bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prompting Is Programming: A Query Language for Large Language Models
Authors: Beurer-Kellner Luca , Fischer Marc , Vechev Martin 
Published: June 2023

Large language models have demonstrated outstanding performance on a wide range of tasks such as question answering and code generation. On a high level, given an input, a language model can be used to automatically complete the sequence in a statistically-likely way. Based on this, users prompt these models with language instructions or examples, to implement a variety of downstream tasks. Advanced prompting methods can even imply interaction between the language model, a user, and external tools such as calculators. However, to obtain state-of-the-art performance or adapt language models for specific tasks, complex task- and model-specific programs have to be implemented, which may still require ad-hoc interaction.Based on this, we present the novel idea of Language Model Programming (LMP). LMP generalizes language model prompting from pure text prompts to an intuitive combination of text prompting and scripting. Additionally, LMP allows constraints to be specified over the language model output. This enables easy adaption to many tasks while abstracting language model internals and providing high-level semantics.To enable LMP, we implement LMQL (short for Language Model Query Language), which leverages the constraints and control flow from an LMP prompt to generate an efficient inference procedure that minimizes the number of expensive calls to the underlying language model.We show that LMQL can capture a wide range of state-of-the-art prompting methods in an intuitive way, especially facilitating interactive flows that are challenging to implement with existing high-level APIs. Our evaluation shows that we retain or increase the accuracy on several downstream tasks, while also significantly reducing the required amount of computation or cost in the case of pay-to-use APIs (26-85% cost savings).
Optimizing Precision Medicine for Breast Cancer Brain Metastases with Functional Drug Response Assessment
Authors: Morikawa Aki , Li Jinju , Ulintz Peter , Cheng Xu , Apfel Athena , Robinson Dan , Hopkins Alex , Kumar-Sinha Chandan , Wu Yi-Mi , Serhan Habib , Verbal Kait , Thomas Dafydd , Hayes Daniel F. , Chinnaiyan Arul M. , Baladandayuthapani Veerabhadran , Heth Jason , Soellner Matthew B. , Merajver Sofia D. , Merrill Nathan 
Published: June 2023

The development of novel therapies for brain metastases is an unmet need. Brain metastases may have unique molecular features that could be explored as therapeutic targets. A better understanding of the drug sensitivity of live cells coupled to molecular analyses will lead to a rational prioritization of therapeutic candidates. We evaluated the molecular profiles of 12 breast cancer brain metastases (BCBM) and matched primary breast tumors to identify potential therapeutic targets. We established six novel patient-derived xenograft (PDX) from BCBM from patients undergoing clinically indicated surgical resection of BCBM and used the PDXs as a drug screening platform to interrogate potential molecular targets. Many of the alterations were conserved in brain metastases compared with the matched primary. We observed differential expressions in the immune-related and metabolism pathways. The PDXs from BCBM captured the potentially targetable molecular alterations in the source brain metastases tumor. The alterations in the PI3K pathway were the most predictive for drug efficacy in the PDXs. The PDXs were also treated with a panel of over 350 drugs and demonstrated high sensitivity to histone deacetylase and proteasome inhibitors. Our study revealed significant differences between the paired BCBM and primary breast tumors with the pathways involved in metabolisms and immune functions. While molecular targeted drug therapy based on genomic profiling of tumors is currently evaluated in clinical trials for patients with brain metastases, a functional precision medicine strategy may complement such an approach by expanding potential therapeutic options, even for BCBM without known targetable molecular alterations.

Significance:
Examining genomic alterations and differentially expressed pathways in brain metastases may inform future therapeutic strategies. This study supports genomically-guided therapy for BCBM and further investigation into incorporating real-time functional evaluation will increase confidence in efficacy estimations during drug development and predictive biomarker assessment for BCBM.
A Mendelian Randomization Analysis of 55 Genetically Predicted Metabolic Traits with Breast Cancer Survival Outcomes in the Pathways Study
Authors: Fiorica Peter N. , Sheng Haiyang , Zhu Qianqian , Roh Janise M. , Laurent Cecile A. , Ergas Isaac J. , Delmerico Jennifer , Kwan Marilyn L. , Kushi Lawrence H. , Ambrosone Christine B. , Yao Song 
Published: June 2023

Previous studies suggest associations of metabolic syndromes with breast cancer prognosis, yet the evidence is mixed. In recent years, the maturation of genome-wide association study findings has led to the development of polygenic scores (PGS) for many common traits, making it feasible to use Mendelian randomization to examine associations between metabolic traits and breast cancer outcomes. In the Pathways Study of 3,902 patients and a median follow-up time of 10.5 years, we adapted a Mendelian randomization approach to calculate PGS for 55 metabolic traits and tested their associations with seven survival outcomes. Multivariable Cox proportional hazards models were used to derive HRs and 95% confidence intervals (CI) with adjustment for covariates. The highest tertile (T3) of PGS for cardiovascular disease was associated with shorter overall survival (HR = 1.34, 95% CI = 1.11–1.61) and second primary cancer–free survival (HR = 1.31, 95% CI = 1.12–1.53). PGS for hypertension (T3) was associated with shorter overall survival (HR = 1.20, 95% CI = 1.00–1.43), second primary cancer–free survival (HR = 1.24, 95% CI = 1.06–1.45), invasive disease-free survival (HR = 1.18, 95% CI = 1.01–1.38), and disease-free survival (HR = 1.21, 95% CI = 1.04–1.39). PGS for serum cystatin C levels (T3) was associated with longer disease-free survival (HR = 0.82, 95% CI = 0.71–0.95), breast event-free survival (HR = 0.74, 95% CI = 0.61–0.91), and breast cancer–specific survival (HR = 0.72, 95% CI = 0.54–0.95). The above associations were significant at a nominal P &lt; 0.05 level but not after correcting for multiple testing (Bonferroni P &lt; 0.0009). Our analyses revealed notable associations of PGS for cardiovascular disease, hypertension, and cystatin C levels with breast cancer survival outcomes. These findings implicate metabolic traits in breast cancer prognosis.

Significance:
To our knowledge, this is the largest study of PGS for metabolic traits with breast cancer prognosis. The findings revealed significant associations of PGS for cardiovascular disease, hypertension, and cystatin C levels with several breast cancer survival outcomes. These findings implicate an underappreciated role of metabolic traits in breast cancer prognosis that would warrant further exploration.
High Serum Brain-Derived Neurotrophic Factor Is Associated With Decreased Risks of Poor Prognosis After Ischemic Stroke
Authors: Zhu Yinwei , Sun Lulu , Huang Tiansheng , Jia Yiming , Yang Pinni , Zhang Qi , Fang Chongquan , Shi Mengyao , Guo Daoxia , Peng Yanbo , Aghi Anushka , Chen Jing , Wang Aili , He Jiang , Zhang Yonghong , Xu Tan , Zhu Zhengbao 
Published: June 2023

BACKGROUND:
BDNF (brain-derived neurotrophic factor) has been implicated in cardiovascular homeostasis and ischemic stroke pathogenesis. We aimed to prospectively investigate the associations between serum BDNF levels and the prognosis of ischemic stroke in a multicenter cohort study.

METHODS:
This prospective study follows the STROBE reporting guideline. Serum BDNF concentrations were measured in 3319 ischemic stroke patients from the China Antihypertensive Trial in Acute Ischemic Stroke between August 2009 and May 2013 in 26 hospitals across China. The primary outcome was the composite outcome of death and major disability (modified Rankin Scale score ≥3) at 3 months after stroke onset. Multivariate logistic regression or Cox proportional hazards regression analysis was used to assess the associations between serum BDNF levels and adverse clinical outcomes.

RESULTS:

During the 3-month follow-up period, 827 (24.92%) patients experienced a primary outcome, including 734 major disabilities and 93 deaths. After adjusting for age, sex, and other important prognostic factors, elevated serum BDNF levels were associated with decreased risks of primary outcome (odds ratio, 0.73 [95% CI, 0.58–0.93]), major disability (odds ratio, 0.78 [95% CI, 0.62–0.99]), death (hazard ratio, 0.55 [95% CI, 0.32–0.97]), and the composite outcome of death and vascular events (hazard ratio, 0.61 [95% CI, 0.40–0.93]) when 2 extreme tertiles were compared. Multivariable-adjusted spline regression analyses showed a linear association between serum BDNF levels and the primary outcome (
P
value for linearity=0.005). The addition of BDNF to conventional risk factors slightly improved reclassification for the primary outcome (net reclassification improvement: 19.33%;
P
<0.001; integrated discrimination index: 0.24%;
P
=0.011).

CONCLUSIONS:
Elevated serum BDNF concentrations were independently associated with decreased risks of adverse outcomes after ischemic stroke, suggesting that serum BDNF may be a potential biomarker for prognosis after ischemic stroke. Further studies are warranted to investigate the potential therapeutic benefit of BDNF for ischemic stroke.
Radiomics Features in Contrast‐Enhanced and Nonenhanced Magnetic Resonance Imaging Images Are Associated With High Intracranial Aneurysmal Risk
Authors: Veeturi Sricharan S. , Raghuram Ashrita , Miller Jacob , Pinter Nandor K. , Sanchez Sebastian , Baig Ammad A. , Siddiqui Adnan H. , Samaniego Edgar A. , Tutino Vincent M. 
Published: June 2023

Background
Aneurysm wall enhancement is a potential imaging biomarker for risk stratification of intracranial aneurysms (IAs). Variations in the texture of the magnetic resonance imaging (MRI) signal could shed light on the underlying pathobiology of the aneurysm wall. Radiomics can help quantify the textural complexity in MRI images, which could lead to better understanding and risk stratification of IAs. Herein, we investigated the potential use of radiomics derived from nonenhanced and contrast‐enhanced MRI to identify high‐risk IAs and evaluated their performance on different data sets.

Methods
We obtained 126 IAs from different centers and extracted radiomics features from nonenhanced and contrast‐enhanced MRI for each aneurysm. We then built a random forest model from a part of the 3‐T data set to identify high‐risk IAs based on the 5‐year population, hypertension, age, size of aneurysm, earlier SAH from another aneurysm, site of aneurysm (PHASES) score. We then tested the performance of this model on a part of the same 3‐T data set, a 7‐T data set, and an external 3‐T data set. We also performed multivariate analysis to understand the significance of radiomics features.

Results
We found that 75 radiomics features were significantly different between high‐ and low‐risk IAs. The radiomics model had good performance when tested on the 3‐T data set (accuracy, 90%; sensitivity, 86%; and specificity, 92%); however, when tested on external data sets, it had a moderate performance (accuracy, 88%; sensitivity, 50%; and specificity, 95% for external 3‐T data set; and accuracy, 62%; sensitivity, 27%; and specificity, 100% for 7‐T data set).

Conclusions
Radiomics derived from nonenhanced and contrast‐enhanced MRI show high accuracy in identifying high‐risk aneurysms from the same data set and could be used as a tool for quantifying aneurysm wall enhancement.
Ἐπιλλίζω (Od. 18.11), from ἐπι(λ)λίγδην ‘Grazing’ (Il. 17.599) to ἰλλός ‘Squint-eyed’: History of a Misunderstanding
Authors: Le Feuvre Claire 
Published: June 2023

Abstract
The article argues that the Odyssean hapax ἐπιλλίζω (Od. 18.11) does not mean ‘to wink’, as traditionally assumed, but ‘to harass, to provoke’, and is the verbal base of the adverb ἐπι(λ)λίγδην ‘grazing’, said of a projectile. It belongs to the PIE root *sleig̑- ‘to rub’ (rather than ‘to slide’). The Odyssey only features the metaphoric use of the verb, but the proper meaning is preserved in Nicander’s fr. 100 ἐπιλλίζοντας ὀϊστούς. Apollonius of Rhodes uses ἐπιλλίζω in agreement with the Odyssean meaning ‘to provoke’. Later, two reinterpretations occurred. The traditional understanding of ‘to wink’ results from a synchronic etymology relating ἐπιλλίζω to ἰλλός ‘squint-eyed’: this accounts for Nicander’s use of ἐπιλλίζω (Ther. 163) and is therefore older than the 2nd c. BCE. Later on, Nicander’s ἐπιλλίζοντας (fr. 100) was erroneously related to λίγξε ‘(the bow) groaned’ by Greek grammarians, and wrongly translated ‘whizzing’.
Pherecydes in Alexandria
Authors: Marshall Laura 
Published: June 2023

Abstract
Pherecydes of Syros’ work is difficult to understand because of its fragmentary nature. A previously unexplored perspective on his work is to analyze how it was understood and used in Ptolemaic Alexandria, particularly by Eratosthenes and Callimachus. Eratosthenes’ distinction between Pherecydes of Syros and Pherecydes of Athens (DL 1.119) has been used as a key piece of evidence that those two authors are, in fact, distinct. However, there has been little discussion of Eratosthenes’ interest in these authors outside of that statement. Callimachus’ interest in Pherecydes has also been ignored by both scholars of Pherecydes and scholars of Alexandrian poetry (except for brief references). Through this examination, I argue that Pherecydes of Syros was an important figure in discussions about the development of prose in Ptolemaic Alexandria.
Figural Realism and the Politics of Literature: Hayden White and Jacques Rancière Read Erich Auerbach
Authors: Muchowski Jakub 
Published: June 2023

Abstract
Hayden White and Jacques Rancière both drew on the account of the history of European literature offered by Erich Auerbach to construct their own theoretical treatments of historical and literary writing: White conceptualized the figure-fulfillment model, modernist realism, and figural realism, while Rancière critically commented on the undemocratic character of the writings of the Annales school and sought egalitarian moments in Western literature. I will examine White’s and Rancière’s readings of Auerbach and partially compare the two theoretical endeavors. The purpose of this analysis will be, first, to critically compare some of the two authors’ proposals and, second, to include Rancière’s work into the English-language debate on historical theory. In bringing them together, I will primarily ask how White and Rancière have articulated the relationship between politics and historical and literary writing in their commentaries on Auerbach’s work.
Understanding the Policy Responses of the Philippines towards China’s Economic Statecraft under the Duterte Administration
Authors: Jung Gratiana 
Published: June 2023

Abstract
This essay is a preliminary study of the Philippines’ foreign policy towards China under President Rodrigo Roa Duterte. It will examine China’s economic statecraft as the sender country towards the Philippines as the target country. The ultimate goal of China’s economic policies is to foster a submissive response from the Philippines over their territorial disputes in the South China Sea. This paper applies the theoretical model proposed by Jean-Marc F. Blanchard and Norrin M. Ripsman (2008 and 2013) to study the political theory of economic statecraft, as applied by the sender and target countries. Blanchard and Ripsman argue that domestic factors serve as significant intervening variables in the strategy of the target country’s leaders towards the sender country. Thus, the target country’s leaders will view the sender country’s economic sanctions or economic inducements differently, depending on the domestic socioeconomic situation. By looking at the Duterte administration in the Philippines, this paper intends to expand upon the research agenda of the theory on economic statecraft and international relations. It will shine a light on the puzzling flip-flop of the Philippines’ foreign policy strategy. It shows that Blanchard and Ripsman’s “stateness” conditionalist approach provides a plausible explanation of the Filipino response to China’s economic statecraft. Instead of relying on conventional neo-realist, economic liberalist, or regime-type conditionalist arguments, this paper will focus on the control of leaders over the decision-making environment. However, it does acknowledge that stateness does not fully explain the Philippines’ strategic adjustment towards China, as international variables could have affected the Philippines’ policy response to China’s economic statecraft. This paper, therefore, argues that domestic and international factors play vital roles in affecting the dynamics in the target state and the effectiveness of the sender state’s economic statecraft.
Improving Seasonal Prediction of Summer Precipitation in the Middle–Lower Reaches of the Yangtze River Using a TU-Net Deep Learning Approach
Authors: Yang Shuxian , Ling Fenghua , Li Yue , Luo Jing-Jia 
Published: June 2023

Abstract
The two-step U-Net model (TU-Net) contains a western North Pacific subtropical high (WNPSH) prediction model and a precipitation prediction model fed by the WNPSH predictions, oceanic heat content, and surface temperature. The data-driven forecast model provides improved 4-month lead predictions of the WNPSH and precipitation in the middle and lower reaches of the Yangtze River (MLYR), which has important implications for water resources management and precipitation-related disaster prevention in China. When compared with five state-of-the-art dynamical climate models including the Climate Forecast System of Nanjing University of Information Science and Technology (NUIST-CFS1.0) and four models participating in the North American Multi-Model Ensemble (NMME) project, the TU-Net produces comparable skills in forecasting 4-month lead geopotential height and winds at the 500- and 850-hPa levels. For the 4-month lead prediction of precipitation over the MLYR region, the TU-Net has the best correlation scores and mean latitude-weighted RMSE in each summer month and in boreal summer [June–August (JJA)], and pattern correlation coefficient scores are slightly lower than the dynamical models only in June and JJA. In addition, the results show that the constructed TU-Net is also superior to most of the dynamical models in predicting 2-m air temperature in the MLYR region at a 4-month lead. Thus, the deep learning-based TU-Net model can provide a rapid and inexpensive way to improve the seasonal prediction of summer precipitation and 2-m air temperature over the MLYR region.

Significance Statement
The purpose of this study is to examine the seasonal predictive skill of the western North Pacific subtropical high anomalies and summer rainfall anomalies over the middle and lower reaches of the Yangtze River region by means of deep learning methods. Our deep learning model provides a rapid and inexpensive way to improve the seasonal prediction of summer precipitation as well as 2-m air temperature. The work has important implications for water resources management and precipitation-related disaster prevention in China and can be extended in the future to predict other climate variables as well.
Tropical Cyclone Rainfall Climatology, Extremes, and Flooding Potential from Remote Sensing and Reanalysis Datasets over the Continental United States
Authors: Mazza Edoardo , Chen Shuyi S. 
Published: June 2023

Abstract
Tropical cyclones (TCs) are high-impact events responsible for devastating rainfall and freshwater flooding. Quantitative precipitation estimates (QPEs) are thus essential to better understand and assess TC impacts. QPEs based on different observing platforms (e.g., satellites, ground-based radars, and rain gauges), however, may vary substantially and must be systematically compared. The objectives of this study are to 1) compute the TC rainfall climatology, 2) investigate TC rainfall extremes and flooding potential, and 3) compare these fundamental quantities over the continental United States across a set of widely used QPE products. We examine five datasets over an 18-yr period (2002–19). The products include three satellite-based products, CPC morphing technique (CMORPH), Integrated Multi-satellitE Retrievals for GPM (IMERG), and Tropical Rainfall Measuring Mission–Multisatellite Precipitation Analysis (TRMM-TMPA); the ground-radar- and rain-gauge-based NCEP Stage IV; and a state-of-the-art, high-resolution reanalysis (ERA5). TC rainfall is highest along the coastal region, especially in North Carolina, northeast Florida, and in the New Orleans, Louisiana, and Houston, Texas, metropolitan areas. Along the East Coast, TCs can contribute up to 20% of the warm season rainfall and to more than 40% of all daily and 6-hourly extreme rain events. Our analysis shows that Stage IV detects far higher precipitation rates in landfalling TCs, relative to IMERG, CMORPH, TRMM, and ERA5. Satellite- and reanalysis-based QPEs underestimate both the TC rainfall climatology and extreme events, particularly in the coastal region. This uncertainty in QPEs is further reflected in the TC flooding potential measured by the extreme rainfall multiplier (ERM) values, whose single-cell maxima are substantially underestimated and misplaced by the satellite and reanalysis QPEs compared to that using NCEP Stage IV.

Significance Statement
Tropical cyclones (TCs) can produce extreme rainfall and widespread flooding. Improvements in our preparedness, mitigation, and adaptation efforts rest on a better understanding of TC rainfall and its impact. Assessment of various rainfall products and uncertainties is urgently needed for decision making and other applications. Different quantitative precipitation estimate (QPE) datasets have been developed over the past decades. This study uses 18 years of data to better understand how key properties of TC rainfall, including its contribution to extreme events and flooding potential, are represented across five widely used QPE products. Our analysis shows that satellite-based, and to a lesser extent, reanalysis-based QPEs underestimate TC rainfall properties both in terms of climatology and extreme events compared to ground-radar-gauge-based QPE. The uncertainty increases in the coastal region and is reflected in the estimated TC flooding potential.