bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum
Authors: Upadhyaya Hari D. , Wang Lihua , Paterson Andrew H. , Gowda C.L.L. , Kumar Rajendra , Li Jieqin , Wang Yi-Hong 
Published: October 2024

Landraces are ideal for identifying genes related to adaptation. The purpose of this study was to map and identify genes related to adaptation. We evaluated a mini core collection that broadly samples the global sorghum landrace gene pool for 11 traits in 4–12 environments. Association mapping with 6094 317 SNPs identified 70 loci for the 11 traits. The key findings include two panicle weight (PWt) and two grain yield (GY) loci overlapped, and two panicle length (PL) and two panicle width (PW) loci overlapped. Some loci for tiller number (TL), PL/PW, PWt, GY, and seed weight (SW) colocalized with previously mapped quantitative trait loci. We identified 33 candidate genes for TL, PL, PW, PWt, GY, SW, and MRC. The overlapping PWt and GY locus on chromosome 9 contained gibberellin receptor GID1 gene that regulates seed development. A TL locus on chromosome 1 that was consistently detected contained Sobic.001G152700 encoding a DUF1618 protein that was the sole horizontally transferred gene from sorghum to the parasitic Striga hermonthica, which was potentially related to environmental adaptation. These results are relevant for sorghum molecular breeding. Future studies are needed to functionally characterize the rich collection of novel candidate genes identified in this study. Key message We mapped 11 sorghum traits, identified 33 candidate genes, and found a grain yield gene ( GID1) that regulates seed development and a grass-specific tillering gene (DUF1618) transferred to Striga hermonthica.
Maximum entropy method for valence quark distributions in exotic hadrons: a study of the $$Z_c(3900)$$ case
Authors: Han Chengdong , Kou Wei , Wang Xiaopeng , Chen Xurong 
Published: October 2024

AbstractIn this study we demonstrate the application of the maximum entropy method (MEM) to determine the valence quark distribution of exotic hadrons. Our investigation yields three key findings. Firstly, we observe a significant shift towards smaller Bjorken scale x in the peak position of the valence quark distribution for hadrons with an increasing number of valence quarks, consistent with previous results by Kawamura and Kumano. Secondly, assuming that the $$Z_c(3900)$$

Z
c

(
3900
)

initially consists of four valence quarks, we employ MEM to determine its initial valence quark distribution, estimating a radius of $$r_c=1.276$$

r
c

=
1.276

fm at an extremely low resolution scale $$Q^2$$

Q
2

. Furthermore, we identify a notable discrepancy between our computed charge form factor $$G_c(q)$$

G
c

(
q
)

at leading order and the outcomes of hadron molecular state calculations. We propose that this form factor can be extracted from the QCD counting rule cross-section, which is grounded in generalized distribution amplitudes (GDA) linked to the multi-quark states.
When an Overwhelming Number of Supernumerary Teeth Provides an Alternative to the Diagnosis of Trichorhinophalangeal Syndrome
Authors: Shaker Nariman , Abdelrady Aya , Haridy Sara F. A. , El-Beialy Waleed 
Published: October 2024

Background: The prevalence of supernumerary teeth is increasing in modern dental practice. However, the presence of multiple supernumerary teeth should be further investigated. Proper diagnosis of an underlying syndrome might save the patient from future health hazards through early diagnosis and optimal follow‐up screening.Case Presentation: A 13‐year‐old female patient presented with multiple retained deciduous teeth and delayed eruption of permanent teeth. Although the medical and family history of the patient did not raise any concerns, the clinical and radiographic examinations yielded intriguing findings. The patient presented with a total of 11 supernumerary teeth, which impeded the normal eruption of permanent dentition in addition to the presence of retained deciduous teeth. Additional clinical and laboratory investigations were conducted in response to the case’s complexity, resulting in the diagnosis of Trichorhinophalangeal Syndrome (TRPS) Type I. The patient underwent a precise treatment plan and then was followed up for 6 months postoperatively to monitor the eruptive movement of the permanent teeth.Conclusion: When a syndrome is the underlying cause, monitoring unusual cases, such as those with multiple supernumerary teeth, can be lifesaving or aid in the early diagnosis of more serious complications.
Development, Validation, and Diagnostic Accuracy of the Fetal Lack of Responsiveness Scale for Diagnosis of Severe Perinatal Hypoxia
Authors: Franco Luis Carlos , Buitrago Sandra M. , Arbelaez Isabel , Pinto Laura F. , Blanco Daniela , Pizarro María C. , Santamaria Laura , Trillos Catalina 
Published: October 2024

Background: There are limitations to predicting perinatal asphyxia, as current tools rely almost entirely on fetal cardiotocography (CTG). The fetal lack of responsiveness scale (FLORS) is a new diagnostic alternative based on the physiological phenomena associated with fetal hypoxia.Objectives: The objective of this study was to develop, validate, and assess the diagnostic accuracy of the FLORS for predicting severe perinatal hypoxia (SPH).Study Design: A two‐phase retrospective observational cross‐sectional analytical study was conducted. Phase 1 involved the formulation and retrospective validation of the FLORS. A total of 366 fetal CTG records were evaluated twice by seven readers. Phase 2 was a collaborative, retrospective, multicenter diagnostic test study that included 37 SPH and 366 non‐SPH cases.Results: Phase 1: A numeric, physiology‐based scale was developed and refined based on expert opinions. The median time to apply the scale per reading was 38 s. Cronbach’s alpha, which is a reliability measure, was significant (p = 0.784). The kappa index for test–retest agreement was moderate to reasonable, with a median value of 0.642. For interobserver agreement, the kappa index per variable was as follows: baseline, 0.669; accelerations, 0.658; variability, 0.467; late/variable decelerations, 0.638; slow response decelerations, 0.617; and trend to change, 0.423. Phase 2, including 37 SPH and 366 non‐SPH cases, showed a sensitivity of 62.2% and specificity of 75.4% for the 2‐point score, whereas the 3‐point score had a sensitivity of 35.1% and specificity of 89.9%. The area under the curve (AUC) was significant at 0.73 (CI 0.645–0.818).Conclusions: FLORS demonstrated significant internal consistency and observer agreement, with a promising sensitivity–specificity balance and significant AUC. Further research is needed to assess its impact on perinatal hypoxia and cesarean delivery.
Ephrin A1 Stimulates CCL2 Secretion to Facilitate Premetastatic Niche Formation and Promote Gastric Cancer Liver Metastasis
Authors: Cui Yun , Chang Yongxia , Ma Xixi , Sun Meng , Huang Yuliang , Yang Feng , Li Shuang , Zhuo Wei , Liu Wei , Yang Bo , Lin Aifu , Ou Guangshuo , Yang Yuehong , Xie Shanshan , Zhou Tianhua 
Published: October 2024

Abstract
The liver is a primary target for distal metastasis of gastric cancer. The hepatic premetastatic niche (PMN) facilitates crucial communications between primary tumor and liver, thereby playing an essential role in hepatic metastasis. Identification of the molecular mechanisms driving PMN formation in gastric cancer could facilitate development of strategies to prevent and treat liver metastasis. Here, we uncovered a role for ephrin A1 (EFNA1) signaling in development of the PMN. EFNA1 overexpression in gastric cancer cells significantly increased C–C motif chemokine ligand 2 (CCL2) secretion through the Hippo–YAP pathway. Secreted CCL2 activated hepatic stellate cells (HStC) within the hepatic PMN via the WNT/β-catenin pathway. Inhibition of CCL2 significantly suppressed HStC activation and reduced liver metastasis triggered by EFNA1 signaling in gastric cancer cells. Moreover, high CCL2 expression correlated with poor survival in patients with cancer. Overall, these findings reveal that EFNA1 signaling in gastric cancer cells upregulates CCL2, which activates HStCs to engender establishment of a hepatic PMN that supports liver metastasis.
Significance: Cross-talk between gastric cancer cells and hepatic stellate cells mediated by the EFNA1/CCL2 axis induces premetastatic niche development to facilitate metastatic spread, nominating CCL2 as a therapeutic target to suppress liver metastasis.
Tumor Hypoxia: Long Ignored but Now Detectable and Potentially Actionable
Authors: Mason Ralph P. 
Published: October 2024

Summary
Oxygen-enhanced MRI was successfully applied to 24 patients with human papillomavirus–associated oropharyngeal cancer. This prospective trial rigorously evaluated reproducibility and changes with respect to tumor radiation. Analyses compared hypoxic volumes and hypoxic fractions. It represents important progress in developing a practical approach to assessing tumor hypoxia in patients noninvasively.
See related article by Dubec et al., p. 5620
The Desert as an Inventarium
Authors: Kiperwasser Reuven 
Published: October 2024

Abstract
This article is about the symbolic representation of the wilderness motif in a selection of rabbinic travel tales, taking into consideration its representation in earlier Jewish writings. The article includes a selection of rabbinic travel narratives found in b. Baba Batra that concern the desert journeys of the remarkable rabbinic protagonist Rabba bar Bar Ḥanna. The hero of the stories is presented as viewing the giant dead bodies of the biblical tribes in the wilderness, Mount Sinai, and Korah and his people, all according to the sequence of biblical events in the books of Moses. Wilderness plays an integral role in these stories. While there is little interest in this motif in Palestinian rabbinic literature, wilderness plays a distinct role in the eschatological process according to the rabbinic theological speculations known from the Babylonian Talmud. According to the selected travel narratives, which all focus on the wilderness, several objects from the biblical past, as well as some items from the dawn of creation, which are designated to play an important role in the eschatological process, are stored there.
“And Judith Set Forth”
Authors: Livneh Atar 
Published: October 2024

Abstract
Judith is a wealthy, pious, celibate, domestic(ated) widow both at the beginning of the story and at its conclusion. Comprising the central section, her peregrinations to Holofernes’ tent (Jdt 10:1–13:20) and the Jerusalem temple (Jdt 15:8–16:21) serve as an “interlude.” Her story (chs. 8–16) is thus structured as a rite de passage, opening and ending in two stable states that enclose a liminal core. This article traces the role her two journeys play in the narrative, comparison of the topographical details, encounters with foreigners, and gender roles, suggesting that Judith’s first voyage marks her separation from her community and position within it, the second her reintegration and restoration to her original status.
Poetic Alchemy: the Rise of Romance from a Persian Perspective
Authors: Cross Cameron 
Published: October 2024

Abstract
The eleventh and twelfth centuries witnessed either the rise or revival of long-form amorous narratives in at least four courtly language traditions across the southwestern flank of Eurasia: Persian, Georgian, Greek, and French. This coeval occurrence of the “rise of romance” offers fruitful grounds for considering broad literary-historical questions about genre, poetics, and interconnectivity in a comparative fashion. The aim of this article is to give an account of this phenomenon in the early Persian context, with special attention to the role of poetry in transforming popular tales into elite literature. Understanding the implications of this practice may shed some light on possible factors contributing to the romance’s (re-)emergence in other twelfth-century literary traditions. As a coda, this article suggests twelfth-century Anatolia and Syria as significant contact zones where all four of the courtly languages mentioned above would have had some opportunity to interact.
Greek Poetry in a Multicultural Society: Sicily and Salento in the Twelfth and Thirteenth Centuries
Authors: Kubina Krystina , Zagklas Nikos 
Published: October 2024

Abstract
In the twelfth and thirteenth centuries, southern Italy experienced a period of relative political stability and economic prosperity under the Normans as well as the Hohenstaufen dynasty that succeeded them. These cultural conditions fostered a cultural resurgence, which included the composition of Greek poetry. Poets in Sicily wrote from within a multicultural context, including the presence of Arabic- and Latin-speaking communities. Many of their poems illustrate the generative intersections between the Byzantine-Constantinopolitan, Latin, and Arabic traditions. Later in Salento, poetry was written in a rather closed Greek-speaking, Orthodox society. Comparing Greek poetry from Sicily and Salento shows some differences between composition in the two regions. Whereas Sicilian poetry includes especially creative narrative poems, composed for the rich and sophisticated courts of the island, the Salentine poetry bears the stamp of the schoolroom. In fact, most poems from both Sicily and Salento survive in manuscripts that can be traced to a pedagogical environment. While the circulation of these poems was limited to their surrounding regions, their literary sophistication betrays remarkable creativity and the multicultural conditions of composition, further evidence of the vitality of Greek literary culture far from the heartland of the Byzantine Empire.
Evolution of Remote Participation of the Accused and Victim in International Criminal Proceedings
Authors: Sobański Kamil 
Published: October 2024

Abstract
The use of technologies in criminal proceedings has become increasingly popular. This has not escaped the attention of international criminal proceedings. Of particular importance are remote communication tools, which are now used in proceedings before the International Criminal Court (icc). These tools enable, among other things, the remote participation of the accused and the victim in the proceedings. In this paper I will analyse how this one form of using technologies in the criminal process has evolved in the changing reality of international criminal proceedings, including how the use of remote communication tools affects the rights of the accused. I will argue that the development of the use of remote communication tools in icc proceedings has so far been evolutionary and that this has been justified differently depending on the approach taken by the accused and victim in the proceedings. The paper also examines the impact of the covid-19 pandemic.
From Face to Facies
Authors: Jones David Houston 
Published: October 2024

Abstract
This article considers Beckett’s faces in the light of Giorgio Agamben’s account of the face as a disputed biopolitical marker. Agamben refers to the face both in terms of social and juridical identity in ancient Rome and as an icon of contemporary biopolitics, as social identity gives way to biometric recognition. Beckett’s own face figures prominently in the series of machine-generated Eigenface portraits created by artist Trevor Paglen in 2017, and whose use of the Eigenface method invokes modern facial recognition technologies. The Eigenface is examined here in relation to a gallery of ghostly progenitors: the faces of Beckett’s late plays.
Projected North Equatorial Current/Countercurrent toward an El Niño–Like Condition in the Western Pacific under Moderate and Worst-Case CO2 Emission Scenarios
Authors: Hsin Yi-Chia , Chiang Tzu-Ling , Hsu Huang-Hsiung 
Published: October 2024

Abstract
Validating the mean state and historical trends of the North Equatorial Current (NEC) and North Equatorial Counter Current (NECC) in 36 phase 5 of the Coupled Model Intercomparison Project (CMIP) models and 32 phase 6 CMIP models with those in ocean reanalysis products, this study extracts the most qualified 17 model outputs to explore the projected changes in NEC and NECC in the western Pacific Ocean under scenarios of moderate- and worst-case CO2 emissions. NEC and NECC are robustly predicted to have an El Niño–like change, in which the NEC (NECC) tends to intensify with a poleward (equatorward) movement, during the twenty-first century under both scenarios. Meanwhile, the Kuroshio and Mindanao Current are projected to become weaker. A change in the meridional gradient of basin-scale wind stress curl in the tropical Pacific Ocean is the major contributor to the centennial changes in NEC and NECC; however, anomalous wind stress curl dipole on the two sides of NEC off the eastern Philippines is the major factor in controlling the western boundary currents. This study not only represents a step forward in understanding the impact of global warming on the western tropical Pacific surface circulation but also serves as a reference for downscaled modeling, which can better resolve regional circulation and western boundary currents, for selecting suitable inputs from a large number of CMIP models.

Significance Statement
The North Equatorial Current and Countercurrent are important surface currents transporting massive heat and mass zonally across the tropical Pacific Ocean. With verified modeling outputs of phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP), this study aims at understanding the 100-yr tendencies of the two currents in the western Pacific Ocean during the twenty-first century. The outcome shows that the North Equatorial Current (Countercurrent) tends to intensify with a poleward (equatorward) movement associated with the changes in the meridional gradient of wind stress curl across the entire tropical Pacific Ocean. The 100-yr tendencies are similar to those during an El Niño event. Meanwhile, Kuroshio and Mindanao Current are projected to be weaker during the twenty-first century due to the anomalous wind stress curl dipole off the Philippines in the western tropical Pacific Ocean. This study provides an understanding about the impact of global warming on the western tropical Pacific surface circulation and helps to select suitable initial conditions, boundary conditions, and forcing from a large number of CMIP models when conducting a downscaling modeling for the western Pacific area.
Tropical Intraseasonal Variability as a Leading Moisture Dynamic Mode of the Warm-Pool Background State
Authors: Hayashi Michiya , Jin Fei-Fei 
Published: October 2024

Abstract
Tropical intraseasonal variability (ISV) is dominated by the Madden–Julian oscillation (MJO), and its spatiotemporal characteristics vary with the Indo-Pacific warm-pool background on seasonal and longer time scales. Previous works have suggested ISV dynamics in various frameworks, whereas a unifying view remains challenging. Motivated by the recent advance in moisture mode theory, we revisit the ISV as a leading moisture mode modulated by varying background states derived from a reanalysis, using a moist linear baroclinic model (mLBM) improved with a simple convective scheme relating convective precipitation to tropospheric and boundary layer moisture anomalies and simple cloud-radiative feedback representations. Under a boreal winter background state, this mLBM yielded a large-scale but local eastward-propagating mode with a phase speed of 3–5 m s−1 over the warm-pool region, resembling the MJO. Background lower-tropospheric winds and thermodynamic fields are important in determining the growth rate and periodicity of the leading mode, whose stability depends on cloud-radiative feedback and background state variations. We further demonstrate why the MJO is locally contained in the Indo-Pacific warm-pool region. The local thermal/moisture condition and Walker circulation greatly enhance its instability, but outside this region, this mode is heavily damped. Thus, the expansion/contraction of this warm-pool condition may enhance/reduce its instability and expand/reduce its domain of activity. Prescribing El Niño background causes eastward displacement of the wintertime ISV activity, reminiscent of the observed MJO modulations by El Niño. Under a summer background state, the eastward-propagating leading mode resembles the boreal summer ISV but is biased, requiring further model improvements.
Scale-Dependent Inflation Algorithms for Ensemble Kalman Filters
Authors: Deng Junjie , Lei Lili , Tan Zhe-Min , Zhang Yi 
Published: October 2024

Abstract
Ensemble-based data assimilation methods often suffer sampling errors due to limited ensemble sizes and model errors, which can result in filter divergence. One method to avoid filter divergence is inflation, which inflates ensemble perturbations to increase ensemble spread and account for model errors. The commonly applied inflation methods, including the multiplicative inflation, relaxation to prior spread (RTPS), and additive inflation, often use a constant inflation parameter. To capture different error growths at different scales, a scale-dependent inflation is proposed here, which applies different inflation magnitudes for variables associated with different scales. Results from the two-scale Lorenz05 model III show that for the ensemble square root filter (EnSRF) and integrated hybrid ensemble Kalman filter with ensemble mean updated by hybrid background error covariances (IHEnKF-Mean), scale-dependent inflation is superior to constant inflation. Constant inflation overinflates small-scale variables and results in increased small-scale errors, which then propagate to large-scale variables through the coupling between large- and small-scale variables and lead to increased large-scale errors. Scale-dependent inflation applies larger inflation for large-scale variables and imposes no inflation for small-scale variables, since large-scale errors have larger magnitudes than small-scale ones and small-scale errors grow faster than large-scale ones. But IHEnKF-Ensemble that updates both the ensemble mean and perturbations with hybrid background error covariances is much less sensitive to scale-dependent inflation, compared to EnSRF and IHEnKF-Mean, because updating ensemble perturbations with hybrid background error covariances can play a role similar to the scale-dependent inflation.

Significance Statement
Ensemble-based data assimilation and ensemble forecasts often have smaller ensemble spread than errors. Strategies used by ensemble-based data assimilation to combat insufficient ensemble spread usually focus on the short-term ensemble forecasts, rather than considering the whole ensemble forecasts over different lead times. Thus, there are obvious gaps between the ensemble-based data assimilation and ensemble forecasts. A scale-dependent inflation that can capture different error growths at different scales is proposed, which obtains improved consistency between ensemble spread and errors at different lead times and effectively links the ensemble-based data assimilation and ensemble forecasts.