bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential of a Second Screening Test for Alloimmunization in Pregnancies of Rhesus-positive Women: A Swedish Population-based Cohort Study
Authors: Lamichhane Nishan , Liu Shengxin , Wikman Agneta , Reilly Marie
Published: September 2024

Introduction:

There is lack of consensus regarding whether a second screening in rhesus-positive pregnant women is worthwhile, with different guidelines, recommendations, and practices. We aimed to estimate the number and timing of missed alloimmunizations in rhesus-positive pregnancies screened once and weigh the relative burden of additional screening and monitoring versus the estimated reduction in adverse pregnancy outcomes.

Methods:

We extracted information on maternal, pregnancy, and screening results for 682,126 pregnancies for 2003–2012 from Swedish national registers. We used data from counties with a routine second screening to develop and validate a logistic model for a positive second test after an earlier negative. We used this model to predict the number of missed alloimmunizations in counties offering only one screening. Interval-censored survival analysis identified an optimal time window for a second test. We compared the burden of additional screening with estimated adverse pregnancy outcomes avoided.

Results:

The model provided an accurate estimate of positive tests at the second screening. For counties with the lowest screening rates, we estimated that a second screening would increase the alloimmunization prevalence by 33% (from 0.19% to 0.25%), detecting the 25% (304/1222) of cases that are currently missed. The suggested timing of a second screen was gestational week 28. For pregnancies currently screened once, the estimated cost of a second test followed by maternal monitoring was approximately 10% of the cost incurred by the excess adverse pregnancy outcomes.

Conclusion:

Investment in routine second screening can identify many alloimmunizations that currently go undetected or are detected late, with the potential for cost savings.
Immediate Breast Reconstruction Outcomes in Patients with Prior Mantle and Whole Breast Irradiation
Authors: Mullen Barbara L. , Mazroua Muhammad S. , Murphy Brenna M. , Boonipat Thanapoom , Gao Robert W. , Mrdutt Mary M. , Shumway Dean A. , Degnim Amy C. , Vijayasekaran Aparna
Published: September 2024

Background:

Limited studies have detailed the risk of mastectomy with immediate breast reconstruction among women who previously received mantle field radiation.

Methods:

A single institution retrospective review from 2010 to 2020 of patients previously treated with mantle field radiation (MF-RT) and subsequent mastectomy with immediate breast reconstruction was performed. Patients with prior whole breast irradiation (WBI) were also included as a reference group. Demographic, comorbidity, and surgical factors were collected. The primary outcome was major complications, defined as those requiring reoperation, intravenous antibiotics, or debridement.

Results:

Fourteen patients with prior MF-RT (27 breasts) and 129 with prior WBI (132 breasts) underwent mastectomy with immediate reconstruction. Prior MF-RT patients were significantly younger (43.8 versus 57.5, P < 0.001) and had significantly lower body mass index (23.6 versus 26.8, P = 0.004) compared with prior WBI patients. Nipple-sparing mastectomy was significantly more common in the mantle than in the WBI patients (78.6% versus 35.9%, P = 0.03). Most (13, 92.9%) prior mantle patients underwent tissue expander/implant-based reconstruction. Three (21.4%) prior MF-RT patients had major complications at any point, but none required an alternative type of reconstruction. On multiple variable analysis, there was no significant difference in major complication risk among prior MF-RT versus WBI patients (HR 0.74, confidence interval 0.20–2.70, P = 0.74).

Conclusion:

Immediate tissue expander/implant-based reconstruction in prior MF-RT patients seems safe, with a complication risk similar to that of prior WBI patients.
Laser-Assisted In Situ Keratomileusis in Flat, Normal, and Steep Corneas
Authors: Arnon Roee , Levinger Eliya , Pikkel Joseph , Yahalomi Tal , Sela Tzahi , Munzer Gur , Kaiserman Igor , Mimouni Michael
Published: September 2024

Purpose:

To compare laser-assisted in situ keratomileusis (LASIK) outcomes in patients with different corneal curvatures.

Methods:

This is a retrospective comparative chart review. Patients included in this study underwent wavefront-optimized myopic LASIK between January 2013 and December 2022 at Care-Vision Laser Center, Tel-Aviv, Israel. Patients were divided into 3 groups based on the steepness of the cornea (steep keratometry) (flat: <42 diopters [D], normal: 42–46 D, and steep: >46 D). Case-by-case matching was performed to verify that baseline parameters (age, preoperative visual acuity, and refractive error) were similar between groups. Primary outcome measures were postoperative corrected/uncorrected distance visual acuity, efficacy index, safety index, spherical equivalence, and astigmatism.

Results:

After matching, 300 eyes were included in each group, which were similar in baseline parameters. There were no significant postoperative differences between flat, normal, and steep corneas regarding safety index (1.01 vs. 1.02 vs. 1.01,P= 0.95), efficacy index (1.03 vs. 1.02 vs. 1.02,P= 0.94), logarithm of the minimum angle of resolution corrected distance visual acuity (0.01 vs. 0.01 vs. 0.01,P= 0.17), logarithm of the minimum angle of resolution uncorrected distance visual acuity (0.02 vs. 0.03 vs. 0.02,P= 0.65), proportion of patients with spherical equivalence within 0.50 D (73.0% vs. 73.7% vs. 69.3%,P= 0.45) or 1.00 D (93.3% vs. 94.7% vs. 91.7%,P= 0.34) of the target, and proportion of patients with astigmatism within 0.50 D (86.7% vs. 82.3% vs. 80.3%,P= 0.11) or 1.00 D (98.7% vs. 98.7% vs. 99.0%,P= 0.91) of the target. Longer term follow-up of a smaller set of patients revealed similar results.

Conclusions:

No significant differences were found between flat, normal, and steep corneas following wavefront-optimized myopic LASIK. Thus, this procedure may be safely and effectively performed across a wide range of corneal curvatures.
Decreased vision due to scarring after phototherapeutic keratectomy
Authors: Nuijts Rudy M.M.A. , Ollivier Robin C.I. , Schlereth Simona , Cursiefen Claus , Busin Massimo , Yu Angeli Christy , Alió Jorge , Borderie Vincent , Shetty Rohit , Nagaraja Harsha , Sethu Swaminathan
Published: September 2024

In May 2023, a 36-year-old carpenter complained of a sudden decrease in visual acuity in both eyes after his fourth COVID-19 vaccination. He underwent extensive evaluation by ophthalmological, neurological, and internal medicine specialists elsewhere, which was unremarkable, except for a computed tomography scan of his brain showing minor occipital calcifications. In 2021, he had been diagnosed with anterior basement membrane dystrophy and treated with phototherapeutic keratectomy (PTK) of the left eye, leading to significant postoperative haze.

On referral in July 2023, slitlamp examination showed significant anterior basement membrane dystrophy in the right eye, whereas the left eye had an extensive central scar in the anterior stroma, measuring up to 6 mm in width and 140 µm in depth (Figures 1–3

JOURNAL/jcrs/04.03/02158034-202410000-00017/figure1/v/2024-09-18T130724Z/r/image-tiff

JOURNAL/jcrs/04.03/02158034-202410000-00017/figure2/v/2024-09-18T130724Z/r/image-tiff

JOURNAL/jcrs/04.03/02158034-202410000-00017/figure3/v/2024-09-18T130724Z/r/image-tiff

). His corrected distance visual acuity was 20/80 in his right eye and 20/200 in his left eye, with a manifest refraction of −0.50 −3.75 × 170 and +0.00 −4.75 × 180, respectively. Corneal Scheimpflug topography showed regular corneal astigmatism of 3.3 diopters (D) and 5.5 D in the right and left eyes, respectively, with a corneal thickness of 550 and 566 µm (Figure 4

JOURNAL/jcrs/04.03/02158034-202410000-00017/figure4/v/2024-09-18T130724Z/r/image-tiff

). The Schirmer tear test was 20-20 mm. Fundoscopy, electrophysiological testing, and retinal optical coherence tomography (OCT) showed no abnormalities. The patient mentioned he had Crohn disease, managed with ustekinumab (a monoclonal antibody inhibitor of cytokines interleukin [IL]-12 and IL-23), but he had discontinued it because of the apparent remission of the disease.

Attempts to improve visual acuity involved a soft bandage contact lens in the right eye, which was discontinued after 2 days because of the occurrence of a small corneal infiltrate that healed with a short course of topical antibiotics. Unfortunately, because of his vision, he cannot perform his tasks as a carpenter anymore.

Which is your recommended treatment for both eyes?
Extensive intraoperative peritoneal lavage with surgery, compared to surgery alone, for patients diagnosed with gastric cancer: a systematic review and meta-analysis of randomized controlled trials
Authors: Adil Mariam , Ghori Dua , Anwar Eman , Shaukat Maryam , Malik Muhammad T.H. , Murtaza Dua A. , Sumra Khadija A. , Essani Rabia , Nizami Urooj , Khan Bakhtawer N. , Abid Hunaina , Oduoye Malik Olatunde
Published: September 2024

Background:

Gastric cancer ranks as the fifth most frequently diagnosed cancer and the seventh most prevalent overall. The lifetime risk of developing gastric cancer is 1.87% for males and 0.79% for females worldwide.

Aim:

This systematic review and meta-analysis aimed to determine whether extensive intraoperative peritoneal lavage (EIPL) provides short-term benefits or improved survival outcomes for patients undergoing gastrectomy.

Methods:

A comprehensive search spanned PubMed, Embase, Cochrane Library, clinicaltrials.gov, and Web of Science, from their inception up to October 2023, adhering to predefined inclusion and exclusion criteria. The quality of the studies was analyzed using the Cochrane Collaboration Risk of Bias Tool. Data analysis was done using Review Manager 5.3, utilizing a random-effects model.

Results:

Our analysis incorporated seven randomized controlled trials with 2602 patients. The follow-up time for all outcomes varied from 30–60 months. For our primary outcomes, EIPL demonstrated a significant benefit over surgery alone in terms of recurrence (RR=0.73; 95% CI: 0.65–0.83, P<0.00001) and postoperative complications (RR=0.67; 95% CI: 0.51–0.87, P=0.003). For our secondary outcomes, postoperative hospital stay (MD=−0.35; 95% CI: −1.11 to 0.41; P=0.37), 3-year overall survival (OR=1.44; 95% CI: 0.84–2.47; P=0.19), 3-year disease-free survival (HR=0.93; 95% CI: 0.78–1.13; P=0.48), and time to first flatus (MD=−0.17; 95% CI: −0.35 to 0.01; P=0.06), no statistically significant differences were observed between the EIPL and control groups.

Conclusion:

While there is a marginal difference in survival outcomes, EIPL holds promise in significantly reducing overall cancer recurrence and suggests an enhancement in postoperative recovery.
Indications for diagnostic whole-body iodine scan: a review of guidelines
Authors: Askari Emran , Saidi Bahare , Evangelista Laura
Published: September 2024

Objectives

Here, we have compiled all key statements derived from these guidelines and delved into details on which scenarios the diagnostic whole-body iodine scan (DxWBIS) might be useful.

Methods

We identified all relevant guidelines by searching the MEDLINE/PubMed databases, Google Scholar, and Ovid from 2006 onwards using keywords related to DxWBIS, RxWBIS, iodine scintigraphy, and iodine scan. We excluded case reports/series, original articles, and clinical trials while including guidelines or consensus opinions. Additionally, we reviewed existing literature to ensure no guidelines were overlooked.

Results

Overall, 23 relevant guidelines or consensus opinions discussed their views on the role of DxWBIS. Different indications for DxWBIS have been largely discussed in the last few years. However, the role of DxWBIS has been well established after treatment with 131I, with still limited evidence in the other clinical assessments.

Conclusions

Most guidelines find DxWBIS appealing for higher-risk patients, particularly those with a chance of recurrence; additional well-designed studies are required to address further indications.
Partner Characteristics and HIV Outcomes Among Partners Reached by Phone Versus In-Person for Assisted Partner Services in Western Kenya
Authors: Roy Paladhi Unmesha , Kariithi Edward , Otieno George , Hughes James P. , Lagat Harison , Sharma Monisha , Masyuko Sarah , Macharia Paul , Bosire Rose , Mugambi Mary , Farquhar Carey , Katz David A.
Published: September 2024

Background

Assisted partner services (APS) is an effective strategy for testing people with undiagnosed HIV, but there is limited information on the relative reach and effectiveness of phone versus in-person contact.

Methods

We analyzed data from 31 facilities in Western Kenya providing APS to female index clients newly HIV diagnosed, their male partners, and female partners of men newly HIV diagnosed. Assisted partner services providers attempted contacting partners using phone first and, if unsuccessful, in-person in the community. Using log-linear mixed models, we estimated relative risks (RRs) between phone being the final contact method and partner characteristics and HIV outcomes.

Results

From May 2018 to March 2020, 2534 female index clients named 7614 male partners, of whom 772 (10.1%) tested positive and named an additional 4956 non-index female partners. Of 11,912 (94.7%) partners reached, 5179 (43.5%) were via phone and 6733 (56.5%) in-person. Of 8076 testing-eligible partners, 99.7% tested and 11.2% first-time tested. Of those tested, 13.1% were newly diagnosed, of whom 87.0% linked to care. Newly diagnosed partners were less likely to have been reached by phone versus in-person (9.8% vs. 15.9%; adjusted relative risk, 0.61; 95% confidence interval, 0.53–0.70). Being reached by phone was not significantly associated with testing, first-time testing, or linkage to care.

Conclusions

In an APS program that reached 94% of elicited partners, fewer than half were successfully contacted by phone. A combined phone and in-person approach is likely essential for equitable, effective APS.
Pelvic and Perineal Reconstruction
Authors: Shahzad Farooq , Ray Edward
Published: September 2024

Learning Objectives:

After studying this article, the participant should be able to: 1. Classify types of bony pelvic resections. 2. Outline reconstructive options for pelvic and perineal defects. 3. Identify advantages and drawbacks of various reconstructive techniques. 4. Recognize the functional benefits of bony and soft-tissue reconstruction.

Defects of the pelvis and perineum arise from tumors, trauma, infection, congenital differences, and gender incongruence. Pelvic resections can result in bony instability and soft-tissue deficiency. The goals of reconstruction are maintenance of spinopelvic continuity, elimination of dead space, resurfacing of cutaneous defects, and prevention of hernias. Perineal reconstruction has important functional considerations. Abdominoperineal resection and pelvic exenteration defects benefit from flap reconstruction to decrease pelvic wound complications. Vulvovaginal reconstruction is performed with flaps from the perineum, thigh, or abdomen. Scrotal and superficial penile defects are most commonly reconstructed with scrotal flaps and skin grafts. Total penile reconstruction most commonly uses a radial forearm free flap.
Evolving Surgical Techniques for Tessier Clefts Number 3 and 4
Authors: Rashid Mamoon , Malik Sakina , Sarwar Saad ur Rehman , Qazi Uzair A. , Salahuddin Omer , Khan Muhammad Ibrahim , Malik Saleem A.
Published: September 2024

Tessier cleft types 3 and 4 are exceptionally rare even within the ambit of rare craniofacial clefts, with very few reported cases worldwide, particularly in the bilateral forms. This rarity combined with the absence of standardized management guidelines poses significant technical challenges for plastic surgeons and suboptimal surgery can leave patients with substantial facial deformity and stigma. In this study, the authors have presented the management guidelines for the repair of these clefts and have discussed some of the cases in detail. The senior author has operated on 15 clefts in 11 patients (4 bilateral). The strategy employed includes components of the techniques described by Longaker and colleagues and Giglio and colleagues. This includes rotation and advancement of lateral cheek flaps and use of naso-jugal flaps. This modified technique incorporates the use of a nasojugal flap for lower eyelid reconstruction, a cheek rotation flap tocover the medial cheeek defect, closure of alveolar cleft with the use of mucoperiosteal flaps and repair of the lip by principles described by Millard. These modifications keep the scars along the facial esthetic units thus achieving better esthetic outcomes. The authors have utilised this technique for both type 3 and 4 clefts with the addition of a glabellar flap in some cases of Tessier No. 3 clefts. Most of these cases were operated on before 6 months of age and the average follow-up time was 28 months after surgery.

Conclusion:

Management of craniofacial clefts has evolved. Due to the rarity of craniofacial clefts, surgical development in this regard is slow and complex. The authors invite the plastic surgery fraternity to apply their technique in the repair of these clefts and recommend giving feedback by conducting further studies to assess this technique’s feasibility, versatility, and cosmetic outcome.
Incidence of Pressure Injuries in Patients at Risk Using a Powered Alternating Pressure Air Mattress
Authors: Meaume Sylvie , Urbinelli Renaud , Marty Marc
Published: September 2024

PURPOSE:

The aim of the study was to determine the clinical value of using a powered alternating pressure air mattress (P-APAM) in the prevention of pressure injury (PI) in patients at medium to high risk.

DESIGN:

Noncomparative, observational study.

SUBJECTS AND SETTING:

The sample comprised 86 patients who were >18 years old, were classified as having medium to high risk of PI, had no PI at baseline, and were lying more than 15 hours a day on a specific P-APAM. Data were collected between September 2018 and July 2019, in 4 nursing homes, and 1 long-term care geriatrics hospital department in France.

METHODS:

In addition to guideline-based care for PI prevention, patients were followed up for 35 days following placement on the P-APAM. The main outcome was the percentage of patients who developed between day 0 and day 35 at least 1 PI of at least stage 2 on the sacrum, spine, or heel. Secondary outcomes were patient assessments of comfort, caregiver satisfaction, mattress noise level, and mattress safety.

RESULTS:

No patients experienced a PI (incidence = 0%; 95% confidence interval, 0.00%-4.28%). Patients were satisfied or very satisfied with the mattress in most cases in terms of comfort (77.9%) and stability (73.0%). Patients also rated the noise level of the mattress as satisfactory or very satisfactory in all cases (100%).

CONCLUSION:

When combined with guideline-based PI prevention measures, use of the P-APAM was associated with a low incidence of PI.
Nursing Care of Patients Managed With a Defunctioning Tube Ileostomy
Authors: Wang Feixia , Wang Qunmin , Li Xia , Wang Qin , Hua Hanju , Zhong Zifeng
Published: September 2024

PURPOSE:

The purpose of this study was to describe nurses’ experiences of caring for patients with colorectal cancer who underwent surgery to create a spontaneously closed defunctioning tube ileostomy after low anterior resection.

DESIGN:

Exploratory, descriptive study.

SUBJECTS AND SETTINGS:

Data were collected from 6 registered nurses specialized in Wound, Ostomy and Continence Care (WOC nurses). The patient cohort comprised 247 hospitalized patients with histologically confirmed colorectal cancer who underwent low anterior resection of the rectum and creation of a closed defunctioning tube ileostomy. The study setting was the First Affiliated Hospital, Zhejiang University School of Medicine.

METHODS:

Semi-structured interviews and content analysis were used to collect and analyze data. The Wound, Ostomy and Continence Care nurses visited patient participants 1 week after hospital discharge and 1 to 2 times per week until the cannula was removed and the ostomy wound closed. Data were collected over a 6-month span after the surgery from January 2016 to December 2018.

RESULTS:

Content analysis identified 7 management strategies unique to caring for patients with a closed defunctioning tube ileostomy. They are: (1) cannula fixation (securement); (2) maintaining inflation of the cannular balloon to prevent fecal flow into the distal bowel, (3) cannular patency, (4) dietary advice for prevention of cannular blockage, (5) selecting an ostomy pouching system, (6) patient education, and (7) care during and following cannula removal (extubation).

CONCLUSIONS:

We identified 7 areas of nursing care unique to the closed defunctioning tube ileostomy that provide a basis for creating clinical guidelines for patients undergoing this procedure.
Infrared Thermometry and Thermography in Detecting Skin Temperature Variations to Predict Venous Leg Ulcer Reulceration
Authors: Kelechi Teresa J. , Prentice Margie , Mueller Martina , Madisetti Mohan
Published: September 2024

BACKGROUND:

We aimed to determine whether monitoring skin temperature (Tsk) over recently healed venous leg ulcers (VLUs) can provide an objective approach to predicting reulceration. The cases presented in this article were part of a larger, multisite, 6-month randomized clinical trial of a cooling intervention to prevent ulcer recurrence among patients with chronic venous disease (CVD) and with recently healed VLUs.

CASES:

We report a series of four patients with CVD, three experienced VLU reulceration, and one case remained free of recurrence. Assessments of recurrence likelihood is based on daily patient Tsk self-reports using a handheld infrared (IR) thermometer and clinic visits using a combination digital and long-wave IR camera. All three cases with reulceration demonstrate a persistent 2°C above baseline average Tsk increase and a “dip-and-spike” pattern from −3°C to +5°C for several days prior to reulceration. In contrast, the patient who remained free of VLU recurrence showed a stable pattern of Tsk with minimal daily fluctuations. Thermal images showed Tsk of the affected extremity is warmer compared with the contralateral limb and increased between visits when ulcers recurred.

CONCLUSION:

Using IR devices to monitor Tsk among patients with CVD at risk of reulceration is an objective and reliable approach to detect changes over time. Consistent Tsk elevation over the affected area as compared to the contralateral limb and a “dip-and-spike” pattern may predict reulceration. Infrared devices showed effectiveness in detecting changes indicative of Tsk changes in recently healed leg skin over scar tissue after VLU healing.
Amplitude modulation structure in French and German poetry: universal acoustic physical structures underpin different poetic rhythm structures
Authors: Daikoku Tatsuya , Lee Charlotte , Goswami Usha
Published: September 2024

French and German poetry are classically considered to utilize fundamentally different linguistic structures to create rhythmic regularity. Their metrical rhythm structures are considered poetically to be very different. However, the biophysical and neurophysiological constraints upon the speakers of these poems are highly similar. Scientifically, this suggests that at the level of the acoustic physical structures that are produced orally, the two poetic genres may be rhythmically extremely similar. Here, we apply a language-blind computational model of linguistic rhythm based on features of the amplitude envelope (AE) to compute these physical stimulus characteristics. The model was applied to recordings of the recitation of metrical French and German poems by native speakers. Poems in free verse were not considered in the study. The results indicated that the acoustic physical structures of the poems were identical for the two languages in terms of temporal modulation patterns in the AE. This challenges the linguistic view that German poetry utilizes lexical stress to create prosodic alternation between strong and weak syllables, while French poetry relies on accentuation at the level of prosodic phrasing. Nevertheless, minor differences in physical structure could be detected by applying further modelling drawn, respectively, from the birdsong and neural connectivity literatures.
Multispecies interactions and the community context of the evolution of virulence
Authors: Evensen Claire , White Andrew , Boots Mike
Published: September 2024

Pairwise host–parasite relationships are typically embedded in broader networks of ecological interactions, which have the potential to shape parasite evolutionary trajectories. Understanding this ‘community context’ of pathogen evolution is vital for wildlife, agricultural and human systems alike, as pathogens typically infect more than one host—and these hosts may have independent ecological relationships. Here, we introduce an eco-evolutionary model examining ecological feedback across a range of host–host interactions. Specifically, we analyse a model of the evolution of virulence of a parasite infecting two hosts exhibiting competitive, mutualistic or exploitative relationships. We first find that parasite specialism is necessary for inter-host interactions to impact parasite evolution. Furthermore, we find generally that increasing competition between hosts leads to higher shared parasite virulence while increasing mutualism leads to lower virulence. In exploitative host–host interactions, the particular form of parasite specialization is critical—for instance, specialization in terms of onward transmission, host tolerance or intra-host pathogen growth rate lead to distinct evolutionary outcomes under the same host–host interactions. Our work provides testable hypotheses for multi-host disease systems, predicts how changing interaction networks may impact virulence evolution and broadly demonstrates the importance of looking beyond pairwise relationships to understand evolution in realistic community contexts.
Widespread scope for coral adaptation under combined ocean warming and acidification
Authors: Jury Christopher P. , Toonen Robert J.
Published: September 2024

Reef-building coral populations are at serious risk of collapse due to the combined effects of ocean warming and acidification. Nonetheless, many corals show potential to adapt to the changing ocean conditions. Here we examine the broad sense heritability (H
2
) of coral calcification rates across an ecologically and phylogenetically diverse sampling of eight of the primary reef-building corals across the Indo-Pacific. We show that all eight species exhibit relatively high heritability of calcification rates under combined warming and acidification (0.23–0.56). Furthermore, tolerance to each factor is positively correlated and the two factors do not interact in most of the species, contrary to the idea of trade-offs between temperature and pH sensitivity, and all eight species can co-evolve tolerance to elevated temperature and reduced pH. Using these values together with historical data, we estimate potential increases in thermal tolerance of 1.0–1.7°C over the next 50 years, depending on species. None of these species are probably capable of keeping up with a high global change scenario and climate change mitigation is essential if reefs are to persist. Such estimates are critical for our understanding of how corals may respond to global change, accurately parametrizing modelled responses, and predicting rapid evolution.
Human-driven breakdown of predator–prey interactions in the northern Adriatic Sea
Authors: Zuschin Martin , Nawrot Rafał , Dengg Markus , Gallmetzer Ivo , Haselmair Alexandra , Kowalewski Michał , Scarponi Daniele , Wurzer Sandra , Tomašových Adam
Published: September 2024

Long-term baseline data that allow tracking how predator–prey interactions have responded to intensifying human impacts are often lacking. Here, we assess temporal changes in benthic community composition and interactions between drilling predatory gastropods and their molluscan prey using the Holocene fossil record of the shallow northern Adriatic Sea, which is characterized by a long history of human transformation. Molluscan assemblages differ between the Isonzo and Po prodelta, but both show consistent temporal trends in the abundance of dominant species. Samples of mollusc prey collected at high stratigraphic resolution indicate that drilling frequencies have drastically declined in the Po prodelta since the mid-twentieth century, while a weaker trend in the more condensed sediments of the Isonzo prodelta is not statistically significant. The decrease in drilling predation intensity and the community turnover are linked to the loss of predatory gastropods and the increased relative abundance of less-preferred prey during the most recent decades. Our results align with data showing the substantial depletion of marine resources at higher trophic levels in the region and indicate that the strong simplification of the food web initiated in the late nineteenth century accelerated further since the mid-twentieth century.
Fish couple forecasting with feedback control to chase and capture moving prey
Authors: Martin Benjamin T. , Sparks David , Hein Andrew M. , Liao James C.
Published: September 2024

Predator
–
prey interactions are fundamental to ecological and evolutionary dynamics. Yet, predicting the outcome of such interactions—whether predators intercept prey or fail to do so—remains a challenge. An emerging hypothesis holds that interception trajectories of diverse predator species can be described by simple feedback control laws that map sensory inputs to motor outputs. This form of feedback control is widely used in engineered systems but suffers from degraded performance in the presence of processing delays such as those found in biological brains. We tested whether delay-uncompensated feedback control could explain predator pursuit manoeuvres using a novel experimental system to present hunting fish with virtual targets that manoeuvred in ways that push the limits of this type of control. We found that predator behaviour cannot be explained by delay-uncompensated feedback control, but is instead consistent with a pursuit algorithm that combines short-term forecasting of self-motion and prey motion with feedback control. This model predicts both predator interception trajectories and whether predators capture or fail to capture prey on a trial-by-trial basis. Our results demonstrate how animals can combine short-term forecasting with feedback control to generate robust flexible behaviours in the face of significant processing delays.
A Machine Learning-Based Investigation of Integrin Expression Patterns in Cancer and Metastasis
Authors: Shadman Hossain , Gomrok Saghar , Cheng Qianyi , Jiang Yu , Huang Xiaohua , Ziebarth Jesse D. , Wang Yongmei
Published: September 2024

Background

Integrins, a family of transmembrane receptor proteins, play complex roles in cancer development and metastasis. These roles could be better delineated through machine learning of transcriptomic data to reveal relationships between integrin expression patterns and cancer.

Methods

We collected publicly available RNA-Seq integrin expression from 8 healthy tissues and their corresponding tumors, along with data from metastatic breast cancer. We then used machine learning methods, including t-SNE visualization and Random Forest classification, to investigate changes in integrin expression patterns.

Results

Integrin expression varied across tissues and cancers, and between healthy and cancer samples from the same tissue, enabling the creation of models that classify samples by tissue or disease status. The integrins whose expression was important to these classifiers were identified. For example, ITGA7 was key to classification of breast samples by disease status. Analysis in breast tissue revealed that cancer rewires co-expression for most integrins, but the co-expression relationships of some integrins remain unchanged in healthy and cancer samples. Integrin expression in primary breast tumors differed from their metastases, with liver metastasis notably having reduced expression.

Conclusions

Integrin expression patterns vary widely across tissues and are greatly impacted by cancer. Machine learning of these patterns can effectively distinguish samples by tissue or disease status.
Trait-dependent biogeography offers insights on the dispersal ofMeiogyne(Annonaceae) across the Australasia-Pacific region
Authors: Liu Ming-Fai , Munzinger Jérôme , Chalermglin Piya , Chen Junhao , Xue Bine , Saunders Richard M. K.
Published: September 2024

Meiogyneis a genus of trees and treelets occurring in Indomalaya and Australasia-Pacific, an unusually wide distribution across Australasia and Western Pacific compared to the rest of the family Annonaceae. Previous chloroplast phylogenies of the genus offered poor resolution and support for many internal nodes. Here, a molecular phylogeny was reconstructed based on seven chloroplast and 11 nuclear markers of 33Meiogynetaxa (ca.70% sampling). The combined dataset generated a well resolved and supported phylogeny. Estimation of divergence time was calibrated with two fossils using uncorrelated lognormal relaxed clock model. Trait-dependent and trait-independent biogeographical models in BioGeoBEARS were compared using AICc weight and likelihood ratio test. The results suggest that narrow monocarp width and fruit colour associated with bird dispersal are correlated with increased macroevolutionary dispersal. Under the best-fitting monocarp width-dependent DEC model, a single colonisation event from Sunda to Sahul during the middle to late Miocene and two dispersal events from New Guinea and Australia into the Pacific during the late Miocene to early Pliocene were detected. BayesTraits analysis strongly supports a correlation between narrow fruits and avian fruit colours. This study reveals thatMeiogynelineages with narrow fruitlets and fruit colour associated to bird dispersal (black, red & orange) are associated with increased macroevolutionary dispersal. Bird dispersal and the associated traits may be important drivers for macroevolutionary dispersal for plants with fleshy fruits in Australasia-Pacific.
Global prevalence of naturally occurringWolbachiain field-collectedAedesmosquitoes: a systematic review and meta-analysis
Authors: Gebremariam Tewelde T. , Leung Polly , Rusanganwa Vincent
Published: September 2024

Background

Dengue is one of the leading causes of morbidity worldwide.Wolbachia-mediated dengue biocontrol has emerged as a novel strategy in recent decades and depends on a lack ofWolbachiain the natural populations ofAedesmosquitoes. Through a systematic review of the published literature, this study sought to estimate the natural occurrence ofWolbachiaamong field-collectedAedesmosquitoes worldwide.

Methods

We conducted hand and systematic searches from PubMed, the Cochrane Library, and Google Scholar for all relevant published articles onWolbachiainfection inAedesmosquitoes published before September 12, 2024. The prevalence estimates were analysed using a random effects meta-analysis, and a random effects meta-regression was performed to determine sources of heterogeneity in prevalence estimates.

Results

Twenty-three studies with 16,997 field-collectedAedesmosquitoes from different countries worldwide were included. The meta-analysis revealed a global pooled prevalence of naturalWolbachiainfection inAedesmosquitoes of 57.7% (95% CI: 41.0–72.8%), which was six times higher inAe. albopictusthanAe. aegypti (p<0.001) and ranged from 6.0% (95% CI: 2.6–13.1%) inAe. aegyptito 87.1% (95% CI: 78.0–92.8%) inAe. albopictus. Continentally, Asia had the highest percentage ofWolbachiainfection inAe. aegypti(7.1%), followed by Europe (5.0%), North America (1.9%), and Africa (0.7%). Similarly, Asia had the highest prevalence ofWolbachiainAe. albopictus(95.5%), followed by Europe (94.8%), North America (91.6%), South America (85.2%), and Africa (71.6%). Overall, dengue incidence was negatively related toWolbachiaprevalence (B = −0.0006,p= 0.0281). Species wise, infection rates inAe. aegyptiwere significantly higher among females than males (OR = 1.72; 95% CI = 1.01, 2.92,p= 0.046), while there was no difference between males and females inAe. albopictus(p= 0.098). Furthermore,Wolbachiainfection rates inAe. albopictuswere inversely correlated with dengue incidence (β = −0.0013, p <0.01) but not inAe. aegypti (p =0.0984). In contrast, higher temperature was negatively associated withWolbachiaprevalence inAe. aegyptibut not inAe. albopictus. In contrast, higher temperature was negatively associated withWolbachiaprevalence inAe. aegypti(β = --2.5736, p <0.001) but not inAe. albopictus (p =0.7050).

Conclusion

Aedesmosquitoes had a high and variable prevalence of naturally occurringWolbachia, and this was negatively correlated with dengue incidence across countries. While the natural infection ofAe. albopictusis more common, detection inAe. aegyptimay reflect contamination and require high-quality multicentre studies to verify the above findings.
Selective preservation of fucose-rich oligosaccharides in the North Atlantic Ocean
Authors: Bligh Margot , Buck-Wiese Hagen , Sichert Andreas , Bercovici Sarah K. , Hellige Inga , Marchant Hannah , Iversen Morten , Sauer Uwe , Dittmar Thorsten , Arnosti Carol , Liebeke Manuel , Hehemann Jan-Hendrik
Published: September 2024

The ocean has a substantial capacity to store carbon dioxide fixed via photosynthesis in dissolved organic molecules. An estimated 20% of the 660 Gt dissolved organic carbon in the ocean pool consists of structurally uncharacterized oligosaccharides, which appear to resist microbial degradation (Aluwihare et al., 1997). Current technologies lack the sensitivity and molecular resolution to identify these oligosaccharides. Here, we adapted graphitized carbon chromatography to extract and separate marine oligosaccharides for liquid chromatography high resolution mass spectrometry analysis. Using a newly-developedde novoannotation tool, we found 110 oligosaccharide structures in surface and deep ocean seawater at two distant locations in the North Atlantic Ocean. One group of the detected oligosaccharides was found only in surface seawater and consisted of larger and more abundant molecules detected by our analysis. A second group of smaller, less abundant oligosaccharides was detected in both the surface and deep ocean seawater of both sampled locations. The composition of oligosaccharides differed between the surface and deep ocean, with deep ocean samples relatively enriched in hard-to-metabolize deoxy-sugars, and xylose, amino sugars and uronic acids compared to simple hexoses. Notably the deoxy-sugar fucose constituted 35-40% of the monomers in deep-sea oligosaccharides, twice the percentage in surface ocean oligosaccharides. The ubiquity of deep ocean oligosaccharides indicates that they represent a preserved fraction of the carbohydrate pool. Their enrichment in specific monosaccharides suggests selective preservation of fucose-rich oligosaccharides in the deep ocean.
The loss of a supergene in obligately polygynousFormicawood ant species
Authors: Sigeman Hanna , Satokangas Ina , De Lamarre Matthieu , Deshmukh Riddhi , Nouhaud Pierre , Helanterä Heikki , Chapuisat Michel , Kulmuni Jonna , Viljakainen Lumi
Published: September 2024

Some of the most striking examples of phenotypic variation within species are controlled by supergenes. However, most research on supergenes has focused on their emergence and long-term maintenance, leaving the later stages of their life cycle largely unexplored. Specifically, what happens to a derived supergene haplotype when the trait it controls reaches fixation? Here we answer this question using the ancient supergene system ofFormicaants, where (monogynous) single-queen colonies carry only the ancestral haplotype M while the derived haplotype P is exclusive to (polygynous) colonies with multiple queens. Through comparative genomics of all seven European wood ant species, we found that the P haplotype was present in only one of the three obligate polygynous species (F. polyctena). In the two others (F. aquiloniaandF. paralugubris) the P haplotype was completely missing except for duplicated P-specific paralogs of two genes,Zasp52andTTLL2, withZasp52being directly involved in wing muscle development. We hypothesize that these genes play a direct role in polygyny and contribute to differences in body size and/or dispersal behaviour between monogynous and polygynous queens. A complete lack of P/P genotypes among the 136 workers suggest strong selection against such genotypes. While our analyses did not reveal evidence of increased mutation load on the P, it is possible that this skew in genotype distributions is driven by a few loci with strong fitness effects. We propose that selection to escape P-associated fitness costs underlies the loss of this haplotype in obligate polygynous wood ants.
Structural Insights into the Role of the Proline Rich Region in Tau Function
Authors: Acosta Karen , Brue Christopher R. , Kim Hee Jong , Holubovska Polina , Mayne Leland , Murakami Kenji , Rhoades Elizabeth
Published: September 2024

Tau is a microtubule-associated protein that plays an important role in modulating axonal microtubules in neurons. Intracellular tau aggregates are found in a broad class of disorders, including Alzheimer’s disease, termed tauopathies. Tau is an intrinsically disordered protein, and its structural disorder appears to be critical to its microtubule-related functions. Tubulin binding sites are found in tau’s proline-rich region (PRR), microtubule binding repeats (MTBR: R1–R4), and pseudo-repeat, R′. While many post-translational modifications have been identified on tau, phosphorylation sites, which both regulate tubulin dimer and microtubule interactions and are correlated with disease, cluster with high frequency within the PRR. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tubulin dimer binding and probe the structure of the PRR-tubulin dimer complex. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two ∼15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Together these measurements provide insight into the previously overlooked relevance of tau’s PRR in functional interactions with tubulin.

GRAPHICAL ABSTRACT
Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma
Authors: Umbaugh Charles S. , Groth Marie , Erkut Cihan , Lee Kwang-Seok , Marinho Joana , Iser Florian , Kapp Jonas N. , Schroeter Petra , Dolaner Simay , Kayserili Asli , Hartmann Julia , Walch Philipp , Barth Thomas F.E. , Mellert Kevin , Dreier Birgit , Schaefer Jonas V. , Plückthun Andreas , Fröhling Stefan , Scholl Claudia
Published: September 2024

Aberrant expression of the embryonal transcription factor TBXT (also known as brachyury) drives chordoma, a rare spinal neoplasm with no effective drug therapies. The gene network regulated by TBXT is poorly understood, and strategies to disrupt its abnormal activity for therapeutic purposes are lacking. Here, we developed TBXT-targeted designed ankyrin repeat proteins (T-DARPins) that selectively bind TBXT, inhibiting its binding to DNA and expression. In chordoma cells, T-DARPins reduced cell cycle progression, spheroid formation, and tumor growth in mice and induced morphologic changes indicative of senescence and differentiation. Combining T-DARPin-mediated TBXT inhibition with transcriptomic and proteomic analyses, we determined the TBXT regulome in chordoma cells, which comprises in particular networks involved in cell cycle regulation, DNA replication and repair, embryonal cell identity, metabolic processes, and interferon response. The analysis of selected TBXT regulome components provided new insights into chordoma biology, such as the strong upregulation of IGFBP3 upon TBXT inhibition to fine-tune part of TBXT’s downstream effectors. Finally, we assigned each TBXT regulome member a druggability status to create a resource for future translational studies and found high interferon response signaling in chordoma cell lines and patient tumors, which was promoted by TBXT and associated with strong sensitivity to clinically approved JAK2 inhibitors. These findings demonstrate the potential of DARPins to investigate the function of nuclear proteins to understand the regulatory networks of cancers driven by aberrant transcription factor activity, including novel entry points for targeted therapies that warrant testing in patients.
Synonymous and single nucleotide changes facilitate the adaptation of a horizontally transferred gene
Authors: Venkataraman Pavithra , Singh Sudeepta , Ahlawat Neetika , Saini Supreet
Published: September 2024

The movement of genes between microbial species, or horizontal gene transfer, is common. While this process speeds up adaptation, the functionality of horizontally transferred genes is highly constrained in the new hosts due to several reasons, and protein localization is one of them. In this study, we ask what is the minimum number of mutations that can resolve a localization problem faced by a horizontally transferred protein in a new host. Using a directed-evolution approach, we show that SNPs and a synonymous mutation can change the localization patterns of an ammonia transporter (AmtA) moved fromDictyostelium discoideumtoSaccharomyces cerevisiae. Interestingly, the mutations that cause this change in localization, confer different fitness effects, are spread throughout the gene, and do not cause a uniform change in amino acids. In a novel attempt, we show how SNPs or a synonymous mutation can alter the membrane affinity of proteins, and as a result, aiding protein evolution and functional diversification.
Mesoscale Modelling of Fibrin Clots: The Interplay between Rheology and Microstructure at the Gel Point
Authors: Zohravi Elnaz , Moreno Nicolas , Hawkins Karl , Curtis Daniel , Ellero Marco
Published: September 2024

This study presents a numerical model for incipient fibrin-clot formation that captures characteristic rheological and microstructural features of the clot at the gel point. Using a mesoscale-clustering framework, we evaluate the effect of gel concentration or gel volume fraction and branching on the fractal dimension, the gel time, and the viscoelastic properties of the clots. We show that variations in the gel concentration of our model can reproduce the effect of thrombin in the formation of fibrin clots. In particular, the model reproduces the fractal dimension’s dependency on gel concentration and the trends in elasticity and gelation time with varying thrombin concentrations. This approach allows us to accurately recreate the gelation point of fibrin-thrombin gels, highlighting the intricate process of fibrin polymerization and gel network formation. This is critical for applications in the clinical and bioengineering fields where precise control over the gelation process is required.