bluuebunny/crossref_metadata_2025 huggingface dataset:
Raising Cultural Awareness and Addressing Barriers to Breast Imaging Care for Black Women
Authors: Jackson Tatianie , Wahab Rifat A , Bankston Karen , Mehta Tejas S
Published: December 2023

Health care disparities, which are differences in the attainment of full health potential among population groups, have been documented across medical conditions, clinical settings, and diagnostic and treatment modalities. Deeply rooted health care disparities due to many factors have affected how Black women (BW) view medical care including screening mammography. This article explores health care disparities around breast cancer in BW and how patient distrust, provider biases, race, and social determinants of health continue to have negative effects on breast cancer outcomes in BW, despite medical advances in breast cancer detection and management. In addition, this article addresses the importance of culturally competent care for BW around breast cancer awareness, screening, and treatment, and offers strategies to address disparities and rebuild trust.
Outcomes of High-Risk Breast MRI Screening in Women Without Prior History of Breast Cancer: Effectiveness Data from a Tertiary Care Center
Authors: Rahman W Tania , Gerard Sarah , Grundlehner Paul , Oudsema Rebecca , McLaughlin Carol , Noroozian Mitra , Neal Colleen H , Helvie Mark
Published: December 2023

Objective

To evaluate the diagnostic performance outcomes of a breast MRI screening program in high-risk women without prior history of breast cancer.

Methods

Retrospective cohort study of 1 405 consecutive screening breast MRI examinations in 681 asymptomatic women with high risk of breast cancer without prior history of breast cancer from January 1, 2015, to December 31, 2019. Outcomes (sensitivity, specificity, positive predictive value, negative predictive value, false-negative rate [FNR], cancer detection rate [CDR]) and characteristics of cancers were determined based on histopathology or 12-month follow-up. MRI examinations performed, BI-RADS assessments, pathology outcomes, and CDRs were analyzed overall and by age decade. Results in incidence screening round (MRI in last 18 months) and nonincidence round were compared.

Results

Breast MRI achieved CDR 20/1000, sensitivity 93.3% (28/30), and specificity 83.4% (1 147/1375). Twenty-eight (28/1 405, CDR 20/1000) screen-detected cancers were identified: 18 (64.3%, 18/28) invasive and 10 (35.7%, 10/28) ductal carcinoma in situ. Overall, 92.9% (26/28) of all cancers were stage 0 or 1 and 89.3% (25/28) were node negative. All 14 incidence screening round malignancies were stage 0 or 1 with N0 disease. Median size for invasive carcinoma was 8.0 mm and for ductal carcinoma in situ was 9.0 mm. There were two false-negative exams for an FNR 0.1% (2/1 405).

Conclusion

High-risk screening breast MRI was effective at detecting early breast cancer and associated with favorable outcomes.
Is the Mediterranean Diet in Inflammatory Bowel Diseases Ready for Prime Time?
Authors: Godny Lihi , Dotan Iris
Published: December 2023

Background

The rising incidence of inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), specifically in the developing world, suggests an important environmental effect. Amongst environmental influences, dietary factors, particularly the adoption of a westernized diet, have been specifically noticed. In contrast, the Mediterranean diet (MED), characterized by high intake of fruits, vegetables, whole grains, legumes, nuts, olive oil, and moderate consumption of animal and ultra processed foods, has shown potential positive effects in IBD.

Methods

Here we conducted a narrative review focusing on the evidence regarding the role of MED in IBD prevention and management.

Results

Epidemiological studies suggest inverse association of MED with CD development. Furthermore, adherence to MED has been associated with clinical improvement in active CD and maintenance of lower levels of inflammatory markers in UC, along with improved quality of life and lower mortality rates in IBD patients. Mechanistically, MED promotes a diverse and beneficial gut microbiota, possesses anti-inflammatory properties through polyphenols and dietary fats, and may modulate oxidative stress. In clinical practice, MED may be adapted to diverse disease phenotypes and cultural preferences, and is a sustainable, easy to maintain dietary approach.

Conclusion

Current evidence may support the integration of MED into clinical practice in IBD care. In future research, the efficacy of MED in specific IBD phenotypes should be assessed.
Insecticide-mediated changes in the population and toxicity of the thrips species, Frankliniella occidentalis (Pergande) and Thrips flavus (Schrank) (Thysanoptera: Thripidae)
Authors: Sun Ying , Hu Changxiong , Chen Guohua , Li Xingxing , Liu Jihuan , Xu Zhengwei , Zhou Yang , Wu Daohui , Zhang Xiaoming
Published: December 2023

Frankliniella occidentalis (Pergande) and Thrips flavus (Schrank) (Thysanoptera: Thripidae) cause considerable damage to agricultural crops. In this study, we investigated the variations in the population density of these 2 thrips species in 2 sites (Dabai and Heilongtan) with different insecticide application levels. Bioassays were performed to determine the susceptibility of both thrips species to imidacloprid, abamectin, and high-bromine cyhalothrin in summer. The results showed that the F. occidentalis species were more abundant in Dabai than in Heilongtan during both winter and summer. The proportions of F. occidentalis in winter and summer were 28.32–43.35% and 61.79–76.02%, respectively. Moreover, F. occidentalis resistance against the 3 insecticides was significantly higher than that of T. flavus in both 2017 and 2019. Compared with 2017, the LC50 values of F. occidentalis populations in Dabai to imidacloprid, abamectin, and lambda-cyhalothrin increased to 100.076, 16.52, and 130.44 mg/liter, respectively. The number of F. occidentalis, reaching the proportion of 91.63% in 90 days, was significantly higher than that of the control after imidacloprid treatment. In conclusion, thrips interspecies competition is affected by the irrational use of insecticides, which may cause the replacement of native species by invasive species, thereby leading to an outbreak.
Structural Reforms and Elections: Evidence from a World-Wide New Dataset
Authors: Alesina Alberto , Furceri Davide , Ostry Jonathan D , Papageorgiou Chris , Quinn Dennis P
Published: December 2023

We present two new databases we have constructed to explore the electoral consequences of structural economic policy reforms. One database measures reforms in domestic finance, external finance, trade, product, and labor markets covering 90 advanced and developing economies from 1973 to 2014. The other chronicles the timing and results of national elections. We find that liberalizing reforms are associated with economic benefits that accrue only gradually over time. Because of this delay, liberalizing reforms are costly to democratic incumbents when they are implemented close to elections. Electoral outcomes also depend on the state of the economy: Reforms are penalized during contractions but are often rewarded in expansions.
Characteristics of gravity and magnetic anomalies and their petroleum geological significance in the Yingen-Ejinaqi Basin, Inner Mongolia, China
Authors: Xu Haihong , Wei Jianshe , Han Xiaofeng , Zhao Fei , Zhou Junlin , Jiang Ting , Shi Jizhong , Xu Wei , Song Bo , Wang Baowen
Published: December 2023

This research aims to explore petroleum resource distribution characteristics in the Yingen-Ejinaqi Basin and provide a basis for assessing the prospect of petroleum potential in the region. Based on recent and previous gravity and aeromagnetic data obtained in the basin, anomalies including regional and residual gravity and magnetic anomalies, various derivative anomalies, and anomalies in structure-enhancing filtering were determined using multiple techniques. By analysing gravity, magnetic, and seismic anomaly characteristics of existing typical oil and gas wells, the petroleum resource distribution was studied by combining such data with exploration results arising from wells where oil and gas have been discovered. The research shows that the distribution ranges of the sags revealed by seismic profiles correspond to those of negative residual gravity anomalies; the distribution ranges of rock masses identified in the sags along the seismic profiles show some correspondence to the positive residual magnetic anomalies. Analysis indicates that various sags corresponding to areas where negative residual gravity anomalies appear in the north and south of the basin are the primary and secondary favourable areas for oil and gas exploration in Mesozoic–Upper Palaeozoic strata. Therefore, breakthroughs in oil and gas exploration should be made by focusing on these sags in the region. The positive residual magnetic anomalies in the basin can reflect the distribution of concealed rocks in the region, while concealed rocks in sags are an important area for oil and gas exploration in igneous rocks in the basin.
Movement response of small mammals to burn severity reveals importance of microhabitat features
Authors: Slovikosky Sandy A , Merrick Melissa J , Morandini Marina , Koprowski John L
Published: December 2023

Disturbance events are increasing at a global scale, with cascading impacts to ecosystems and residents therein that include fragmentation and altered vegetation structure and composition. Such changes may disproportionately impact small mammal movements, risk perception, and community dynamics as smaller species perceive such changes at finer spatial scales. We examined movement response to burn severity, vegetation structure, and composition in Mexican woodrats (Neotoma mexicana), a common but understudied small mammal species. The study was conducted on Mt. Graham in southeastern Arizona, United States, following a fire that burned over 19,400 ha. We measured path tortuosity of woodrats translocated over patches of different burn severity. Tortuosity can indicate microhabitat selection, foraging behavior, and perceived predation risk—features affecting population-level processes that changes in community composition alone cannot fully demonstrate. We captured woodrats, released them 50 m away from their midden, and used fluorescent powder to track woodrat movement paths through areas of low–severe burn severity. We analyzed features of the resulting powder trails including straightness, average step length, fractal dimension, and squared displacement. We also compared used versus expected vegetation structure and composition along movement paths across burn severities. Analyses indicated shorter step length with increased bare ground, as well as higher squared displacement in areas with more logs. Vegetation analyses likewise showed that logs were heavily used in low-burned areas, whereas dense vegetation was avoided in highly burned areas. Burn severity alone did not have a direct effect on movement parameters, rather its influence on vegetative composition and structure appears to be most important. Selection for logs and avoidance of dense vegetation may be attributed to auditory concealment and ease of travel. With projected increases in wildfire extent and severity, this work represents an understudied approach to understanding these disturbances and their effects on ecological communities.
Ontogenetic and static scaling of antler mass in White-tailed Deer (Odocoileus virginianus)
Authors: Sontheimer Willis P , Pfeffer Deanna , Weckerly Floyd W
Published: December 2023

Antlers are a costly trait that require skeletal reserves to grow to a large size. Thus, insight into variation in antler size requires understanding the connection between antler and body size, which can be summarized through ontogenetic and static scaling relationships. Both types of scaling relationships are also needed to examine the influence of factors besides body mass on antler growth at different ages and whether the effects of these factors diminish with age. Dietary and maternal effects might decline with age as individuals attempt to mitigate size deficits. We examined the potential effects of diet and maternal attributes of dam (mother) age at birth and litter size on body–antler mass relationships throughout ontogeny and at discrete ages. Data on age, maternal characteristics, body mass, and antler mass were gathered from captive, pen-raised White-tailed Deer (n = 168) that consumed either a low-energy (1.77 kcal/g) or standard-energy diet (2.65 kcal/g) from the time they were weaned until they perished by 5.5 years of age. Both types of scaling relationships were estimated with linear mixed-effects models to account for repeated measurements of males, dams, and sires. Diet affected ontogenetic scaling relationships. Males eating the low-energy diet had faster antler growth when young and lighter in body mass than when they were older and heavier—whereas males fed the standard-energy diet had a similar rate of antler growth across the range of body masses. A Bayesian Information Criterion model selection analysis indicated that diet and litter size (singleton, multiple births), but not dam age at birth influenced static scaling relationships. Static scalar coefficients up to 3.5 years of age were positively allometric (>1.0), but isometric (1.0) in 4.5- and 5.5-year-old males. Furthermore, diet and litter size influenced both intercepts and slopes in only the youngest males (1.5 years) indicating that dietary and maternal effects can diminish with age. Body–antler mass relationships are complex. Young males that are small because of maternal effects, for example, might still be able to mitigate smaller body and antler sizes at older ages.
Role distance. An ethnographic study on how street-level managers cope
Authors: Wong Jade
Published: December 2023

Policy is not only made by street-level bureaucrats at the frontlines. It is also made by their superiors—street-level managers—who set the organizational conditions through which street-level bureaucrats act. Although scholars have documented how street-level bureaucrats cope with the pressures of their work by, for instance, breaking or bending rules, the question of how street-level managers cope with the pressures of their own work has received less attention. Drawing from ethnographic data of a network of publicly funded health centers in the Midwestern US, I show how street-level managers use an interaction ritual with role distance to cope. Role distance is mobilized when the person uses communicative expressions such as laughter or cries of frustration to convey a critical distance from what her organizational role prescribes. Based on classic sociological insights, I posit that role distance can function as follows. It can help managers preserve self by allowing them to define their putatively “more-human self” from their work, create a feeling of collectiveness as they orient themselves to the shared frustrations yet obligations that their role engenders, which enables them to coordinate on carrying out tasks, even those that rub against their preferences and well-intentions. Taken together, I suggest that role distance can offer a coping function, which enables them to hold in abeyance individual and collective responsibility for the decisions they make. I then highlight the benefits and unintended consequences of role distance and posit what academics and practitioners can do to ensure that street-level managers use role distance toward more productive ends.
Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection
Authors: Belongia Edward A , Petrie Joshua G , Feldstein Leora R , Guan Lizheng , Halfmann Peter J , King Jennifer P , Neumann Gabriele , Pattinson David , Rolfes Melissa A , McLean Huong Q , Kawaoka Yoshihiro
Published: December 2023

We assessed serum neutralization of Omicron BA.5 in children following SARS-CoV-2 infection during the Delta or Omicron BA.1/BA.2 variant period. Convalescent BA.5 titers were higher following infections during the Omicron BA.1/BA.2 vs Delta variant period, and in vaccinated vs unvaccinated children. Titers against BA.5 did not differ by age group.
Heidenhain variant of Creutzfeldt-Jakob disease masquerading as neuromyelitis optica spectrum disorder: recognizing when apheresis is not the answer
Authors: Burke Olivia , Jacobs Jeremy W , Tormey Christopher A , Rinder Henry M , Figueroa Villalba Cristina A , Lee Edward S , Silva Campos Juan J , Abels Elizabeth , Yurtsever Nalan
Published: December 2023

The Heidenhain variant of Creutzfeld-Jakob disease (CJD) is a rare form that initially presents with visual disturbances. In early stages, the presentation can mimic neuromyelitis optica spectrum disorders (NMOSD) and lead to unnecessary treatment modalities. Herein, we describe a case of a 66-year-old man who presented with bilateral vision loss and retro-orbital discomfort. In addition to immunosuppressive therapy, he received 4 rounds of therapeutic plasma exchange after his preliminary diagnosis of NMOSD. We were surprised to note that his condition did not show improvement but deteriorated, with severe neurocognitive symptoms. Eventually, CJD was suspected, and real-time quaking-induced conversion (RT-QuIC) was performed. By the time the diagnosis of Heidenhain variant of CJD was confirmed, the patient was discharged to hospice care and died shortly after.
Impact of COVID-19 pandemic on accredited programs and graduates who sat for the American Society for Clinical Pathology Board of Certification examination: graduates’ perspective
Authors: Duzan Dana , Fong Karen , Freeman Vicki S , Goodyear Nancy , Nadder Teresa S , Spiczka Amy , Taff Teresa , Tanabe Patricia
Published: December 2023

Objective

Students in health profession education programs were severely affected by the COVID-19 pandemic at both didactic and clinical training levels. The purpose for this American Society for Clinical Pathology Board of Certification (ASCP BOC) study was to determine the impact of the COVID-19 pandemic on graduates. This study represents the perspectives of laboratory professional graduates who sat for the BOC certification in their respective professional disciplines.

Methods

A survey was sent to all graduates from the National Accrediting Agency for Clinical Laboratory Science (NAACLS), Accrediting Bureau of Health Education Schools (ABHES), and Commission on Accreditation of Allied Health Education Programs (CAAHEP) accredited programs who sat for the ASCP BOC examination in 2020 and 2021 to determine the impact of COVID-19 on laboratory professional graduates during the pandemic.

Results

A total of 180 graduates responded to the survey. The majority of graduates indicated that at least 1 didactic program component was shifted to an online system during the pandemic and that both clinical and nonclinical student laboratories were affected. Although program completion for most graduates was not delayed, one-third of graduates delayed taking their respective BOC exam. Due to the lack of knowledge application through practical hands-on laboratory experience in their educational programs, graduates reported feeling a lack of readiness with regards to preparing for the national certification examination as well as for employment.

Conclusion

The study results showed the pandemic greatly impacted the education experience and readiness for the ASCP BOC examinations for graduates. Factors such as the absence of in-person learning and hands-on experience—both crucial aspects in laboratory training—and the ripple effects as a result of the pandemic, such as job loss, financial constraints, and health concerns, contributed to the decreased quality of education for graduates.
Du Fu’s conspicuous negativity and Li Bai’s hidden positivity: a sentiment comparison and exploration
Authors: Meng Yingying , Wan Yuwei , Kit Chunyu
Published: December 2023

In the studies of classical Chinese poetry, the comparison between Li Bai and Du Fu is an everlasting topic, yielding many qualitative interpretations, among which a widely known but disputable one is Li’s positivity versus Du’s negativity. With the development of digital means, distant reading has become possible, and the sentiment issue can be further explored in quantitative ways. This research conducts a corpus-based sentiment comparison of Li and Du with a self-constructed sentiment dictionary. The Complete Collection of Tang Poems is used as a representative of Tang poets, and sentiment comparisons are made at the levels of poems, verses, and characters, as well as key characters extracted with the log-likelihood measure. Analyses show that (1) among Tang poets, Du is more negative at all of the above textual levels, while Li is only more positive at the key character level, proving the importance of key characters in readers’ perception of sentiment; (2) Li and Du both stand out among Tang poets with a negative depiction of the dark reality and a positive expression of grand ideals; and (3) Li’s positivity is largely embodied in his depictions of color, light, and temperature, while Du’s negativity is closely related to his psychological description. To conclude, this research has not only determined the sentiment difference between Li and Du but also located its sources in texts with a novel key character-based sentiment analysis approach.

Keywords:
AI-assisted super-resolution cosmological simulations III: time evolution
Authors: Zhang Xiaowen , Lachance Patrick , Ni Yueying , Li Yin , Croft Rupert A C , Matteo Tiziana Di , Bird Simeon , Feng Yu
Published: December 2023

In this work, we extend our recently developed super-resolution (SR) model for cosmological simulations to produce fully time-consistent evolving representations of the particle phase-space distribution. We employ a style-based constrained generative adversarial network (StyleGAN), where the changing cosmic time is an input style parameter to the network. The matter power spectrum and halo mass function agree well with results from high-resolution N-body simulations over the full trained redshift range (10 ≤ z ≤ 0). Furthermore, we assess the temporal consistency of our SR model by constructing halo merger trees. We examine progenitors, descendants, and mass growth along the tree branches. All statistical indicators demonstrate the ability of our SR model to generate satisfactory high-resolution simulations based on low-resolution inputs.
Mapping out the parameter space for photoevaporation and core-powered mass-loss
Authors: Owen James E , Schlichting Hilke E
Published: December 2023

Understanding atmospheric escape in close-in exoplanets is critical to interpreting their evolution. We map out the parameter space over which photoevaporation and core-powered mass-loss dominate atmospheric escape. Generally, the transition between the two regimes is determined by the location of the Bondi radius (i.e. the sonic point of core-powered outflow) relative to the penetration depth of extreme ultra-violet (XUV) photons. Photoevaporation dominates the loss when the XUV penetration depth lies inside the Bondi radius (RXUV < RB) and core-powered mass-loss when XUV radiation is absorbed higher up in the flow (RB < RXUV). The transition between the two regimes occurs at a roughly constant ratio of the planet’s radius to its Bondi radius, with the exact value depending logarithmically on planetary and stellar properties. In general, core-powered mass-loss dominates for lower gravity planets with higher equilibrium temperatures, and photoevaporation dominates for higher gravity planets with lower equilibrium temperatures. However, planets can transition between these two mass-loss regimes during their evolution, and core-powered mass-loss can ‘enhance’ photoevaporation over a significant region of parameter space. Interestingly, a planet that is ultimately stripped by core-powered mass-loss has likely only ever experienced core-powered mass-loss. In contrast, a planet that is ultimately stripped by photoevaporation could have experienced an early phase of core-powered mass-loss. Applying our results to the observed super-Earth population suggests that it contains significant fractions of planets where each mechanism controlled the final removal of the H/He envelope, although photoevaporation appears to be responsible for the final carving of the exoplanet radius valley.
Estimating photometric redshift from mock flux for CSST survey by using weighted Random Forest
Authors: Lu Junhao , Luo Zhijian , Chen Zhu , Fu Liping , Du Wei , Gong Yan , Li Yicheng , Meng Xian-Min , Tang Zhirui , Zhang Shaohua , Shu Chenggang , Zhou Xingchen , Fan Zuhui
Published: December 2023

Accurate estimation of photometric redshifts (photo-z) is crucial in studies of both galaxy evolution and cosmology using current and future large sky surveys. In this study, we employ Random Forest (RF), a machine learning algorithm, to estimate photo-z and investigate the systematic uncertainties affecting the results. Using galaxy flux and colour as input features, we construct a mapping between input features and redshift by using a training set of simulated data, generated from the Hubble Space Telescope Advanced Camera for Surveys (HST-ACS) and COSMOS catalogue, with the expected instrumental effects of the planned China Space Station Telescope (CSST). To improve the accuracy and confidence of predictions, we incorporate inverse variance weighting and perturb the catalogue using input feature errors. Our results show that weighted RF can achieve a photo-z accuracy of $\rm \sigma _{NMAD}=0.025$ and an outlier fraction of $\rm \eta =2.045\ \hbox{per cent}$, significantly better than the values of $\rm \sigma _{NMAD}=0.043$ and $\rm \eta =6.45\ \hbox{per cent}$ obtained by the widely used Easy and Accurate Zphot from Yale (EAZY) software, which uses template-fitting method. Furthermore, we have calculated the importance of each input feature for different redshift ranges and found that the most important input features reflect the approximate position of the break features in galaxy spectra, demonstrating the algorithm’s ability to extract physical information from data. Additionally, we have established confidence indices and error bars for each prediction value based on the shape of the redshift probability distribution function, suggesting that screening sources with high confidence can further reduce the outlier fraction.
Internal shocks hydrodynamics: the collision of two cold shells in detail
Authors: Rahaman Sk Minhajur , Granot Jonathan , Beniamini Paz
Published: December 2023

Emission in many astrophysical transients originates from a shocked fluid. A central engine typically produces an outflow with varying speeds, leading to internal collisions within the outflow at finite distances from the source. Each such collision produces a pair of forward and reverse shocks with the two shocked regions separated by a contact discontinuity (CD). As a useful approximation, we consider the head-on collision between two cold and uniform shells (a slower leading shell and a faster trailing shell) of finite radial width, and study the dynamics of shock propagation in planar geometry. We find significant differences between the forward and reverse shocks, in terms of their strength, internal energy production efficiency, and the time it takes for the shocks to sweep through the respective shells. We consider the subsequent propagation of rarefaction waves in the shocked regions and explore the cases where these waves can catch up with the shock fronts and thereby limit the internal energy dissipation. We demonstrate the importance of energy transfer from the trailing to leading shell through pdV work across the CD. We outline the parameter space regions relevant for models of different transients,e.g. Gamma-ray burst internal shock model, fast radio burst blast wave model, Giant flare due to magnetars, and superluminous supernovae ejecta. We find that the reverse shock likely dominates the internal energy production for many astrophysical transients.
Exploration of faint X-ray and radio sources in the massive globular cluster M14: a UV-bright counterpart to Nova Ophiuchus 1938
Authors: Zhao Yue , D’Antona Francesca , Milone Antonino P , Heinke Craig , Zhao Jiaqi , Lugger Phyllis , Cohn Haldan
Published: December 2023

Using a 12 ks archival Chandra X-ray Observatory ACIS-S observation on the massive globular cluster (GC) M14, we detect a total of 7 faint X-ray sources within its half-light radius at a $0.5{\small --}7\, \mathrm{keV}$ depth of $2.5\times 10^{31}\, \mathrm{erg s^{-1}}$. We cross-match the X-ray source positions with a catalogue of the Very Large Array radio point sources and a Hubble Space Telescope (HST) UV/optical/near-IR photometry catalogue, revealing radio counterparts to 2 and HST counterparts to 6 of the X-ray sources. In addition, we also identify a radio source with the recently discovered millisecond pulsar PSR 1737−0314A. The brightest X-ray source, CX1, appears to be consistent with the nominal position of the classic nova Ophiuchi 1938 (Oph 1938), and both Oph 1938 and CX1 are consistent with a UV-bright variable HST counterpart, which we argue to be the source of the nova eruption in 1938. This makes Oph 1938 the second classic nova recovered in a Galactic GC since Nova T Scorpii in M80. CX2 is consistent with the steep-spectrum radio source VLA8, which unambiguously matches a faint blue source; the steepness of VLA8 is suggestive of a pulsar nature, possibly a transitional millisecond pulsar with a late K dwarf companion, though an active galactic nucleus (AGN) cannot be ruled out. The other counterparts to the X-ray sources are all suggestive of chromospherically active binaries or background AGNs, so their nature requires further membership information.
Performance of Topology Tests under Extreme Selection Bias
Authors: Markowski Etai , Susko Edward
Published: December 2023

Tree tests like the Kishino–Hasegawa (KH) test and chi-square test suffer a selection bias that tests like the Shimodaira–Hasegawa (SH) test and approximately unbiased test were intended to correct. We investigate tree-testing performance in the presence of severe selection bias. The SH test is found to be very conservative and, surprisingly, its uncorrected analog, the KH test has low Type I error even in the presence of extreme selection bias, leading to a recommendation that the SH test be abandoned. A chi-square test is found to usually behave well and but to require correction in extreme cases. We show how topology testing procedures can be used to get support values for splits and compare the likelihood-based support values to the approximate likelihood ratio test (aLRT) support values. We find that the aLRT support values are reasonable even in settings with severe selection bias that they were not designed for. We also show how they can be used to construct tests of topologies and, in doing so, point out a multiple comparisons issue that should be considered when looking at support values for splits.
PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation
Authors: Hu Mengwen , Yeh Yu-Han , Maezawa So , Nakagawa Toshinori , Yoshida Shosei , Namekawa Satoshi H
Published: December 2023

Spermatogonial stem cells functionality reside in the slow-cycling and heterogeneous undifferentiated spermatogonia cell population. This pool of cells supports lifelong fertility in adult males by balancing self-renewal and differentiation to produce haploid gametes. However, the molecular mechanisms underpinning long-term stemness of undifferentiated spermatogonia during adulthood remain unclear. Here, we discover that an epigenetic regulator, Polycomb repressive complex 1 (PRC1), shields adult undifferentiated spermatogonia from differentiation, maintains slow cycling, and directs commitment to differentiation during steady-state spermatogenesis in adults. We show that PRC2-mediated H3K27me3 is an epigenetic hallmark of adult undifferentiated spermatogonia. Indeed, spermatogonial differentiation is accompanied by a global loss of H3K27me3. Disruption of PRC1 impairs global H3K27me3 deposition, leading to precocious spermatogonial differentiation. Therefore, PRC1 directs PRC2-H3K27me3 deposition to maintain the self-renewing state of undifferentiated spermatogonia. Importantly, in contrast to its role in other tissue stem cells, PRC1 negatively regulates the cell cycle to maintain slow cycling of undifferentiated spermatogonia. Our findings have implications for how epigenetic regulators can be tuned to regulate the stem cell potential, cell cycle and differentiation to ensure lifelong fertility in adult males.
piRNA generation is associated with the pioneer round of translation in stem cells
Authors: Allikka Parambil Sudheesh , Li Danyan , Zelko Michael , Poulet Axel , van Wolfswinkel Josien C
Published: December 2023

Much insight has been gained on how stem cells maintain genomic integrity, but less attention has been paid to how they maintain their transcriptome. Here, we report that the PIWI protein SMEDWI-1 plays a role in the filtering of dysfunctional transcripts from the transcriptome of planarian stem cells. SMEDWI-1 accomplishes this through association with the ribosomes during the pioneer round of translation, and processing of poorly translated transcripts into piRNAs. This results in the removal of such transcripts from the cytoplasmic pool and at the same time creates a dynamic pool of small RNAs for post-transcriptional surveillance through the piRNA pathway. Loss of SMEDWI-1 results in elevated levels of several non-coding transcripts, including rRNAs, snRNAs and pseudogene mRNAs, while reducing levels of several coding transcripts. In the absence of SMEDWI-1, stem cell colonies are delayed in their expansion and a higher fraction of descendants exit the stem cell state, indicating that this transcriptomic sanitation mediated by SMEDWI-1 is essential to maintain stem cell health. This study presents a new model for the function of PIWI proteins in stem cell maintenance, that complements their role in transposon repression, and proposes a new biogenesis pathway for piRNAs in stem cells.
Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
Authors: Badet Thomas , Tralamazza Sabina Moser , Feurtey Alice , Croll Daniel
Published: December 2023

Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate the spread of the pathogenicity-associated Styx element across five species that last diverged ∼11 000 years ago. We show that the element likely originated in the Zymoseptoria fungal pathogen genus and underwent multiple independent reactivation events. Using a global 900-genome panel of the wheat pathogen Zymoseptoria tritici, we assess Styx copy number variation and identify renewed transposition activity in Oceania and South America. We show that the element can mobilize to create additional Styx copies in a four-generation pedigree. Importantly, we find that new copies of the element are not affected by genomic defenses suggesting minimal control against the element. Styx copies are preferentially located in recombination breakpoints and likely triggered multiple types of large chromosomal rearrangements. Taken together, we establish the origin, diversification and reactivation of a highly active TE with likely major consequences for chromosomal integrity and the expression of disease.
Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae
Authors: Yu Lifang , Marchisio Mario Andrea
Published: December 2023

New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal transcriptional activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.
Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella
Authors: Liu Xiaoxiao , Li Jun , Zhang Zhixuan , He Yizhou , Wang Mingfang , Zhao Yunhu , Lin Shituan , Liu Tianlang , Liao Yiwen , Zhang Ni , Yuan Kaixuan , Ling Yong , Liu Ziyao , Chen Xiaozhong , Chen Zhe , Chen Ran , Wang Xiaoxue , Gu Bing
Published: December 2023

Adjusting intracellular metabolic pathways and adopting suitable live state such as biofilms, are crucial for bacteria to survive environmental changes. Although substantial progress has been made in understanding how the histone-like nucleoid-structuring (H-NS) protein modulates the expression of the genes involved in biofilm formation, the precise modification that the H-NS protein undergoes to alter its DNA binding activity is still largely uncharacterized. This study revealed that acetylation of H-NS at Lys19 inhibits biofilm development in Shewanella oneidensis MR-1 by downregulating the expression of glutamine synthetase, a critical enzyme in glutamine synthesis. We further found that nitrogen starvation, a likely condition in biofilm development, induces deacetylation of H-NS and the trimerization of nitrogen assimilation regulator GlnB. The acetylated H-NS strain exhibits significantly lower cellular glutamine concentration, emphasizing the requirement of H-NS deacetylation in Shewanella biofilm development. Moreover, we discovered in vivo that the activation of glutamine biosynthesis pathway and the concurrent suppression of the arginine synthesis pathway during both pellicle and attached biofilms development, further suggesting the importance of fine tune nitrogen assimilation by H-NS acetylation in Shewanella. In summary, posttranslational modification of H-NS endows Shewanella with the ability to respond to environmental needs by adjusting the intracellular metabolism pathways.
The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination
Authors: Alvaro-Aranda Lucia , Petitalot Ambre , Djeghmoum Yasmina , Panigada Davide , Singh Jenny Kaur , Ehlén Åsa , Vugic Domagoj , Martin Charlotte , Miron Simona , Contreras-Perez Aida , Nhiri Naima , Boucherit Virginie , Lafitte Philippe , Dumoulin Isaac , Quiles Francisco , Rouleau Etienne , Jacquet Eric , Feliubadaló Lidia , del Valle Jesús , Sharan Shyam K , Stoppa-Lyonnet Dominique , Zinn-Justin Sophie , Lázaro Conxi , Caputo Sandrine M , Carreira Aura
Published: December 2023

BRCA2 tumor suppressor protein ensures genome integrity by mediating DNA repair via homologous recombination (HR). This function is executed in part by its canonical DNA binding domain located at the C-terminus (BRCA2CTD), the only folded domain of the protein. Most germline pathogenic missense variants are located in this highly conserved region which binds to single-stranded DNA (ssDNA) and to the acidic protein DSS1. These interactions are essential for the HR function of BRCA2. Here, we report that the variant R2645G, identified in breast cancer and located at the DSS1 interface, unexpectedly increases the ssDNA binding activity of BRCA2CTDin vitro. Human cells expressing this variant display a hyper-recombination phenotype, chromosomal instability in the form of chromatid gaps when exposed to DNA damage, and increased PARP inhibitor sensitivity. In mouse embryonic stem cells (mES), this variant alters viability and confers sensitivity to cisplatin and Mitomycin C. These results suggest that BRCA2 interaction with ssDNA needs to be tightly regulated to limit HR and prevent chromosomal instability and we propose that this control mechanism involves DSS1. Given that several missense variants located within this region have been identified in breast cancer patients, these findings might have clinical implications for carriers.
Does exogenous hormonal therapy affect the risk of glioma among females: A systematic review and meta-analysis
Authors: Alfuridy Ghady , Alghamdi Rana , Alkhoshi Abdulaziz , Mahjari Ahood , Alhussein Abdullah , Alshehri Ebtihaj , Lary Ahmed , Sabbagh Abdulrahman , Alomar Soha
Published: December 2023

Background

The effect of exogenous hormone replacement therapy (HRT) and oral contraceptive pills (OCPs) on glioma risk in females is unclear despite numerous studies; hence, we conducted a meta-analysis to evaluate this relationship.

Methods

Studies investigating the impact of exogenous female hormones on glioma risk were retrieved by searching 4 databases from inception until September 2022. Articles of any design, such as case–control and cohort studies, proving the relative risk (RR), odds ratio (OR), or hazard ratio were included. Summary OR values were calculated using a random effects model.

Results

Both HRT and OCP use of any duration decreased the risk of developing glioma [HRT OR = 0.78, 95% CI 0.66–0.91, P = .00; OCP: OR = 0.80, 95% CI 0.67–0.96, P = .02]. When stratified by duration of use, HRT use >1 year significantly reduced glioma risk (<1 year: OR = 0.82, 95% CI 0.63–1.07, P = 0.15; 1–5 years: OR = 0.79, 95% CI 0.67–0.92, P = .00; 5–10 years: OR = 0.80, 95% CI 0.66–0.97, P = .02; >10 years: OR = 0.69, 95% CI 0.54–0.88, P = .00). In contrast, only OCP use for >10 years significantly reduced glioma risk (<1 year: OR = 0.72, 95% CI 0.49–1.05, P = .09; 1–5 years: OR = 0.88, 95% CI 0.72–1.02, P = .09; 5–10 years: OR = 0.85, 95% CI 0.65–1.1, P = 0.21; >10 years: OR = 0.58, 95% CI 0.45–0.74, P = .00).

Conclusions

Our pooled results strongly suggest that sustained HRT and OCP use is associated with reduced risk of glioma development.
Root branching under high salinity requires auxin-independent modulation of LATERAL ORGAN BOUNDARY DOMAIN 16 function
Authors: Zhang Yanxia , Li Yiyun , de Zeeuw Thijs , Duijts Kilian , Kawa Dorota , Lamers Jasper , Munzert Kristina S , Li Hongfei , Zou Yutao , Meyer A Jessica , Yan Jinxuan , Verstappen Francel , Wang Yixuan , Gijsberts Tom , Wang Jielin , Gigli-Bisceglia Nora , Engelsdorf Timo , van Dijk Aalt D J , Testerink Christa
Published: December 2023

Salinity stress constrains lateral root (LR) growth and severely affects plant growth. Auxin signaling regulates LR formation, but the molecular mechanism by which salinity affects root auxin signaling and whether salt induces other pathways that regulate LR development remains unknown. In Arabidopsis thaliana, the auxin-regulated transcription factor LATERAL ORGAN BOUNDARY DOMAIN 16 (LBD16) is an essential player in LR development under control conditions. Here, we show that under high-salt conditions, an alternative pathway regulates LBD16 expression. Salt represses auxin signaling but, in parallel, activates ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6), a transcriptional activator of LBD16. ZAT6 activates LBD16 expression, thus contributing to downstream cell wall remodeling and promoting LR development under high-salt conditions. Our study thus shows that the integration of auxin-dependent repressive and salt-activated auxin-independent pathways converging on LBD16 modulates root branching under high-salt conditions.
Molecular and phylogenetic evidence of parallel expansion of anion channels in plants
Authors: Li Shanshan , Wei Lanlan , Gao Qiang , Xu Min , Wang Yizhou , Lin Zhenguo , Holford Paul , Chen Zhong-Hua , Zhang Liangsheng
Published: December 2023

Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.
An artificial intelligence model based on transrectal ultrasound images of biopsy needle tract tissues to differentiate prostate cancer
Authors: Li Shiyu , Ye Xiuqin , Tian Hongtian , Ding Zhimin , Cui Chen , Shi Siyuan , Yang Yang , Li Guoqiu , Chen Jing , Lin Ziwei , Ni Zhipeng , Xu Jinfeng , Dong Fajin
Published: December 2023

Purpose

We aimed to develop an artificial intelligence (AI) model based on transrectal ultrasonography (TRUS) images of biopsy needle tract (BNT) tissues for predicting prostate cancer (PCa) and to compare the PCa diagnostic performance of the radiologist model and clinical model.

Methods

A total of 1696 2D prostate TRUS images were involved from 142 patients between July 2021 and May 2022. The ResNet50 network model was utilized to train classification models with different input methods: original image (Whole model), BNT (Needle model), and combined image [Feature Pyramid Networks (FPN) model]. The training set, validation set, and test set were randomly assigned, then randomized 5-fold cross-validation between the training set and validation set was performed. The diagnostic effectiveness of AI models and image combination was accessed by an independent testing set. Then, the optimal AI model and image combination were selected to compare the diagnostic efficacy with that of senior radiologists and the clinical model.

Results

In the test set, the area under the curve, specificity, and sensitivity of the FPN model were 0.934, 0.966, and 0.829, respectively; the diagnostic efficacy was improved compared with the Whole and Needle models, with statistically significant differences (P < 0.05), and was better than that of senior radiologists (area under the curve: 0.667). The FPN model detected more PCa compared with senior physicians (82.9% vs. 55.8%), with a 61.3% decrease in the false-positive rate and a 23.2% increase in overall accuracy (0.887 vs. 0.655).

Conclusion

The proposed FPN model can offer a new method for prostate tissue classification, improve the diagnostic performance, and may be a helpful tool to guide prostate biopsy.