES) group, in which foam-mediated external suction at −100 mm Hg was used 5 hours a day for 6 days, and the flap was elevated on the seventh day; and a hybrid flap preconditioning (HFP) group, in which silicone strips were applied along the contour of the foam interface. The same negative-pressure protocol was used as in the FMES group. Seven days after flap elevation, macroscopic, histologic, and Western blot analyses were performed.

Results:

The flap survival rate was 46.25% (8.12%) in the control group, 68.72% (7.00%) in the surgical delay group, 57.03% (8.17%) in the FMES group, and 80.66% (3.27%) in the HFP group. Immunohistologic analysis of CD31+ cells in the distal end of viable tissue procured 7 days after flap elevation showed significantly higher angiogenesis in the surgical delay and HFP groups. Western blot results showed an increased expression of vascular endothelial growth factor in the surgical delay and HFP groups.

Conclusions:

The authors developed and fabricated a novel HFP device combining foam-mediated external suction and nonsurgical delay. The concept of HFP has proved to promote flap survival better than surgical delay.

Clinical Relevance Statement:

This study presented an innovative noninvasive method of flap preconditioning, which has been demonstrated to be superior to surgical delay in a murine model and holds promise for potential application in clinical settings.
Low Strip Unifying Hybrid Rhinoseptoplasty: A Novel Classification in Dorsal Preservation Surgery
Authors: Taglialatela Scafati Salvatore , Rasulo Mario , Göksel Abdülkadir
Published: January 2024

Background:

Preservation rhinoplasty techniques continue to evolve. Suture tip-plasty with minimal resection and grafting, lateral crural tensioning, minimal excision from the lateral crura, dorsal preservation, subperichondrial dissection, and preservation of the ligaments have become the milestones of modern rhinosurgery. However, every time the dorsal frame is modified by means of rasping, shaving, or osteotomy, or the nasal tip is structured using grafts, surgeons are essentially applying structural concepts to their technique. The term “hybrid rhinoplasty” seems to include a more appropriate definition of this approach.

Methods:

The authors performed a retrospective analysis of the medical records of patients who underwent primary septorhinoplasty using the low strip unifying hybrid rhinoseptoplasty concept from December of 2019 to June of 2022. Patient functional satisfaction and cosmetic satisfaction were evaluated using the Rhinoplasty Health Inventory and Nose Outcome scale.

Results:

All reported procedures had low revision rates with good cosmetic and functional outcomes.

Conclusions:

Tailoring the surgical technique is essential in rhinoplasty. The authors present a new technical paradigm to help surgeons choose the best approach for dorsal preservation surgery.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Association of Frailty With Health Care Utilization for Patients Over One Year Following Surgical Evaluation
Authors: Flinn Stephen J. , Silver David S. , Hodges Jacob , Bilderback Andrew L. , Buchanan Dan , Ludwig Justin M. , Schuster James , Hall Daniel E.
Published: January 2024

Objective:

Characterize the distribution of health care utilization associated with preoperative frailty in the year following evaluation by a surgeon.

Background:

Frailty is associated with increased morbidity, mortality, and costs for surgical patients. However, the total financial burden for frail patients beyond the index surgery and inpatient stay remains unknown.

Methods:

Prospective cohort assembled from February 2016 to December 2020 within a multihospital integrated health care delivery and finance system, from patients evaluated with the Risk Analysis Index of frailty. Inclusion criteria: age greater than 18 years, valid Risk Analysis Index, and membership in the integrated health care delivery and finance system health plan. Data were stratified by frailty and surgical status.

Results:

The mean (SD) age was 54.7 (16.1) years and 58.2% females of the cohort (n=86,572). For all patients with reimbursement for surgery (n=53,856), frail and very frail patients incurred respective increases of 8% (P=0.027) and 29% (P<0.001) in utilization relative to the normal group. Robust patients saw a 52% (P<0.001) decrease. This pattern was more pronounced in the cohort without surgery (n=32,716). The increase over normal utilization for frail and very frail patients increased to 23% (P=0.004) and 68% (P<0.001), respectively. Utilization among robust patients decreased by 62% (P<0.001). Increases among the frail were primarily due to increased inpatient medical and postacute care services (all P<0.001).

Conclusions:

Patient frailty is associated with increased total health care utilization, primarily via increased inpatient medical and postacute care following surgery. Quantifying these frailty-related financial burdens may inform clinical decision-making as well as the design of value-based reimbursement strategies.
In
silico
modelling of the effect of pyloric intervention procedures on gastric flow and emptying in a stomach with gastroparesis
Authors: Kuhar Sharun , Seo Jung-Hee , Pasricha Pankaj J , Mittal Rajat
Published: January 2024

Pyloric interventions are surgical procedures employed to increase the gastric emptying rate in gastroparesis patients. In this study, we use an
in silico
model to investigate the consequences of pyloric intervention on gastric flow and emptying for two phenotypes of gastroparesis: antral hypomotility and decreased gastric tone. The transpyloric pressure gradient predicted by the
in silico
model, based on viscous fluid flow equations, is compared against
in vivo
measurements. Both phenotypes exhibit a similar pre-procedural emptying rate reduction, but after pyloric surgery, antral hypomotility case with preserved gastric tone shows significant improvements in emptying rates, up to 131%, accompanied by bile reflux from the duodenum into the stomach. Conversely, severely reduced gastric tone cases exhibited a post-procedural reduction in the net emptying rate due to the relatively larger bile reflux. In cases with a combination of antral hypomotility and reduced gastric tone, post-procedural improvements were observed only when both conditions were mild. Our findings highlight the pivotal role of the relative increase in pyloric orifice diameter in determining post-operative emptying rates. The study suggests a possible explanation for the selective response of patients toward these procedures and underscores the potential of
in silico
modelling to generate valuable insights to inform gastric surgery.
Single-cell expression predicts neuron-specific protein homeostasis networks
Authors: Pechmann Sebastian
Published: January 2024

The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
Are regulations addressing farm animal welfare issues during live transportation fit for purpose? A multi-country jurisdictional check
Authors: Duval Eugénie , Lecorps Benjamin , von Keyserlingk Marina A. G.
Published: January 2024

Growing animal welfare concerns have pushed some jurisdictions to strengthen regulations addressing live farm animal transportation, but whether they provide satisfactory levels of protection for animals remains to be shown. Using the recent peer-reviewed literature, we identified four major risk factors associated with live animal transportation (fitness for transport, journey duration, climatic conditions and space allowances) and explored how regulations were structured to prevent animal welfare issues in five English-speaking Western jurisdictions (Australia, Canada, New Zealand, the EU and the USA). All legally binding federal regulations were systematically reviewed and compared. Whether these rules were fit for purpose was assessed using the relevant peer-reviewed scientific literature. Our findings indicate the majority of regulations in most jurisdictions are often insufficient or too vague to be deemed fit for purpose. All five jurisdictions fall short in guaranteeing adequate protection to livestock during transport. Using recent changes as well as future policy proposals under discussion, we identify future directions that could form the basis for regulatory changes that may significantly improve the welfare of farm animals during transportation.
Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model
Authors: Selvakumar Pavitra , Siddharthan Rahul
Published: January 2024

Transcription factor binding sites (TFBS), like other DNA sequence, evolve via mutation and selection relating to their function. Models of nucleotide evolution describe DNA evolution via single-nucleotide mutation. A stationary vector of such a model is the long-term distribution of nucleotides, unchanging under the model. Neutrally evolving sites may have uniform stationary vectors, but one expects that sites within a TFBS instead have stationary vectors reflective of the fitness of various nucleotides at those positions. We introduce ‘position-specific stationary vectors’ (PSSVs), the collection of stationary vectors at each site in a TFBS locus, analogous to the position weight matrix (PWM) commonly used to describe TFBS. We infer PSSVs for human TFs using two evolutionary models (Felsenstein 1981 and Hasegawa-Kishino-Yano 1985). We find that PSSVs reflect the nucleotide distribution from PWMs, but with reduced specificity. We infer ancestral nucleotide distributions at individual positions and calculate ‘conditional PSSVs’ conditioned on specific choices of majority ancestral nucleotide. We find that certain ancestral nucleotides exert a strong evolutionary pressure on neighbouring sequence while others have a negligible effect. Finally, we present a fast likelihood calculation for the F81 model on moderate-sized trees that makes this approach feasible for large-scale studies along these lines.
Improved estimates for the number of non-negative integer matrices with given row and column sums
Authors: Jerdee Maximilian , Kirkley Alec , Newman M. E. J.
Published: January 2024

The number of non-negative integer matrices with given row and column sums features in a variety of problems in mathematics and statistics but no closed-form expression for it is known, so we rely on approximations. In this paper, we describe a new such approximation, motivated by consideration of the statistics of matrices with non-integer numbers of columns. This estimate can be evaluated in time linear in the size of the matrix and returns results of accuracy as good as or better than existing linear-time approximations across a wide range of settings. We show that the estimate is asymptotically exact in the regime of sparse tables, while empirically performing at least as well as other linear-time estimates in the regime of dense tables. We also use the new estimate as the starting point for an improved numerical method for either counting or sampling matrices with given margins using sequential importance sampling. Code implementing our methods is available.
Numerical direct scattering transform for breathers
Authors: Mullyadzhanov I. I. , Gudko A. S. , Mullyadzhanov R. I. , Gelash A. A.
Published: January 2024

We consider the model of the focusing one-dimensional nonlinear Schrödinger equation (fNLSE) in the presence of an unstable constant background, which exhibits coherent solitary wave structures—breathers. Within the inverse scattering transform (IST) method, we study the problem of the scattering data numerical computation for a broad class of breathers localized in space. Such a direct scattering transform (DST) procedure requires a numerical solution of the auxiliary Zakharov–Shabat system with boundary conditions corresponding to the background. To find the solution, we compute the transfer matrix using the second-order Boffetta–Osborne approach and recently developed high-order numerical schemes based on the Magnus expansion. To recover the scattering data of breathers, we derive analytical relations between the scattering coefficients and the transfer matrix elements. Then we construct localized single- and multi-breather solutions and verify the developed numerical approach by recovering the complete set of scattering data with the built-in accuracy providing the information about the amplitude, velocity, phase and position of each breather. To combine the conventional IST approach with the efficient dressing method for multi-breather solutions, we derive the exact relation between the parameters of breathers in these two frameworks.
Explorations of the holonomy of a rolling sphere
Authors: Honein Theresa E. , O’Reilly Oliver M.
Published: January 2024

Consider a rigid body rolling with one point in contact with a fixed surface. Now suppose that the instantaneous point of contact traces out a closed path. As a demonstration of a phenomenon known as holonomy, the body will typically not return to its original orientation. The simplest demonstration of this phenomenon in rigid body dynamics occurs in the motion of a rolling sphere and finds application to path planning and reorientation of spherical robots. Motivated by earlier works of Bryant and Johnson, we establish expressions for the change in orientation of a rolling sphere after completing a rectangular path. We use numerical methods to show that all possible changes in orientation are possible using a single rectangular path. Based on the Euler angle parameterization of a rotation, we develop a more intuitive method to achieve a desired orientation using three rectangular paths. With regards to applications, the paths we discuss can be employed to achieve any desired reorientation of a spherical robot.
Environmental drivers of Arctic communities based on metabarcoding of marine sediment eDNA
Authors: Geraldi Nathan R. , Krause-Jensen Dorte , Ørberg Sarah B. , Frühe Larissa , Sejr Mikael K. , Hansen Jørgen L. S. , Lund-Hansen Lars , Duarte Carlos M.
Published: January 2024

Our ability to assess biodiversity at relevant spatial and temporal scales for informing management is of increasing importance given this is foundational to identify and mitigate the impacts of global change. Collecting baseline information and tracking ecological changes are particularly important for areas experiencing rapid changes and representing data gaps such as Arctic marine ecosystems. Environmental DNA has the potential to provide such data. We extracted environmental DNA from 90 surface sediment samples to assess eukaryote diversity around Greenland and Svalbard using two separate primer pairs amplifying different sections of the 18S rRNA gene. We detected 27 different phyla and 99 different orders and found that temperature and the change in temperature explained the most variation in the community in a single linear model, while latitude, sea ice cover and change in temperature explained the most variation in the community when assessed by individual non-linear models. We identified potential indicator taxa for Arctic climate change, including a terebellid annelid worm. In conclusion, our study demonstrates that environmental DNA offers a feasible method to assess biodiversity and identifies warming as a key driver of differences in biodiversity across these remote ecosystems.
Anti-predator defences are linked with high levels of genetic differentiation in frogs
Authors: Medina Iliana , Dong Caroline , Marquez Roberto , Perez Daniela M. , Wang Ian J. , Stuart-Fox Devi
Published: January 2024

Predator–prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.
The causes of species richness patterns among clades
Authors: Yu Dan , Wiens John J.
Published: January 2024

Two major types of species richness patterns are spatial (e.g. the latitudinal diversity gradient) and clade-based (e.g. the dominance of angiosperms among plants). Studies have debated whether clade-based richness patterns are explained primarily by larger clades having faster rates of species accumulation (speciation minus extinction over time; diversification-rate hypothesis) or by simply being older (clade-age hypothesis). However, these studies typically compared named clades of the same taxonomic rank, such as phyla and families. This study design is potentially biased against the clade-age hypothesis, since clades of the same rank may be more similar in age than randomly selected clades. Here, we analyse the causes of clade-based richness patterns across the tree of life using a large-scale, time-calibrated, species-level phylogeny and random sampling of clades. We find that within major groups of organisms (animals, plants, fungi, bacteria, archaeans), richness patterns are most strongly related to clade age. Nevertheless, weaker relationships with diversification rates are present in animals and plants. These overall results contrast with similar large-scale analyses across life based on named clades, which showed little effect of clade age on richness. More broadly, these results help support the overall importance of time for explaining diverse types of species richness patterns.
My host’s enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages
Authors: Siedentop Berit , Rüegg Dario , Bonhoeffer Sebastian , Chabas Hélène
Published: January 2024

Bacteria are infected by mobile genetic elements like plasmids and virulent phages, and those infections significantly impact bacterial ecology and evolution. Recent discoveries reveal that some plasmids carry anti-phage immune systems like CRISPR-Cas, suggesting that plasmids may participate in the coevolutionary arms race between virulent phages and bacteria. Intuitively, this seems reasonable as virulent phages kill the plasmid’s obligate host. However, the efficiency of CRISPR-Cas systems carried by plasmids can be expected to be lower than those carried by the chromosome due to continuous segregation loss, creating susceptible cells for phage amplification. To evaluate the anti-phage protection efficiency of CRISPR-Cas on plasmids, we develop a stochastic model describing the dynamics of a virulent phage infection against which a conjugative plasmid defends using CRISPR-Cas. We show that CRISPR-Cas on plasmids provides robust protection, except in limited parameter sets. In these cases, high segregation loss favours phage outbreaks by generating a population of defenceless cells on which the phage can evolve and escape CRISPR-Cas immunity. We show that the phage’s ability to exploit segregation loss depends strongly on the evolvability of both CRISPR-Cas and the phage itself.
Investigating trade-offs between ovary activation and immune protein expression in bumble bee (
Bombus impatiens
) workers and queens
Authors: McAfee Alison , Chapman Abigail , Bao Grace , Tarpy David R. , Foster Leonard J.
Published: January 2024

Evidence for a trade-off between reproduction and immunity has manifested in many animal species, including social insects. However, investigations in social insect queens present a conundrum: new gynes of many social hymenopterans, such as bumble bees and ants, must first mate, then transition from being solitary to social as they establish their nests, thus experiencing confounding shifts in environmental conditions. Worker bumble bees offer an opportunity to investigate patterns of immune protein expression associated with ovary activation while minimizing extraneous environmental factors and genetic differences. Here, we use proteomics to interrogate the patterns of immune protein expression of female bumble bees (
Bombus impatiens
) by (i) sampling queens at different stages of their life cycle, then (ii) by sampling workers with different degrees of ovary activation. Patterns of immune protein expression in the haemolymph of queens are consistent with a reproduction–immunity trade-off, but equivalent samples from workers are not. This brings into question whether queen bumble bees really experience a reproduction–immunity trade-off, or if patterns of immune protein expression may actually be due to the selective pressure of the different environmental conditions they are exposed to during their life cycle.
MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers
Authors: Wang Haihua , Wu Steven , Zhang Kaile , Chen Ko-Hsuan , Vilgalys Rytas , Liao Hui-Ling
Published: January 2024

Profiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome– or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.
Burkholderia cenocepaciaepigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation
Authors: Quintana-Feliciano Richard , Kottur Jithesh , Ni Mi , Ghosh Rikhia , Salas-Estrada Leslie , Rechkoblit Olga , Filizola Marta , Fang Gang , Aggarwal Aneel K.
Published: January 2024

Burkholderia cenocepaciais an opportunistic and infective bacterium containing an orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates the N6 of the adenine at the fifth base position (GTWWAC). Here, we present a high-resolution crystal structure of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structure shows not one, but two DNA substrates bound to the M.BceJIV dimer, wherein each monomer contributes to the recognition of two recognition sequences. This unexpected mode of DNA binding and methylation has not been observed previously and sets a new precedent for a DNA methyltransferase. We also show that methylation at two recognition sequences occurs independently, and that GTWWAC motifs are enriched in intergenic regions of a strain ofB. cenocepacia’sgenome. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limitingB. cenocepaciainfection.
Freshwater ‘microcroissants’ shed light on a novel higher-level clade within Trebouxiophyceae and reveal the genusChlorolobionas a trebouxiophyte
Authors: Barcytė Dovilė , Hodač Ladislav , Eliáš Marek
Published: January 2024

Trebouxiophyceae is a widespread and species-rich green algal class encompassing mostly coccoid algae with a simple ovoid or ellipsoidal outline. However, some poorly-sampled lineages have evolved more elaborate shapes or even complex thalli, adding to the class’s morphological diversity. Led by new and previously established strains, this study additionally uncovered a clade of croissant-like trebouxiophytes. Phylogenetic analyses inferred from nuclear 18S rDNA and chloroplastrbcLsequences confirmed the monophyly of the ‘microcroissant’ clade, which we propose to be classified as a new family, Ragelichloridaceae. This family includes two novel genera,RagelichlorisandNavichloris, and the previously describedThorsmoerkia. The position of Ragelichloridaceae within Trebouxiophyceae stayed unresolved but chloroplast phylogenomics showed that the family belongs to the broaderincertae sedisgroup, which also includesXylochlorisandLeptosira. In addition, our study showed that the microcroissant-like genusChlorolobion, previously classified within Chlorophyceae, is a genuine trebouxiophyte, potentially related to Ragelichloridaceae.

Highlights

A new family-level clade uncovered within Trebouxiophyceae.

Two new genera described.

The genusChlorolobionshown to be a trebouxiophyte.
The blast effector Pwl2 is a virulence factor that modifies the cellular localisation of host protein HIPP43 to suppress immunity
Authors: Were Vincent , Yan Xia , Foster Andrew J. , Sklenar Jan , Langner Thorsten , Gentle Amber , Sahu Neha , Bentham Adam , Zdrzałek Rafał , Ryder Lauren , Kaimenyi Davies , Gomez De La Cruz Diana , Petit-Houdenot Yohan , Eseola Alice Bisola , Smoker Matthew , Bautista Mark Jave , Ma Weibin , Kourelis Jiorgos , Maclean Dan , Banfield Mark J. , Kamoun Sophien , Menke Frank L.H. , Moscou Matthew J. , Talbot Nicholas J.
Published: January 2024

The rice blast fungusMagnaporthe oryzaesecretes a battery of effector proteins to facilitate host infection. Among these effectors, Pwl2 was first identified as a host specificity determinant for infection of weeping lovegrass (Eragrostis curvula) and is also recognised by the barley Mla3 resistance gene. However, its biological activity is not known. Here we show thatPWL2expression is regulated by the Pmk1 MAP kinase during cell-to-cell movement byM. oryzaeat plasmodesmata (PD)-containing pit field sites. Consistent with its regulation, we provide evidence that Pwl2 binds to a barley heavy metal-binding isoprenylated protein HIPP43, which results in its displacement from plasmodesmata. Transgenic barley lines overexpressing eitherPWL2or HIPP43 exhibit attenuated immune responses and increased disease susceptibility. By contrast, a Pwl2SNDEYWYmutant that does not interact with HIPP43, fails to alter the PD localisation of HIPP43. Targeted deletion of three copies ofPWL2inM. oryzaeresults in aΔpwl2mutant showing gain-of-virulence to weeping lovegrass and barley Mla3 lines, but also a reduction in severity of blast disease on susceptible host plants. Taken together, our results provide evidence that Pwl2 is a virulence factor that acts by suppressing host immunity through perturbing the plasmodesmatal deployment of HIPP43.
Deregulation of multiple mechanisms shapes the onset ofLAMA2-congenital muscular dystrophy
Authors: Martins Susana G , Ribeiro Vanessa , Melo Catarina , Paulino-Cavaco Cláudia , Antonini Dario , Naidu Sharadha Dayalan , Murtinheira Fernanda , Fonseca Inês , Saget Bérénice , Pita Mafalda , Fernandes Diogo R , dos Santos Pedro G , Rodrigues Gabriela , Zilhão Rita , Herrera Federico , Dinkova-Kostova Albena T , Carlos Ana Rita , Thorsteinsdóttir Sólveig
Published: January 2024

LAMA2-congenital muscular dystrophy (LAMA2-CMD) is the most common congenital muscular dystrophy. This often-lethal disease is triggered by mutations inLAMA2, coding for laminin-α2 chain, a key extracellular matrix (ECM) component, prevalent in the skeletal muscle. Several phenotypes have been associated with LAMA2-CMD, however, it is not yet known what mechanisms are faulty, right at disease onsetin utero. Using thedyWmouse model of LAMA2-CMD we showed that the disease onset is characterized by a profound downregulation of gene expression, with a marked effect on cytoskeletal organization, myoblast differentiation and fusion and altered DNA repair and oxidative stress responses. Concordantly, we found thatLama2-deficient myoblast cells displayed proliferation and differentiation defects, increased oxidative stress and DNA damage. Together, our findings provide unique insights into the processes dependent on laminin-α2 chain during muscle development, revealing its critical importance to maintain muscle cell homeostasis already at fetal stages.