bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Attack With Constants On μ2 Block Cipher
Authors: Shi Jiali , Li Chao , Liu Guoqiang 
Published: December 2022

Abstract
Differential attack is one of the most important methods in cryptanalysis. When finding a high-probability differential trail, the effect of constant has long been ignored. In this paper, we focus on the effect of constants on the differential attack against $\mu ^2$. $\mu ^2$ is a newly proposed block cipher based on a Type-II generalized Feistel structure. Its 16-bit F function (denoted as F-box) is an ultra-lightweight permutation equipped with different constants. The designer applied the minimum number of active S-boxes to determine $\mu ^2$’ security margin in the design document. However, the F-boxes use different round constants in different rounds; the constants may lead to incompatibility of differential trails of F-boxes. Therefore, to provide a more precise differential attack on $\mu ^2$, we construct an model based on STP (Simple Theorem Prover) constraint solver to search for the valid differential trails with a more precise probability of $\mu ^2$ for different starting rounds. Finally, the related-key differential trail covers one more round than the existing methods. Analyzing the effect of constants on the validity and the probability of the differential trail reminds the designers and the attackers to have a more comprehensive analysis of specific ciphers.
Juvenile survival curves in a solitary ground squirrel with a prolonged hibernation: effects of individual characteristics, environment, and maternal investment
Authors: Vasilieva Nina A , Savinetskaya Liudmila E , Tchabovsky Andrey V 
Published: December 2022

Abstract
Juvenile survival is a key life-history influence on population dynamics and adaptive evolution. We analyzed the effects of individual characteristics, early environment, and maternal investment on juvenile survival in a large solitary hibernating rodent—yellow ground squirrel Spermophilus fulvus using Cox mixed-effects models. Only 48% of weaned pups survived to dispersal and 17% survived to hibernation. Early life expectancy was primarily determined by individual characteristics and, to a lesser extent, by the early environment. The strongest and positive predictor of juvenile survival was body mass which crucially affected mortality immediately after weaning. Males suffered higher mortality than females after the onset of dispersal; however, the overall difference between sexes was partly masked by high rates of mortality in the first days after emergence in both sexes. Later emerged juveniles had lower life expectancy than the earliest pups. The overall effect of local juvenile density was positive. Prolonged lactation did not enhance juvenile survival: Pups nursed longer survived shorter than the young nursed for a shorter period. Our findings support the hypothesis that females of S. fulvus cannot effectively regulate maternal expenditures to mitigate the effects of unfavorable conditions on their offspring. The strategy to deal with seasonal time constraints on life history in female S. fulvus suggests an early termination of maternal care at the cost of juvenile quality and survival. This female reproductive strategy corresponds to a “fast-solitary” life of folivorous desert-dwelling S. fulvus and other solitary ground squirrels with prolonged hibernation.
A highly quality genome sequence of Penicillium oxalicum species isolated from the root of Ixora chinensis in Vietnam
Authors: Pham Huong Mai , Le Dung Thi , Le Lam Tung , Chu Phuong Thi Minh , Tran Linh Huyen , Pham Tung Thanh , Nguyen Hung Mau , Luu Tien Thuy , Hoang Ha , Chu Hoang Ha 
Published: December 2022

Abstract
Penicillium oxalicum has been reported as a multienzyme-producing fungus and is widely used in industry due to great potential for cellulase release. Until now, there are only 10 available genome assemblies of P. oxalicum species deposited in the GenBank database. In this study, the genome of the I1R1 strain isolated from the root of Ixora chinensis was completely sequenced by Pacbio Sequel sequencing technology, assembled into 8 chromosomes with the genome size of 30.8 Mb, as well as a mitogenome of 26 kb. The structural and functional analyses of the I1R1 genome revealed gene model annotations encoding an enzyme set involved in significant metabolic processes, along with cytochrome P450s and secondary metabolite biosynthesis. The comparative analysis of the P. oxalicum species based on orthology and gene family duplications indicated their large and closed pan-genome of 9,500 orthologous groups. This is valuable data for future phylogenetic and population genomics studies.
A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)
Authors: Velasco Vera Marjorie Elauria , Ferreira Alyssa , Zaman Sumaira , Noordermeer Devin , Ensminger Ingo , Wegrzyn Jill L 
Published: December 2022

Abstract
Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more “complete” genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.
A Local Trace Formula for p-adic Infinitesimal Symmetric Spaces: the Case of Guo–Jacquet
Authors: Li Huajie 
Published: December 2022

Abstract
We establish an invariant local trace formula for the tangent space of some symmetric spaces over a non-archimedean local field of characteristic zero. These symmetric spaces are studied in Guo–Jacquet trace formulae, and our methods are inspired by works of Waldspurger and Arthur. Some other results are given during the proof including a noninvariant local trace formula, Howe’s finiteness for weighted orbital integrals, and the representability of the Fourier transform of weighted orbital integrals. These local results are preparations for the comparison of regular semi-simple terms, which are weighted orbital integrals, appearing in an infinitesimal variant of Guo–Jacquet trace formulae.
On a Conjecture of Khoroshkin and Tolstoy
Authors: Appel Andrea , Gautam Sachin , Wendlandt Curtis 
Published: December 2022

Abstract
We prove a no-go theorem on the factorization of the lower triangular part in the Gaussian decomposition of the Yangian’s universal $R$-matrix, yielding a negative answer to a conjecture of Khoroshkin and Tolstoy from [11].
Emergency Department Presentation of Life-threatening Symptomatic Hyperkalemia From an Angiotensin Receptor Blocker in a Low-risk Individual
Authors: Dockery Samuel , Dupré Alan , Deflorio Paul , Murray Brian Patrick 
Published: December 2022

ABSTRACT
Hyperkalemia is a common electrolyte abnormality with characteristic electrocardiogram changes. Both angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) increase the risk of developing hyperkalemia. This case highlights a rare life-threatening episode of hyperkalemia in an individual whose only risk factor was an ARB. A 58-year-old female presented with sudden-onset chest pressure, light-headedness, and diaphoresis. Her initial electrocardiogram showed a nearly sinusoidal rhythm with a widened ventricular depolarization (QRS) and prolonged QT-interval (QTc). Life-threatening hyperkalemia of 9.1 mmol/L was confirmed with a rapid point-of-care electrolyte panel. She was rapidly treated with calcium, potassium-shifting and eliminating medications, and emergent hemodialysis. After stabilization, a thorough workup found that the patient’s only risk factor for hyperkalemia was her use of an ARB. While both ARBs and ACEIs are commonly associated with mild hyperkalemia, life-threatening hyperkalemia is rare, particularly in patients without concomitant renal failure, diabetes mellitus, adrenal disease, or potassium-sparing diuretic use. However, this case illustrates that life-threatening hyperkalemia is possible in patients solely taking an ARB without prior significant risk factors. Despite normal renal function in an individual without heart failure or diabetes, this patient developed life-threatening hyperkalemia.
Cerebrospinal fluid methylome-based liquid biopsies for accurate malignant brain neoplasm classification
Authors: Zuccato Jeffrey A , Patil Vikas , Mansouri Sheila , Voisin Mathew , Chakravarthy Ankur , Shen Shu Yi , Nassiri Farshad , Mikolajewicz Nicholas , Trifoi Mara , Skakodub Anna , Zacharia Brad , Glantz Michael , De Carvalho Daniel D , Mansouri Alireza , Zadeh Gelareh 
Published: December 2022

Abstract

Background
Resolving the differential diagnosis between brain metastases (BM), glioblastomas (GBM), and central nervous system lymphomas (CNSL) is an important dilemma for the clinical management of the main three intra-axial brain tumor types. Currently, treatment decisions require invasive diagnostic surgical biopsies that carry risks and morbidity. This study aimed to utilize methylomes from cerebrospinal fluid (CSF), a biofluid proximal to brain tumors, for reliable non-invasive classification that addresses limitations associated with low target abundance in existing approaches.

Methods
Binomial GLMnet classifiers of tumor type were built, in fifty iterations of 80% discovery sets, using CSF methylomes obtained from 57 BM, GBM, CNSL, and non-neoplastic control patients. Publicly-available tissue methylation profiles (N = 197) on these entities and normal brain parenchyma were used for validation and model optimization.

Results
Models reliably distinguished between BM (area under receiver operating characteristic curve [AUROC] = 0.93, 95% confidence interval [CI]: 0.71–1.0), GBM (AUROC = 0.83, 95% CI: 0.63–1.0), and CNSL (AUROC = 0.91, 95% CI: 0.66–1.0) in independent 20% validation sets. For validation, CSF-based methylome signatures reliably distinguished between tumor types within external tissue samples and tumors from non-neoplastic controls in CSF and tissue. CSF methylome signals were observed to align closely with tissue signatures for each entity. An additional set of optimized CSF-based models, built using tumor-specific features present in tissue data, showed enhanced classification accuracy.

Conclusions
CSF methylomes are reliable for liquid biopsy-based classification of the major three malignant brain tumor types. We discuss how liquid biopsies may impact brain cancer management in the future by avoiding surgical risks, classifying unbiopsiable tumors, and guiding surgical planning when resection is indicated.
Meeting the Challenges of Sepsis in Severe Coronavirus Disease 2019: A Call to Arms
Authors: Walsh Thomas J , Bright Rick A , Ahuja Aparna , McCarthy Matthew W , Marfuggi Richard A , Simpson Steven Q 
Published: December 2022

Abstract
Sepsis is a life-threatening organ dysfunction that is caused by a dysregulated host response to infection. Sepsis may be caused by bacterial, fungal, or viral pathogens. The clinical manifestations exhibited by patients with severe coronavirus disease 2019 (COVID-19)-related sepsis overlap with those exhibited by patients with sepsis from secondary bacterial or fungal infections and can include an altered mental status, dyspnea, reduced urine output, tachycardia, and hypotension. Critically ill patients hospitalized with severe acute respiratory syndrome coronavirus 2 infections have increased risk for secondary bacterial and fungal infections. The same risk factors that may predispose to sepsis and poor outcome from bloodstream infections (BSIs) converge in patients with severe COVID-19. Current diagnostic standards for distinguishing between (1) patients who are critically ill, septic, and have COVID-19 and (2) patients with sepsis from other causes leave healthcare providers with 2 suboptimal choices. The first choice is to empirically administer broad-spectrum, antimicrobial therapy for what may or may not be sepsis. Such treatment may not only be ineffective and inappropriate, but it also has the potential to cause harm. The development of better methods to identify and characterize antimicrobial susceptibility will guide more accurate therapeutic interventions and reduce the evolution of new antibiotic-resistant strains. The ideal diagnostic test should (1) be rapid and reliable, (2) have a lower limit of detection than blood culture, and (3) be able to detect a specific organism and drug sensitivity directly from a clinical specimen. Rapid direct detection of antimicrobial-resistant pathogens would allow targeted therapy and result in improved outcomes in patients with severe COVID-19 and sepsis.
Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis
Authors: Farrell Martilias , Dietterich Tyler E , Harner Matthew K , Bruno Lisa M , Filmyer Dawn M , Shaughnessy Rita A , Lichtenstein Maya L , Britt Allison M , Biondi Tamara F , Crowley James J , Lázaro-Muñoz Gabriel , Forsingdal Annika E , Nielsen Jacob , Didriksen Michael , Berg Jonathan S , Wen Jia , Szatkiewicz Jin , Mary Xavier Rose , Sullivan Patrick F , Josiassen Richard C 
Published: December 2022

AbstractBackgroundIt remains unknown why ~30% of patients with psychotic disorders fail to respond to treatment. Previous genomic investigations of treatment-resistant psychosis have been inconclusive, but some evidence suggests a possible link between rare disease-associated copy number variants (CNVs) and worse clinical outcomes in schizophrenia. Here, we identified schizophrenia-associated CNVs in patients with treatment-resistant psychotic symptoms and then compared the prevalence of these CNVs to previously published schizophrenia cases not selected for treatment resistance.MethodsCNVs were identified using chromosomal microarray (CMA) and whole exome sequencing (WES) in 509 patients with treatment-resistant psychosis (a lack of clinical response to ≥3 adequate antipsychotic medication trials over at least 5 years of psychiatric hospitalization). Prevalence of schizophrenia-associated CNVs in this sample was compared to that in a previously published large schizophrenia cohort study.ResultsIntegrating CMA and WES data, we identified 47 cases (9.2%) with at least one CNV of known or possible neuropsychiatric risk. 4.7% (n = 24) carried a known neurodevelopmental risk CNV. The prevalence of well-replicated schizophrenia-associated CNVs was 4.1%, with duplications of the 16p11.2 and 15q11.2-q13.1 regions, and deletions of the 22q11.2 chromosomal region as the most frequent CNVs. Pairwise loci-based analysis identified duplications of 15q11.2-q13.1 to be independently associated with treatment resistance.ConclusionsThese findings suggest that CNVs may uniquely impact clinical phenotypes beyond increasing risk for schizophrenia and may potentially serve as biological entry points for studying treatment resistance. Further investigation will be necessary to elucidate the spectrum of phenotypic characteristics observed in adult psychiatric patients with disease-associated CNVs.
Do the Components of Attenuated Positive Symptoms Truly Represent One Construct?
Authors: Pratt Danielle N , Bridgwater Miranda , Schiffman Jason , Ellman Lauren M , Mittal Vijay A 
Published: December 2022

Abstract

Background and Hypotheses
Psychosis-risk inventories, like the Structured Interview for Psychosis-Risk Syndromes (SIPS), utilize symptom components and coalesce the information into a single-severity rating. These components include frequency, duration, in-the-moment conviction, retrospective insight, distress, and effect on social/role functioning. While combining components distills a great deal of important information into one practical symptom rating, this approach may mask important details of the greater clinical picture.

Study Design
Individuals at clinical high risk for psychosis (n = 115) were assessed with the SIPS Score Separable Components (SSSC) scale, created to accompany the SIPS positive items by dividing each item into the 7 components identified above. The latent structure of the SSSC was identified with an exploratory factor analysis (EFA). The factors were followed up with validation analyses including hypothesized cognitive, functioning, and symptom measures. Finally, clinical utility analyses were conducted to understand relationships between psychosis risk and common comorbidities.

Study Results
EFA revealed that the SSSC had 3 interpretable factors with the appropriate fit (rmsr = 0.018, TLI = 0.921): Conviction (in-the-moment conviction, retrospective insight), Distress-Impairment (distress, social/role functioning), and Frequency/Duration (frequency, duration). Conviction was minimally valid, Distress-Impairment had excellent validity, and Frequency/Duration was not related to any of the candidate validators. Conviction significantly predicted elevated psychosis risk. Distress-Impairment was related to common comorbid symptoms. Notably, the factors associated more strongly with clinical features than the traditional SIPS scores.

Conclusions
The SSSC offers a supplemental approach to single-severity ratings, providing useful clinical insight, mechanistic understanding, and the potential for better capturing heterogeneity in this population.
Maternal exposure to perfluorobutane sulfonate (PFBS) during pregnancy: evidence of adverse maternal and fetoplacental effects in New Zealand White (NZW) rabbits
Authors: Crute Christine E , Landon Chelsea D , Garner Angela , Hall Samantha M , Everitt Jeffery I , Zhang Sharon , Blake Bevin , Olofsson Didrik , Chen Henry , Stapleton Heather M , Murphy Susan K , Feng Liping 
Published: December 2022

AbstractPerfluorobutanesulfonic acid (PFBS) is a replacement for perfluorooctanesulfonic acid (PFOS) that is increasingly detected in drinking water and human serum. Higher PFBS exposure is associated with risk for preeclampsia, the leading cause of maternal and infant morbidity and mortality in the United States. This study investigated relevant maternal and fetal health outcomes after gestational exposure to PFBS in a New Zealand White rabbit model. Nulliparous female rabbits were supplied drinking water containing 0 mg/l (control), 10 mg/l (low), or 100 mg/l (high) PFBS. Maternal blood pressure, body weights, liver and kidney weights histopathology, clinical chemistry panels, and thyroid hormone levels were evaluated. Fetal endpoints evaluated at necropsy included viability, body weights, crown-rump length, and liver and kidney histopathology, whereas placenta endpoints included weight, morphology, histopathology, and full transcriptome RNA sequencing. PFBS-high dose dams exhibited significant changes in blood pressure markers, seen through increased pulse pressure and renal resistive index measures, as well as kidney histopathological changes. Fetuses from these dams showed decreased crown-rump length. Statistical analysis of placental weight via a mixed model statistical approach identified a significant interaction term between PFBS high dose and fetal sex, suggesting a sex-specific effect on placental weight. RNA sequencing identified the dysregulation of angiotensin (AGT) in PFBS high-dose placentas. These results suggest that PFBS exposure during gestation leads to adverse maternal outcomes, such as renal injury and hypertension, and fetal outcomes, including decreased growth parameters and adverse placenta function. These outcomes raise concerns about pregnant women’s exposure to PFBS and pregnancy outcomes.
Multistate Modeling of Clinical Trajectories and Outcomes in the ICU: A Proof-of-Concept Evaluation of Acute Kidney Injury Among Critically Ill Patients With COVID-19
Authors: Lyons Patrick G. , Mody Aaloke , Bewley Alice F. , Schoer Morgan , Neelam Raju Bharat , Geng Elvin , Payne Philip R. O. , Sinha Pratik , Vijayan Anitha 
Published: December 2022

IMPORTANCE:
Multistate models yield high-fidelity analyses of the dynamic state transition and temporal dimensions of a clinical condition’s natural history, offering superiority over aggregate modeling techniques for addressing these types of problems.

OBJECTIVES:
To demonstrate the utility of these models in critical care, we examined acute kidney injury (AKI) development, progression, and outcomes in COVID-19 critical illness through multistate analyses.

DESIGN, SETTING, AND PARTICIPANTS:
Retrospective cohort study at an urban tertiary-care academic hospital in the United States. All patients greater than or equal to 18 years in an ICU with COVID-19 in 2020, excluding patients with preexisting end-stage renal disease.

MAIN OUTCOMES AND MEASURES:
Using electronic health record data, we determined AKI presence/stage in discrete 12-hour time windows and fit multistate models to determine longitudinal transitions and outcomes.

RESULTS:
Of 367 encounters, 241 (66%) experienced AKI (maximal stages: 88 stage-1, 49 stage-2, 104 stage-3 AKI [51 received renal replacement therapy (RRT), 53 did not]). Patients receiving RRT overwhelmingly received invasive mechanical ventilation (IMV) (n = 60, 95%) compared with the AKI-without-RRT (n = 98, 53%) and no-AKI groups (n = 39, 32%; p < 0.001), with similar mortality patterns (RRT: n = 36, 57%; AKI: n = 74, 40%; non-AKI: n = 23, 19%; p < 0.001). After 24 hours in the ICU, almost half the cohort had AKI (44.9%; 95% CI, 41.6–48.2%). At 7 days after stage-1 AKI, 74.0% (63.6–84.4) were AKI-free or discharged. By contrast, fewer patients experiencing stage-3 AKI were recovered (30.0% [24.1–35.8%]) or discharged (7.9% [5.2–10.7%]) after 7 days. Early AKI occurred with similar frequency in patients receiving and not receiving IMV: after 24 hours in the ICU, 20.9% of patients (18.3–23.6%) had AKI and IMV, while 23.4% (20.6–26.2%) had AKI without IMV.

CONCLUSIONS AND RELEVANCE:
In a multistate analysis of critically ill patients with COVID-19, AKI occurred early and heterogeneously in the course of critical illness. Multistate methods are useful and underused in ICU care delivery science as tools for understanding trajectories, prognoses, and resource needs.