bluuebunny/crossref_metadata_2025 huggingface dataset:
Blood transfusion in the Caribbean: Historical perspective in the context of Trinidad and Tobago
Authors: Charles Kenneth Stering , Wilson Keith M.O. , Roberts David
Published: October 2024

To compare the historical development of blood transfusion in Britain and a former British West Indian colony. International transfusion bodies recommend national coordination and exclusively voluntary non‐remunerated donation as essential pre‐requisites for blood safety. These ideals have been achieved in high‐income countries including Great Britain, the United States of America and Canada. However, most West Indian countries have fragmented, hospital‐based blood services that rely on family replacement and remunerated donors. Comparative historical analysis of blood transfusion service development in Great Britain and Trinidad and Tobago was undertaken to provide insight into their dichotomous development and inform policy decisions to bridge the gap between the two types of transfusion service. The British National Blood Transfusion service was based on voluntary non‐remunerated blood donation from its inception but achieved national coordination over 50 years that included a period of regional control during which incoordination contributed to a tainted blood scandal. Failure to establish community voluntary non‐remunerated donation in Trinidad and Tobago during the colonial period, before independence in 1962, allowed regionally‐controlled family replacement and remunerated blood donation to become entrenched then perpetuated by path dependence. A university‐led programme has recently used historically‐proven methods, drawing on the experiences of the British National Blood Transfusion Service, to establish a model for developing a voluntary non‐remunerated programme. The programme aims to avoid historical pitfalls during its national extension. Historical analysis provided information for introducing voluntary non‐remunerated blood donation and planning a nationally‐coordinated blood transfusion service.
Efficacy of an oral chew containing fibre and Bacillus velezensis C‐3102 in the management of anal sac impaction in dogs
Authors: Salichs Marta , Beasley Shea , Homedes Josep
Published: October 2024

Background

Anal sac impaction is common in dogs. Manual expression may be effective, yet recurrence can be problematic. To facilitate physiological emptying of the sacs, it is important to maintain bulky stool consistency.

Objectives

The study evaluated if supplementation with a complementary feed product formulated as a chew containing Bacillus velezensis C‐3102 and fibre sources, reduced anal sac impaction recurrence.

Animals

Thirty‐five client‐owned dogs with anal sac impaction were enrolled.

Materials and Methods

Prospective, randomised, negative controlled field clinical trial with 22 dogs receiving the chew orally for 90 consecutive days and 13 dogs with no treatment. Dogs were evaluated on Day (D) 30, 60, 90 and 120 for the presence of clinical signs of anal sac impaction and the need to empty the sacs. Any animal that required manual expression of the sacs was classified as a failure and was withdrawn from the study.

Results

The cumulative percentage of failures in the untreated group increased steadily from the first follow‐up visit on D30 (15%) to the last visit on D120 (61.5%). However, in the group receiving the chew the cumulative percentage of failures increased at a much slower rate and stabilised at 19% from the D90 visit (last administration day) until the end of the study on D120, with statistically significant differences (p = 0.025). Animals receiving the chew also showed reduction in clinical signs.

Conclusion and Clinical Relevance

The probiotic and fibre chew was a safe and effective management option for recurrent anal sac impaction in dogs.
A novel approach to simultaneous genotyping of human platelet antigen systems and human leucocyte antigen class I loci using PacBio long‐read sequencing
Authors: Zhao Peizhe , Lyu Qilu , Xu Yi , Liang Yajun , Wu Yunxiang , Li Qing , Wang Hua , Yuan Yao , He Runjun , Fu Weiyi , Zhang Demei , Kong Yujie
Published: October 2024

Background and Objectives

Accurate human leucocyte antigen (HLA) and human platelet antigen (HPA) typing is essential for establishing a blood platelet donor bank to deal with refractoriness in patients undergoing multiple platelet transfusions. Current methods, such as Sanger and next‐generation sequencing, encounter difficulties in haplotyping. Herein, the aim of this study was to establish a method for HLA and HPA typing based on the long read sequencing.

Study Design and Methods

The HPA and HLA class I genotypes of 268 platelet donors from the Taiyuan Blood Center, China were identified using long‐read sequencing on the PacBio platform. Allele frequencies for HPA systems and HLA class I genes were calculated, and genetic variability within HPA system genes was analysed.

Results

Polymorphisms were identified in 8 of the 35 HPA systems (HPA‐1 to HPA‐6w, HPA‐15 and HPA‐21w), with the frequencies of the ‘b’ allele at 0.0187, 0.0709, 0.4086, 0.0075, 0.0149, 0.0317, 0.4310 and 0.0019, respectively. The alleles with the highest frequencies at the HLA‐A, HLA‐B and HLA‐C loci are HLA‐A02:01, B51:01, B46:01 and C06:02, respectively. Additionally, several genetic patterns in HPA systems were identified, including the c.166‐1029C>T variant, which was found exclusively in samples carrying the HPA‐1b allele.

Conclusion

This study developed a targeted long‐read sequencing method characterized by high throughput and simultaneity, capable of resolving allele ambiguities for effective HLA class I genotyping in establishing a platelet donor bank.
Diagnostic imaging findings in lame Warmblood horses with bone injuries of the medial proximal phalanx glenoid cavity
Authors: Vandersmissen Maxime , Evrard Laurence , Charles Alexandre , Audigié Fabrice , Busoni Valeria
Published: October 2024

This retrospective study aims to describe baseline and follow‐up imaging findings in subchondral and trabecular bone damage occurring outside of the sagittal groove in the proximal phalanx (P1) glenoid in a case series of lame Warmblood horses. Thirteen lame horses (16 forelimbs) with standing magnetic resonance imaging (sMRI) evidence of nonsagittal groove glenoid subchondral and trabecular bone injury of P1 as the main lesion were included. All injuries were located at the medial aspect of the P1 glenoid. At sMRI, changes included subchondral bone plate thickening and trabecular sclerosis, bone marrow edema‐like signal, subchondral bone resorption (11/16), and new bone production (8/16). Subchondral bone resorption in the transverse plane was linear (8/11), round (2/11), or ill‐defined (1/11). Sclerosis, bone resorption, and new bone production were seen radiographically in 10, 4, and 5 limbs, respectively. All limbs had concurrent metacarpal condyle sMRI imaging abnormalities, osteophytosis, and joint effusion. Follow‐up sMRIs were obtained in 8 of 16 limbs, five of which showing progression of the resorptive lesion. One horse encountered a comminuted fracture of the affected P1 18 months after the follow‐up sMRI examination. The imaging appearance of the medial glenoid bone injuries of P1 in this case series is consistent with chronic bone overload. The linear configuration of bone resorption seen in eight lesions suggests short, incomplete stress fractures, which is supported by the ultimate catastrophic fracture occurring in one case.
Characteristics of advanced practice nurses’ clinical competence in primary health care settings: a scoping review protocol
Authors: Troncoso-Valenzuela Bernardita , de Almeida Lopes Monteiro da Cruz Diná , Quiroga Toledo Natalia
Published: October 2024

Objective:

This scoping review aims to identify the clinical competency characteristics, in terms of knowledge, skills, and attitudes, of advanced practice nurses in primary health care settings.

Introduction:

Although much has been written about the competencies of advanced practice nurses, more detail about the skills, knowledge, and attitudes that inform their clinical competence in primary health care needs to be ascertained. This will promote the development, implementation, and evaluation of advanced nursing practice in contexts where it is unavailable.

Inclusion criteria:

Studies that address the clinical competency characteristics of advanced practice nurses in primary health care settings will be considered for inclusion.

Methods:

This review will be conducted according to JBI methodology for scoping reviews. A comprehensive search will be conducted in PubMed, CINAHL (EBSCOhost), Web of Science Core Collection, Scopus, Virtual Health Library, Scientific Electronic Library Online, Embase, ScienceDirect, Cochrane Library, and Google Scholar for primary and secondary qualitative, quantitative, and mixed methods studies on the topic of relevance. Gray literature will be searched in DART-E, TESES CAPES, CAUL (Australian Digital Theses), and Theses Canada Editorials. Letters, editorials, commentaries, conference abstracts, and documents published by advanced practice nurses’ associations will also be considered for inclusion. Two independent reviewers will screen the studies at title and abstract and at full text. The same reviewers will extract relevant data using an instrument developed by the reviewers. These data will be presented in a narrative synthesis to facilitate the analysis of the evidence found.

Review registration:

Open Science Framework https://osf.io/zbqdn
Detection of mild sensory hearing loss using a joint reflection-distortion otoacoustic emission profile
Authors: Abdala Carolina , Benjamin Tricia , Stiepan Samantha , Luo Ping , Shera Christopher A.
Published: October 2024

Measuring and analyzing both nonlinear-distortion and linear-reflection otoacoustic emissions (OAEs) combined creates what we have termed a “joint-OAE profile.” Here, we test whether these two classes of emissions have different sensitivities to hearing loss and whether our joint-OAE profile can detect mild-moderate hearing loss better than conventional OAE protocols have. 2f1-f2 distortion-product OAEs and stimulus-frequency OAEs were evoked with rapidly sweeping tones in 300 normal and impaired ears. Metrics included OAE amplitude for fixed-level stimuli as well as slope and compression features derived from OAE input/output functions. Results show that mild-moderate hearing loss impacts distortion and reflection emissions differently. Clinical decision theory was applied using OAE metrics to classify all ears as either normal-hearing or hearing-impaired. Our best OAE classifiers achieved 90% or better hit rates (with false positive rates of 5%–10%) for mild hearing loss, across a nearly five-octave range. In summary, results suggest that distortion and reflection emissions have distinct sensitivities to hearing loss, which supports the use of a joint-OAE approach for diagnosis. Results also indicate that analyzing both reflection and distortion OAEs together to detect mild hearing loss produces outstanding accuracy across the frequency range, exceeding that achieved by conventional OAE protocols.
A low-complexity error-feedback lattice-equalizer with phase tracking for underwater acoustic communications
Authors: Wu Fei-Yun , Yang Hui-Zhong , Liu Shengxing
Published: October 2024

Recursive least squares (RLS)–based equalizers are hindered by their high complexity in underwater acoustic (UWA) communications. This article proposes an adaptive equalizer with a phase tracking method for the UWA communication, named the error-feedback lattice-equalizer (EFLE). First, we derive the algorithm for recursively solving the least squares problem from EFLE, introducing a lattice structure using time and order updates, thereby reducing the complexity to be linearly related to its length. The error-feedback mechanism used in computing reflection coefficients ensures the numerical stability of the algorithm. By focusing on the rapid tap rotation in time-varying channels, we design phase tracking in EFLE to further improve equalization performance. To verify the bit error rate (BER) performance of the proposed EFLE, we study the UWA communication system and conduct UWA simulations and at-sea experiments. Comparisons include linear complexity equalizers such as least mean square (LMS), leaky LMS, least mean mixed-norm, and ϵ-normalized LMS equalizers, and quadratic complexity RLS equalizers. At-sea experiment results show that the BER performance of EFLE significantly outperforms its counterparts.
Association Between Accelerometer-Measured Physical Activity and Mobility Limitations in Twins
Authors: Pullinen Pia , Parkkari Jari , Kaprio Jaakko , Vähä-Ypyä Henri , Sievänen Harri , Kujala Urho , Waller Katja
Published: October 2024

Background: The associations between mobility limitations and device-measured physical activity are sparsely studied. In this study, these associations are studied among community-dwelling older twins. Methods: This cross-sectional study utilized data gathered in 2014–2016 for the MOBILETWIN study. Participants were twins born in Finland between 1940 and 1944 (774 participants, mean age 73 years). Physical activity was measured with a hip-worn accelerometer. Mobility limitations were assessed with a questionnaire. Results: Individual-level analyses revealed that physical activity was associated with mobility limitations. Participants with severe mobility limitations took 2,637 (SD = 1,747) steps per day, those with some mobility limitations 4,437 (SD = 2,637) steps, and those without mobility limitations 7,074 (SD = 2,931) steps (p < .05). The within-twin pair analyses revealed the same pattern for the 144 dizygotic twin pairs, but no associations were seen for the 117 monozygotic twin pairs. Conclusions: Accelerometer-measured physical activity and mobility limitations were associated in community-dwelling older adults. Genetic factors may explain some of the variations in physical activity. Significance: A personalized exercise program to promote increased physical activity should be provided for older adults who report mobility difficulties. Future research is needed to examine causality between physical activity and mobility limitations.
Screening and functional characterization of isocitrate lyase AceA in the biofilm formation of
Vibrio alginolyticus
Authors: Shi Weibo , Li Ya , Zhang Weiwei
Published: October 2024

Biofilm is a well-known sessile lifestyle for bacterial pathogens, but a little is known about the mechanism on biofilm formation in
Vibrio alginolyticus
. In this study, we screened
V. alginolyticus
strains with strong biofilm formation ability from coastal seawater. The antibiotic resistance of the biofilm cells (BFs) was higher than that of the planktonic cells (PTs). To study the genes and pathways involved in biofilm formation, we performed transcriptome analysis of the BFs and PTs of
V. alginolyticus
R9. A total of 685 differentially expressed genes (DEGs) were upregulated, and 517 DEGs were downregulated in the BFs. The upregulated DEGs were significantly enriched in several pathways including glyoxylate and dicarboxylate metabolism, while the downregulated genes were significantly enriched in the flagellar assembly pathways. The key gene involved in glyoxylate shunt,
aceA
, was cloned, and Δ
aceA
mutant was constructed to determine the function of AceA in carbon source utilization, biofilm formation, and virulence. Real-time reverse transcription PCR showed that the expression of
aceA
was higher at the mature stage but lower at the disperse stage of biofilm formation, and the expression of the flagellar related genes was upregulated in Δ
aceA
. This is the first study to illustrate the global gene expression profile during the biofilm formation of
V. alginolyticus
, and isocitrate lyase AceA, the key enzyme involved in glyoxylate shunt, was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the late stage.

IMPORTANCE

Biofilms pose serious public problems, not only protecting the cells in it from environmental hazard but also affecting the composition and abundance of bacteria, algae, fungi, and protozoa. The important opportunistic pathogen
Vibrio alginolyticus
is extremely ubiquitously present in seawater, and it also exhibited a strong ability to form biofilm; thus, investigation on the biofilm formation of
V. alginolyticus
at molecular level is fundamental for the deeper exploration of the environmental concerns arose by biofilm. In this study, transcriptome analysis of biofilm cells (BFs) and planktonic cells (PTs) from
V. alginolyticus
was performed and AceA was screened to play an important role in biofilm formation. AceA was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the disperse stage. This method was helpful to further understand the ability and mechanism of
V. alginolyticus
biofilm formation and provide clues for prevention of
V. alginolyticus
infection.
Complete genome sequence of a potentially probiotic cheese isolate
Lactiplantibacillus plantarum
LP140 from the Nordbiotic collection
Authors: Szczepankowska Agnieszka , Cukrowska Bożena , Aleksandrzak-Piekarczyk Tamara
Published: October 2024

We report the complete genome sequence of
Lactiplantibacillus plantarum
LP140, a cheese isolate from the Nordbiotic collection, comprising 3,371,266 bp with 44.4% GC content. Our data provide insight into the potential of LP140 for use as a probiotic strain.
Ash deposits link Oceanic Anoxic Event 2 to High Arctic volcanism
Authors: Dummann Wolf , Wennrich Volker , Schröder-Adams Claudia J. , Leicher Niklas , Herrle Jens O.
Published: October 2024

Oceanic Anoxic Event 2 (OAE 2) was a major environmental perturbation that occurred ∼94 million years ago. It is associated with profound changes in global climate and carbon cycling, which are commonly attributed to large-scale carbon release from large igneous province (LIP) volcanism. However, the specific LIP(s) involved and the mechanisms of carbon release remain poorly understood, as indicated by discrepancies between carbon release rates suggested by numerical models and LIP degassing estimates. Our study refines the eruptive history of the High Arctic large igneous province (HALIP) by dating ashfall deposits in marine sediments from the Canadian High Arctic using an integrated stratigraphic approach. Our results show that silicic HALIP volcanism began tens of thousands of years before OAE 2, suggesting a strong causal link. Volcanic activity coincides with a marked shift in carbon isotope values, linked to the degassing of HALIP magmas and/or thermogenic gas release. We propose that the concurrent activity of two LIPs—the HALIP and the Kerguelen Plateau—could account for the high rates of carbon release inferred for OAE 2, providing a hypothesis for its pervasive environmental impact.
Supplemental Material: Origin of the Oligocene–Miocene Sailipu ultrapotassic volcanic rocks in southern Tibet: Melting of Asian mantle pyroxenites triggered by eastward tearing of the subducting Indian continental slab
Authors: Liu Lin , al. et
Published: October 2024

Table S1: The mineral assemblage, whole-rock major and trace element data for the Sailipu ultrapotassic rocks. Table S2: U-Pb age data of zircons from Sailipu ultrapotassic rocks. Table S3: Trace element data of zircons from Sailipu ultrapotassic rocks. Table S4: Hf isotopic data of zircons from the Sailipu ultrapotassic rocks. Table S5: Major element and trace element data of olivine from Sailipu ultrapotassic rocks. Table S6: Major element and trace element data of clinopyroxene from Sailipu ultrapotassic rocks. Table S7: Estimation of redox condition of the Sailipu ultrapotassic rocks based on olivine-liquid equilibrium. Table S8: Estimation of crystallization temperature of the Sailipu ultrapotassic rocks based on olivine-liquid equilibrium. Table S9: Estimation of crystallization temperature and pressure of the Sailipu ultrapotassic rocks based on clinopyroxene-liquid equilibrium. Table S10: Pressure-temperature estimates of the Sailipu ultrapotassic rocks. 
Falciform ligament abscess management
Authors: Tran Elisa , Colbran Rachel , Sethi Harsheet
Published: October 2024

Falciform ligament abscess (FLA) is a rare occurrence as a consequence of local inflammation. This report presents a case of FLA on a background of recent cholangitis and laparoscopic cholecystectomy complicated by superficial umbilical wound infection. Diagnosis was by clinical examination and CT imaging. Management was by laparoscopic drainage.
Fungal community composition varies spatially in a commercial potato field in response to soil properties and topographic features
Authors: Neupane Saraswoti , Goyer Claudia , Zebarth Bernie J. , Li Sheng , Mills Aaron , Whitney Sean
Published: October 2024

The factors influencing the spatial distribution of fungal communities are commonly examined over large spatial scales but not at smaller scales. Given this, the extent to which soil properties and topographic features contribute to the diversity and distribution of fungal communities in an agricultural field needs to be further explored. We investigated the spatial distribution of soil fungal community composition from an ∼1100 m long transect with 83 sampling points in a commercial potato field with a rolling landform. The relative abundance of Ascomycota, Basidiomycota, and Mortierellomycota showed medium to strong spatial dependence with an autocorrelation range varying from ∼43 to 92 m, similar to the autocorrelation range of soil properties and topographic features. Most of the variability in fungal and saprotrophic community composition was explained by soil properties (15% and 11%, respectively) and spatial distance (16% and 15%, respectively) while topographic features contributed 8% and 5% of variability to total fungi and saprotrophic community composition, respectively. The fungal and saprotrophic community compositions were correlated with soil organic carbon, pH, and slope curvature, however, richness and Pielou’s evenness of the fungal communities and fungal biomass were not correlated with soil properties or topographic features. The results suggest that the spatial variation in fungal and saprotrophic community composition in response to soil properties and topographic features in this agricultural landscape was due to differences in assemblages of fungal amplicon sequence variants (ASVs) but not in differences in the number of fungal ASVs or fungal biomass measured using phospholipids fatty acids.
Charmless decays of the spin-2 partner of X(3872)
Authors: Cai Zu-Xin , Jia Zhao-Sai , Li Gang , Liu Shi-Dong , Xie Ju-Jun
Published: October 2024

The Belle collaboration recently reported a pro-mising candidate for the spin-2 $$D^*\bar{D}^*$$

D
∗

D

¯

∗

partner of the X(3872), called the $$X_2$$

X
2

for short, having a mass of $$(4014.3 \pm 4.0 \pm 1.5)~\textrm{MeV}$$

(
4014.3
±
4.0
±
1.5
)

MeV

and a width of $$(4 \pm 11 \pm 6)~\textrm{MeV} $$

(
4
±
11
±
6
)

MeV

. In present work, we assume the $$X_2$$

X
2

as a pure molecule of the $$D^*\bar{D}^*$$

D
∗

D

¯

∗

under four cases, i.e., pure neutral components ($$\theta = 0$$

θ
=
0

), isospin singlet ($$\theta = \pi /4$$

θ
=
π
/
4

), neutral components dominant ($$\theta = \pi /6$$

θ
=
π
/
6

), and purely charged components ($$\theta = \pi /2$$

θ
=
π
/
2

), where $$\theta $$
θ
is a phase angle describing the proportion of neutral and charged constituents. Using an effective Lagrangian approach, we calculated the partial widths of $$X_2\rightarrow VV$$

X
2

→
V
V

and $$X_2 \rightarrow PP$$

X
2

→
P
P

(V and P stand for light vector and pseudoscalar mesons, respectively). The predicted decay widths of $$X_2 \rightarrow VV$$

X
2

→
V
V

can reach a few hundreds of $$\textrm{keV}$$
keV
, while the decay widths of $$X_2 \rightarrow PP$$

X
2

→
P
P

are about several tens of $$\textrm{keV}$$
keV
. In addition, the effects from the proportion of neutral and charged constituent on the decay widths of $$X_2\rightarrow VV$$

X
2

→
V
V

and PP are also investigated. We hope that the present calculations will be checked experimentally in the future.
The Role of Confirmatory Testing in Carpal Tunnel Syndrome: Electrodiagnostic Study, Ultrasound and CTS-6
Authors: GABRIEL Daniel C. , DEMETRI Leah , ZHANG Dafang
Published: October 2024

Carpal tunnel syndrome (CTS) is the most common upper extremity compressive neuropathy. The reference standard for the diagnosis of CTS remains an area of controversy. The diagnosis can be established clinically, but options for confirmatory testing include electrodiagnostic studies, ultrasound and diagnostic aids such as the CTS-6 score. This review article summarises the current evidence for each confirmatory testing modality, contrasts their advantages and disadvantages and discusses future directions for investigation.

Level of Evidence: Level V (Diagnostic)
Assessment of Fracture Line Angle in Mallet Fractures
Authors: ATEŞ Erdem , GÜMÜŞOĞLU Ender , ARIKAN Anıl , ESKANDARİ Metin Manouchehr
Published: October 2024

Background: Surgery is often offered to patients with mallet fractures that have a large, displaced fragment and/or joint subluxation. However, the surgical approach remains a subject of debate, and surgery is frequently associated with unsatisfactory outcomes. We felt that the angle formed by the fracture line and the long axis of the distal phalanx on a lateral view radiograph (fracture line angle [FLA]) could be useful in determining the appropriate treatment strategy. The aim of this study was to assess the FLA and its distribution in mallet fractures.

Methods: Three researchers measured the mallet FLA and the percentage of articular surface (PAS) involved in the lateral radiographs of 103 patients with a mallet fracture.

Results: There was a strong correlation between the mallet FLA and the percentage of joint surface involvement between the three researchers. The mean FLA was 42.59° (±11.54) and it ranged from −1 to +1 standard deviation in 73 individuals (70.87%). The FLA varied over a wide range, while clustering near the average value. The average PAS involvement was 46.5% (±8.7%). There was no correlation between FLA and PAS involvement (p > 0.05).

Conclusions: It is possible to quantify the mallet FLA accurately and consistently. It varies widely, regardless of the PAS involvement. When choosing the type of treatment and making prognostic predictions, the mallet FLA may be a helpful guide.

Level of Evidence: Level IV (Diagnostic)
The Transverse Sigmoid Notch Morphology Unravelled
Authors: KRAMER Simon B. , RAAD Frederike , HAUSER Alexander , SCHIPPER Inger B. , SCHEP Niels W. L.
Published: October 2024

Background: Several studies have described pathology in relation to transverse sigmoid notch morphology, using the Tolat transverse sigmoid notch classification. It is believed that the entire shape of a sigmoid notch can be described using Tolat sigmoid types. We hypothesised that the determination of the sigmoid notch shape (SNS) depends on the level of the transverse CT plane on the axial axis of the distal radius. The aim of this study was to determine and compare the transverse SNS on different axial CT levels in the same wrist.

Methods: The transverse SNS of 53 participants were independently qualitatively classified by two researchers in accordance with the four morphologies described by Tolat et al. The SNS was determined at two levels on the axial axis of the distal radius; at the level of the most prominent part of Lister tubercle, determined on the sagittal plane and at the level of the ‘smallest distance between the ulnar head and sigmoid notch’ (SDUS).

Results: Forty-seven percent of the wrists demonstrated different SNS types according to Tolat classification, depending on the axial level of the CT scan. Interobserver agreement on the transverse sigmoid shape was 87% at Lister tubercle and 85% at SDUS, which can both be interpreted as ‘excellent’.

Conclusions: Despite an excellent interobserver agreement, 47% of the study population had different transverse sigmoid notch types within the same wrist. We, therefore, conclude that Tolat transverse sigmoid classification may not be useful for the description of potential pathology in relation to the sigmoid notch morphology.
Fracture length data for geothermal applications
Authors: Forstner Stephanie R. , Corrêa Rodrigo , Wang Qiqi , Laubach Stephen E.
Published: October 2024

Fracture lengths govern permeability and are unknowns in geothermal assessment. Along their lengths, fracture widths vary due to growth by linkage. Under the influence of diagenesis, narrow widths seal, breaking porosity continuity and reducing open length. The largest range of widths and thus susceptibility to fill occurs where fractures are linked by narrow segments. Outcrops of a geothermal target, Cambrian Potsdam quartz arenite, contain opening-mode fractures having lengths spanning five orders of magnitude from 0.082 mm to 17.9 m. Combined lengths measured at a range of scales can be described by power laws, but at a given image resolution, lengths are best fit by exponential functions. Owing to preferential sealing of small fractures, open fractures follow exponential functions, but values depend on rules for designating fractures as continuous. En échelon segments, offset 10 mm, are connected by narrow fractures or microfractures (hard linked) not evident on outcrop 1 m-elevation LiDAR or 30 m-height drone images. A rule that identifies where narrow and likely connected segments are located can yield lengths meaningful for flow simulation. Depending on diagenesis, continuity rules can halve or double average and maximum length values. Length values from outcrop for geothermal applications should be adjusted based on wellsite-specific diagenesis information.
Fracturability of shale based on rock brittleness and natural fracture tensile reactivation
Authors: Zhao Zhihong , Wu Tianyu , Liang Hao , Guo Jianchun , Zhou Xiaoyu
Published: October 2024

Exploration and development practices have proved that fracturability evaluation is the primary basis for successful fracturing operations. Current studies mainly rely on using traditional physical parameters to evaluate shale fracturability. However, fracture morphology and the extension of natural fractures during fracturing are also crucial for shale fracturability evaluation. In this study, correlations between factors and rock fracture complexity and the degree of natural fracture opening were analysed using 40 sets of related experiments, and a new method is proposed for shale fracturability evaluation that considers Young's modulus, the shear expansion angle, residual strain, the approach angle and the stress variance coefficient. Finally, taking the shale gas field in the Sichuan Basin as an example, a comprehensive evaluation model of shale fracturability was established using the grey correlation method combined with core experimental data. One well was selected in order to compare and analyse the fracturability profile with the stimulated reservoir volume. The results show that peak strain has the most significant influence on shale fracture complexity, followed by the shear expansion angle and Young's modulus. The approach angle and the stress difference coefficient affect the degree of natural fracture opening at the same time. The model is accurate because the fracturability values match the study block's stimulated reservoir volume data. This new method of shale fracturability evaluation provides important technology for predicting the fracturability of shale gas reservoirs and optimizing operation schemes.
SMT2Test: From SMT Formulas to Effective Test Cases
Authors: Zhang Chengyu , Su Zhendong
Published: October 2024

One of the primary challenges in software testing is generating high-quality test inputs and obtaining corresponding test oracles. This paper introduces a novel methodology to mitigate this challenge in testing program verifiers by employing SMT (Satisfiability Modulo Theories) formulas as a universal test case generator. The key idea is to transform SMT formulas into programs and link the satisfiability of the formulas with the safety property of the programs, allowing the satisfiability of the formulas to act as a test oracle for program verifiers. This method was implemented as a framework named SMT2Test, which enables the transformation of SMT formulas into Dafny and C programs. An intermediate representation was designed to augment the flexibility of this framework, streamlining the transformation for other programming languages and fostering modular transformation strategies. We evaluated the effectiveness of SMT2Test by finding defects in two program verifiers: the Dafny verifier and CPAchecker. Utilizing the SMT2Test framework with the SMT formulas from the SMT competition and SMT solver fuzzers, we discovered and reported a total of 14 previously unknown defects in these program verifiers that were not found by previous methods. After reporting, all of them have been confirmed, and 6 defects have been fixed. These findings show the effectiveness of our method and imply its potential application in testing other programming language infrastructures.
libLISA: Instruction Discovery and Analysis on x86-64
Authors: Craaijo Jos , Verbeek Freek , Ravindran Binoy
Published: October 2024

Even though heavily researched, a full formal model of the x86-64 instruction set is still not available. We present libLISA, a tool for automated discovery and analysis of the ISA of a CPU. This produces the most extensive formal x86-64 model to date, with over 118000 different instruction groups. The process requires as little human specification as possible: specifically, we do not rely on a human-written (dis)assembler to dictate which instructions are executable on a given CPU, or what their in- and outputs are. The generated model is CPU-specific: behavior that is "undefined" is synthesized for the current machine. Producing models for five different x86-64 machines, we mutually compare them, discover undocumented instructions, and generate instruction sequences that are CPU-specific. Experimental evaluation shows that we enumerate virtually all instructions within scope, that the instructions' semantics are correct w.r.t. existing work, and that we improve existing work by exposing bugs in their handwritten models.
SparseAuto: An Auto-scheduler for Sparse Tensor Computations using Recursive Loop Nest Restructuring
Authors: Dias Adhitha , Anderson Logan , Sundararajah Kirshanthan , Pelenitsyn Artem , Kulkarni Milind
Published: October 2024

Automated code generation and performance enhancements for sparse tensor algebra have become essential in many real-world applications, such as quantum computing, physical simulations, computational chemistry, and machine learning. General sparse tensor algebra compilers are not always versatile enough to generate asymptotically optimal code for sparse tensor contractions. This paper shows how to generate asymptotically better schedules for complex sparse tensor expressions using kernel fission and fusion. We present generalized loop restructuring transformations to reduce asymptotic time complexity and memory footprint.

Furthermore, we present an auto-scheduler that uses a partially ordered set (poset)-based cost model that uses both time and auxiliary memory complexities to prune the search space of schedules. In addition, we highlight the use of Satisfiability Module Theory (SMT) solvers in sparse auto-schedulers to approximate the Pareto frontier of better schedules to the smallest number of possible schedules, with user-defined constraints available at compile-time. Finally, we show that our auto-scheduler can select better-performing schedules and generate code for them. Our results show that the auto-scheduler provided schedules achieve orders-of-magnitude speedup compared to the code generated by the Tensor Algebra Compiler (TACO) for several computations on different real-world tensors.
Fully Verified Instruction Scheduling
Authors: Yang Ziteng , Shirako Jun , Sarkar Vivek
Published: October 2024

CompCert project, the state-of-the-art compiler that achieves the first end-to-end formally verified C compiler, does not support fully verified instruction scheduling. Instead, existing research that works on such topics only implements translation validation. This means they do not have direct formal proof that the scheduling algorithm is correct, but only a posterior validation to check each compiling case. Using such a method, CompCert accepts a valid C program and compiles correctly only when the untrusted scheduler generates a correct result. However, it does not guarantee the complete correctness of the scheduler. It also causes compile-time validation overhead in the view of runtime performance.

In this work, we present the first achievement in developing a mechanized library for fully verified instruction scheduling while keeping the proof workload acceptably lightweight. The idea to reduce the proof length is to exploit a simple property that the topological reordering of a topological sorted list is equal to a sequence of swapping adjacent unordered elements. Together with the transitivity of semantic simulation relation, the only burden will become proving the semantic preservation of a transition that only swaps two adjacent independent instructions inside one block. After successfully proving this result, proving the correctness of any new instruction scheduling algorithm only requires proof that it preserved the syntax-level dependence among instructions, instead of reasoning about semantics details every time. We implemented a mechanized library of such methods in the Coq proof assistant based on CompCert's library as a framework and used the list scheduling algorithm as a case study to show the correctness can be formally proved using our theory.

We show that with our method that abstracts away the semantics details, it is flexible to implement any scheduler that reorders instructions with little extra proof burden. Our scheduler in the case study also abstracts away the outside scheduling heuristic as a universal parameter so it is flexible to modify without touching any correctness proof.
Computing Precise Control Interface Specifications
Authors: Campbell Eric Hayden , Hojjat Hossein , Foster Nate
Published: October 2024

Verifying network programs is challenging because of how they divide labor: the control plane computes high level routes through the network and compiles them to device configurations, while the data plane uses these configurations to realize the desired forwarding behavior. In practice, the correctness of the data plane often assumes that the configurations generated by the control plane will satisfy complex specifications. Consequently, validation tools such as program verifiers, runtime monitors, fuzzers, and test-case generators must be aware of these
control interface specifications
(ci-specs) to avoid raising false alarms. In this paper, we propose the first algorithm for computing
precise
ci-specs for network data planes. Our specifications are designed to be
efficiently monitorable
—concretely, checking that a fixed configuration satisfies a ci-spec can be done in polynomial time. Our algorithm, based on modular program instrumentation, quantifier elimination, and a path-based analysis, is more expressive than prior work, and is applicable to practical network programs. We describe an implementation and show that ci-specs computed by our tool are useful for finding real bugs in real-world data plane programs.
Effects and Coeffects in Call-by-Push-Value
Authors: Torczon Cassia , Suárez Acevedo Emmanuel , Agrawal Shubh , Velez-Ginorio Joey , Weirich Stephanie
Published: October 2024

Effect and coeffect tracking integrate many types of compile-time

analysis, such as cost, liveness, or dataflow, directly into a language's type

system. In this paper, we investigate the addition of effect and coeffect

tracking to the type system of call-by-push-value (CBPV), a computational

model useful in compilation for its isolation of effects and for its ability

to cleanly express both call-by-name and call-by-value computations. Our

main result is effect-and-coeffect soundness, which asserts that the

type system accurately bounds the effects that the program may trigger

during execution and accurately tracks the demands that the program may make

on its environment. This result holds for two different dynamic semantics: a

generic one that can be adapted for different coeffects and one that is

adapted for reasoning about resource usage. In particular, the second

semantics discards the evaluation of unused values and pure computations

while ensuring that effectful computations are always evaluated, even if

their results are not required. Our results have been mechanized using

the Coq proof assistant.
Tachis: Higher-Order Separation Logic with Credits for Expected Costs
Authors: Haselwarter Philipp G. , Li Kwing Hei , de Medeiros Markus , Gregersen Simon Oddershede , Aguirre Alejandro , Tassarotti Joseph , Birkedal Lars
Published: October 2024

We present Tachis, a higher-order separation logic to reason about the expected cost of probabilistic programs. Inspired by the uses of time credits for reasoning about the running time of deterministic programs, we introduce a novel notion of probabilistic cost credit. Probabilistic cost credits are a separation logic resource that can be used to pay for the cost of operations in programs, and that can be distributed across all possible branches of sampling instructions according to their weight, thus enabling us to reason about expected cost. The representation of cost credits as separation logic resources gives Tachis a great deal of flexibility and expressivity. In particular, it permits reasoning about amortized expected cost by storing excess credits as potential into data structures to pay for future operations. Tachis further supports a range of cost models, including running time and entropy usage. We showcase the versatility of this approach by applying our techniques to prove upper bounds on the expected cost of a variety of probabilistic algorithms and data structures, including randomized quicksort, hash tables, and meldable heaps. All of our results have been mechanized using Coq, Iris, and the Coquelicot real analysis library.
Scaling Abstraction Refinement for Program Analyses in Datalog using Graph Neural Networks
Authors: Yan Zhenyu , Zhang Xin , Di Peng
Published: October 2024

Counterexample-guided abstraction refinement (CEGAR) is a popular approach for automatically selecting abstractions with high precision and low time costs. Existing works cast abstraction refinements as constraint-solving problems. Due to the complexity of these problems, they cannot be scaled to large programs or complex analyses. We propose a novel approach that applies graph neural networks to improve the scalability of CEGAR for Datalog-based program analyses. By constructing graphs directly from the Datalog solver’s calculations, our method then uses a neural network to score abstraction parameters based on the information in these graphs. Then we reform the constraint problems such that the constraint solver ignores parameters with low scores. This in turn reduces the solution space and the size of the constraint problems. Since our graphs are directly constructed from Datalog computation without human effort, our approach can be applied to a broad range of parametric static analyses implemented in Datalog. We evaluate our approach on a pointer analysis and a typestate analysis and our approach can answer 2.83× and 1.5× as many queries as the baseline approach on large programs for the pointer analysis and the typestate analysis, respectively.
Reward Augmentation in Reinforcement Learning for Testing Distributed Systems
Authors: Borgarelli Andrea , Enea Constantin , Majumdar Rupak , Nagendra Srinidhi
Published: October 2024

Bugs in popular distributed protocol implementations have been the source of many downtimes in popular internet services. We describe a randomized testing approach for distributed protocol implementations based on reinforcement learning. Since the natural reward structure is very sparse, the key to successful exploration in reinforcement learning is reward augmentation. We show two different techniques that build on one another. First, we provide a decaying exploration bonus based on the discovery of new states---the reward decays as the same state is visited multiple times. The exploration bonus captures the intuition from coverage-guided fuzzing of prioritizing new coverage points; in contrast to other schemes, we show that taking the maximum of the bonus and the Q-value leads to more effective exploration. Second, we provide waypoints to the algorithm as a sequence of predicates that capture interesting semantic scenarios. Waypoints exploit designer insight about the protocol and guide the exploration to "interesting" parts of the state space. Our reward structure ensures that new episodes can reliably get to deep interesting states even without execution caching. We have implemented our algorithm in Go. Our evaluation on three large benchmarks (RedisRaft, Etcd, and RSL) shows that our algorithm can significantly outperform baseline approaches in terms of coverage and bug finding.
Imperative Compositional Programming: Type Sound Distributive Intersection Subtyping with References via Bidirectional Typing
Authors: Ye Wenjia , Sun Yaozhu , Oliveira Bruno C. d. S.
Published: October 2024

Compositional programming is a programming paradigm that emphasizes modularity and is implemented in the CP programming language. The foundations for compositional programming are based on a purely functional variant of System F with intersection types, called Fi+, which includes distributivity rules for subtyping.

This paper shows how to extend compositional programming and CP with mutable references, enabling a modular, imperative compositional programming style. A technical obstacle solved in our work is the interaction between distributive intersection subtyping and mutable references. Davies and Pfenning [2000] studied this problem in standard formulations of intersection type systems and argued that, when combined with references, distributive subtyping rules lead to type unsoundness. To recover type soundness, they proposed dropping distributivity rules in subtyping. CP cannot adopt this solution, since it fundamentally relies on distributivity for modularity. Therefore, we revisit the problem and show that, by adopting bidirectional typing, a more lightweight and type sound restriction is possible: we can simply restrict the typing rule for references. This solution retains distributivity and an unrestricted intersection introduction rule. We present a first calculus, based on Davies and Pfenning's work, which illustrates the generality of our solution. Then we present an extension of Fi+ with references, which adopts our restriction and enables imperative compositional programming. We implement an extension of CP with references and show how to model a modular live-variable analysis in CP. Both calculi and their proofs are formalized in the Coq proof assistant.