Miracle-dz/UniFAR-FTUs huggingface dataset:
Closing the Performance Gap between Leveling and Tiering Compaction via Bundle Compaction

So far, most LSM-tree-based storage engines adopt either leveling or tiering compaction. We note that while leveling compaction can deliver high search performance and low space amplification, it has a high rate of write amplification (therefore delivering poor write performance). On the other hand, tiering compaction has a low rate of write amplification (therefore delivering good write performance) but has poor search performance and high space amplification. Aiming to close the performance gap between leveling and tiering databases, this paper proposes a new storage engine called B+LSM. The novel ideas of B+LSM lie in two aspects: (1) B+LSM replaces the underlying level structure of LSM-tree with a B+-tree-like tree, and each tree node is defined as a Bundle Compaction Unit (BCU), whose size is allowed to be dynamically changed with workload statistics to balance read and write performance. (2) B+LSM proposes a new node-grained compaction scheme called Bundle Compaction. Bundle compaction is always triggered to merge all the data within a BCU node, partition them into bundles, and then send bundles to the children. Such a compaction scheme can take advantage of leveling and tiering compaction by auto-tuning the size of BCU nodes. We implemented B+LSM and compared it with LevelDB, RocksDB, PebblesDB, and L2SM on the YCSB workloads. The results show that B+LSM can achieve high time performance and reduce space amplification on both static and dynamic workloads.
Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly

Ebola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 (BSL-4) laboratories hinders experimental work to advance our understanding of EBOV and evaluation of treatment. In this work, we use a computational model to study the assembly and budding process of EBOV and evaluate the effect of fendiline on these processes. Our results indicate that the assembly of VP40 filaments may follow the nucleation-elongation theory, as it is critical to maintain a pool of VP40 dimer for the maturation and production of virus-like particles (VLPs). We further find that the nucleation-elongation process can also be influenced by phosphatidylserine (PS), which can complicate the efficacy of fendiline, a drug that lowers cellular PS levels. We observe that fendiline may increase VLP production at earlier time points (24 h) and under low concentrations (≤ 2 μM). But this effect is transient and does not change the conclusion that fendiline generally decreases VLP production. We also conclude that fendiline can be more efficient at the stage of VLP budding relative to earlier phases. Combination therapy with a VLP budding step-targeted drug may further increase the treatment efficiency of fendiline. Finally, we also show that fendiline has higher efficacy when VP40 expression is high. While these are single-cell level results based on the VP40 system, it points out a potential way of fendiline application affecting EBOV assembly, which can be further tested in experimental studies with multiple EBOV proteins or live virus. Importance EBOV infection can cause deadly hemorrhagic fever, which has a mortality rate around 90% without treatment. The recent outbreaks in Uganda and Democratic Republic of the Congo illustrate its treat to human health. Though two antibody-based treatments are approved, mortality rates in the last outbreak is still higher than 30%. This can partly be due to the requirement of advanced medical facilities for current treatments. As a result, it is very important to develop and evaluate new therapies for EBOV infection, especially those can be easily applied in the developing world. The significance of our research is that we evaluate the potential treatment effect of fendiline on EBOV infection in the VP40 system with a computational approach, which both greatly saves time and lowers cost compared to traditional experimental studies, and provides innovative new tools to study viral protein dynamics.
Functional architecture of the aging brain

The intrinsic functional connectome can reveal how a lifetime of learning and lived experience is represented in the functional architecture of the aging brain. We investigated whether network dedifferentiation, a hallmark of brain aging, reflects a global shift in network dynamics, or comprises network-specific changes that reflect the changing landscape of aging cognition. We implemented a novel multi-faceted strategy involving multi-echo fMRI acquisition and de-noising, individualized cortical parcellation, and multivariate (gradient and edge-level) functional connectivity methods. Twenty minutes of resting-state fMRI data and cognitive assessments were collected in younger (n=181) and older (n=120) adults. Dimensionality in the BOLD signal was lower for older adults, consistent with global network dedifferentiation. Functional connectivity gradients were largely age-invariant. In contrast, edge-level connectivity showed widespread changes with age, revealing discrete, network-specific dedifferentiation patterns. Visual and somatosensory regions were more integrated within the functional connectome; default and frontoparietal regions showed greater coupling; and the dorsal attention network was less differentiated from transmodal regions. Associations with cognition suggest that the formation and preservation of integrated, large-scale brain networks supports complex cognitive abilities. However, into older adulthood, the connectome is dominated by large-scale network disintegration, global dedifferentiation and network-specific dedifferentiation associated with age-related cognitive change.
Common clinicopathological and immunological features of sarcomatoid carcinoma across organs: A histomorphology‐based cross‐organ study

Sarcomatoid carcinoma (SC), which can occur in any organ, is a rare disease. To elucidate common characteristics of SC beyond organs, we evaluated clinicopathological and immunological features of SC defined by the single histological criterion beyond organs compared to randomly matched conventional carcinoma (non‐SC) adjusted for the disease stage. Immunological features were assessed by multiplex immunohistochemistry, comparing immune cell density in tumor tissues and tumor programmed death‐ligand 1 (PD‐L1) expression. A total of 101 patients with SC or non‐SC (31 lung, 19 esophagus, 22 pancreas, 15 liver, 4 bile duct, 6 kidney, 2 uterus and 2 ovary) were identified among 7197 patients who underwent surgery at our institute (1997‐2020). SC was significantly associated with worse survival (HR: 1.571; 95% CI: 1.084‐2.277; P = .017). The frequency of postoperative progression within 6 months was significantly higher for SC patients (54% vs 28%; P = .002). The immune profiling revealed the densities of CD8+ T cells (130 vs 72 cells/mm2; P = .004) and tumor‐associated macrophages (566 vs 413 cells/mm2; P < .0001) and the tumor PD‐L1 expression score (40% vs 5%; P < .0001) were significantly higher in SCs than in non‐SCs. Among 73 SC patients with postoperative progression, multivariate Cox regression analysis showed that immunotherapy tended to be associated with favorable survival (HR: 0.256; 95% CI: 0.062‐1.057; P = .060). Collectively, SCs shared clinicopathological and immunological features across organs. Our study can initiate to standardize the pathological definition of SC and provide a rationale for the investigation and development for this rare disease in a cross‐organ manner.
The high prevalence of occult hepatitis B infections among the partners of chronically infected HBV blood donors emphasizes the potential residual risk to blood safety

A small percentage of couples who regularly donated blood in China tested positive for HBsAg. Although it is well known that blood donors can acquire hepatitis B virus (HBV) infection from a chronically infected sexual partner, the prevalence of occult hepatitis B infections (OBIs) among blood donations from partners of HBV‐infected chronically infected spouses and the risk to blood safety remain poorly understood. Among 212 763 blood donors, 54 pairs of couples (108 donations) were enrolled because one partner tested positive for HBsAg. Several molecular and serological examinations were conducted. The origin of HBV transmission between sexual partners was investigated further. Also evaluated was the potential risk of HBV infection with OBIs. We identified 10 (10/54, 18.6%) sexual partners of chronically infected HBV donors who were positive for HBV DNA, including five samples (9.3%) with OBIs, of which 3 (3/54, 5.6%, 1 in 70 921 donations) passed the routine blood screening tests. Seven of the 10 HBV‐DNA‐positive couples contracted the virus possibly through sexual or close contact. Among infected couples, immune escape mutations were observed. A high prevalence of OBIs was found among the partners of chronically infected HBV blood donors, posing a potential threat to blood safety.
Hypoconnectivity within the cingulo‐opercular network in patients with mild cognitive impairment in Chinese communities

At rest, the brain's higher cognitive systems engage in correlated activity patterns, forming networks. With mild cognitive impairment (MCI), it is essential to understand how functional connectivity within and between resting‐state networks changes. This study used resting‐state functional connectivity to identify significant differences within and between the cingulo‐opercular network (CON) and default mode network (DMN).
Differential sensory and immune gene evolution in sea turtles with contrasting demographic and 1 life histories 2 3

3 Blair P. Bentley , Tomás Carrasco-Valenzuela, Elisa K. S. Ramos, Harvinder Pawar, Larissa Souza 4 Arantes, Alana Alexander, Shreya M. Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel, 5 Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano Silva, Giulio Formenti, Kerstin Howe, William 6 Chow, Alan Tracey, Yumi Sims, Sarah Pelan, Jonathan Wood, Justin R. Perrault, Kelly Stewart, Scott R. 7 Benson, Yaniv Levy, Erica V. Todd, H. Bradley Shaffer, Peter Scott, Brian T. Henen, Robert W. 8 Murphy, David W. Mohr, Alan F. Scott, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Françoise 9 Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho Antunes, Yaron Tikochinski, 10 Peter H. Dutton, Olivier Fedrigo, Eugene W. Myers, Erich D. Jarvis, Camila J. Mazzoni*, and Lisa 11 M. Komoroske* 12
Changes in process and outcome for ST elevation myocardial infarction in central China from 2011 to 2018

Abstract Background: Limited data are available on the changes in the quality of care for ST elevation myocardial infarction (STEMI) during China's health system reform from 2009 to 2020. This study aimed to assess the changes in care processes and outcome for STEMI patients in Henan province of central China between 2011 and 2018. Methods: We compared the data from the Henan STEMI survey conducted in 2011–2012 (n = 1548, a cross-sectional study) and the Henan STEMI registry in 2016–2018 (n = 4748, a multicenter, prospective observational study). Changes in care processes and in-hospital mortality were determined. Process of care measures included reperfusion therapies, aspirin, P2Y12 antagonists, β-blockers, angiotensin-converting enzyme inhibitors or angiotensin receptor blockers, and statins. Therapy use was analyzed among patients who were considered ideal candidates for treatment. Results: STEMI patients in 2016–2018 were younger (median age: 63.1 vs. 63.8 years) with a lower proportion of women (24.4% [1156/4748] vs. 28.2% [437/1548]) than in 2011–2012. The composite use rate for guideline-recommended treatments increased significantly from 2011 to 2018 (60.9% [5424/8901] vs. 82.7% [22,439/27,129], P <0.001). The proportion of patients treated by reperfusion within 12 h increased from 44.1% (546/1237) to 78.4% (2698/3440) (P <0.001) with a prolonged median onset-to-first medical contact time (from 144 min to 210 min, P <0.001). The use of antiplatelet agents, statins, and β-blockers increased significantly. The risk of in-hospital mortality significantly decreased over time (6.1% [95/1548] vs. 4.2% [198/4748], odds ratio [OR]: 0.67, 95% confidence interval [CI]: 0.50–0.88, P = 0.005) after adjustment. Conclusions: Gradual implementation of the guideline-recommended treatments in STEMI patients from 2011 to 2018 has been associated with decreased in-hospital mortality. However, gaps persist between clinical practice and guideline recommendation. Public awareness, reperfusion strategies, and construction of chest pain centers need to be further underscored in central China.
Single-linkage molecular clustering of viral pathogens

Introduction Public health faces the ongoing mission of safeguarding the population’s health against various infectious diseases caused by a great number of pathogens. Epidemiology is an essential discipline in this field. With the rise of more advanced technologies, new tools are emerging to enhance the capability to intervene and control an epidemic. Among these approaches, molecular clustering comes forth as a promising option. However, appropriate genetic distance thresholds for defining clusters are poorly explored in contexts outside of Human Immunodeficiency Virus-1 (HIV-1). Methods In this work, using the well-used pairwise Tamura-Nei 93 (TN93) distance threshold of 0.015 for HIV-1 as a point of reference for molecular cluster properties of interest, we perform molecular clustering on whole genome sequence datasets from HIV-1, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Zaire ebolavirus, and Mpox virus, to explore potential pairwise distances thresholds for these other viruses. Results We found the following pairwise TN93 distance thresholds as potential candidates for use in molecular clustering: 0.00016 (3 mutations) for Ebola, 0.00014 (4 mutations) for SARS-CoV-2, and 0.0000051 (1 mutation) for Mpox. Conclusion This study provides valuable information for epidemic control strategies, and public health efforts in managing infectious diseases caused by these viruses. The identified pairwise distance thresholds for molecular clustering can serve as a foundation for future research and intervention to combat epidemics effectively. Availability and implementation All relevant data and results can be found in the following repository: https://github.com/Niema-Lab/ENLACE-2023
Gbx2 controls amacrine cell dendrite stratification through Robo1/2 receptors

Within the neuronal classes of the retina, amacrine cells (ACs) exhibit the greatest neuronal diversity in morphology and function. We show that the selective expression of the transcription factor Gbx2 is required for cell fate specification and dendritic stratification of an individual AC subtype in the mouse retina. We identify Robo1 and Robo2 as downstream effectors that when deleted, phenocopy the dendritic misprojections seen in Gbx2 mutants. Slit1 and Slit2, the ligands of Robo receptors, are localized to the OFF layers of the inner plexiform layer where we observe the dendritic misprojections in both Gbx2 and Robo1/2 mutants. We show that Robo receptors also are required for the proper dendritic stratification of additional AC subtypes, such as Vglut3+ ACs. These results show both that Gbx2 functions as a terminal selector in a single AC subtype and identify Slit-Robo signaling as a developmental mechanism for ON-OFF pathway segregation in the retina.
Dynamics of cerebrospinal fluid pressure alterations and bilateral transverse–sigmoid sinus morphologies in Asian patients with venous pulsatile tinnitus

Objective This study was performed to investigate the dynamics of intracranial pressure (ICP) alterations and bilateral transverse–sigmoid sinus morphologies in patients with venous pulsatile tinnitus (PT). Methods This retrospective study involved 27 patients with venous PT associated with sigmoid sinus wall anomalies. ICP and ICP metrics were measured by cerebrospinal fluid manometry and internal jugular vein compression tests. Correlation analysis was performed to determine the statistical correlation between ICP and the morphological metrics. Results The mean ICP was 212.5 ± 47.3 mmH2O. The median Δ ICP total was 130 (range, 55–150) mmH2O. The Δ ICP total was linearly correlated with the open lumbar pressure, and a significant difference was found between patients with normal and elevated cerebrospinal fluid pressure. The Δ ICP difference was linearly correlated with the Len difference and Vol difference . Δ ICP was linearly correlated with Len difference . Conclusions Complete obstruction of flow patency should be avoided in patients with low ICP and large volumetric/patency differences in the bilateral transverse–sigmoid sinus systems.
A Radiostereometric Analysis of Tendon Migration After Arthroscopic and Mini-Open Biceps Tenodesis: Interference Screw Versus Single Suture Anchor Fixation

Background: Studies suggest that similar clinical results are achieved via arthroscopic and open biceps tenodesis (BT) techniques. Purpose: To quantify the postoperative migration of the BT construct between arthroscopic suprapectoral BT (ASPBT) and open subpectoral BT (OSPBT) techniques via interference screw (IS) or single-suture suture anchor (SSSA) fixation using radiostereometric analysis. Study Design: Cohort study; Level of evidence, 2. Methods: Distal migration of the biceps tendon after OSPBT with a polyetheretherketone IS, OSPBT with 1 SSSA, ASPBT with polyetheretherketone IS, and ASPBT with 2 SSSAs was measured prospectively. Patients with symptomatic biceps tendinopathy and preoperative patient-reported outcome measures (PROMs) including Constant-Murley subjective, Single Assessment Numeric Evaluation, or Patient-Reported Outcomes Measurement Information System–Upper Extremity scores were included. A tantalum bead was sutured on the proximal end of the long head of the biceps tendon before fixation of tendon tissue. Anteroposterior radiographs were performed immediately postoperatively, at 1 week, and at 3 months. Bead migration was measured, and preoperative PROMs were compared with those at latest follow-up. Results: Of 115 patients, 94 (82%) were available for final follow-up. IS fixation yielded the least tendon migration with no difference between the open and arthroscopic approaches (4.31 vs 5.04 mm; P = .70). Fixation with 1 suture anchor demonstrated significantly greater migration than that achieved with an IS at both 1 week (6.47 vs 0.1 mm, 6.47 vs 1.75 mm, P < .001;) and 3 months (14.76 vs 4.31 mm, 14.76 vs 5.04 mm, P < .001) postoperatively. Two-suture anchor fixation yielded significantly greater migration than IS fixation at 1 week (7.02 vs 0.1 mm, P < .001; 7.02 vs 1.75 mm, P = .003) but not 3 months postoperatively (8.06 vs 4.31 mm, P = .10; 8.06 vs 5.04 mm, P = .07). Four patients with suture anchor fixation (3 patients in the OSPBT 1 SSSA group, 9.4%, and 1 patient in the ASPBT 2 SSSAs group, 3.8%) developed a Popeye deformity, whereas no Popeye deformities occurred in the IS groups. Mean 3-month bead migration in patients with and without a Popeye deformity was 60.8 and 11.2 mm, respectively (P < .0001). PROMs did not differ among groups at final follow-up. Conclusion: Interference screw fixation yielded the least tendon migration whether achieved arthroscopically or open. The available data indicated that fixation with 1 SSSA but not 2 SSSAs resulted in significantly greater migration than that achieved with an IS. Despite variations in tendon migration, PROMs were similar among all groups. When SSSAs are used, tendon migration may be minimized by using ≥2 anchors.
China's Muslim Hui Community: Migration, Settlement and Sects

This is a reconstruction of the history of the Muslim community in China known today as the Hui or often as the Chinese Muslims as distinct from the Turkic Muslims such as the Uyghurs. It traces their history from the earliest period of Islam in China up to the present day, but with particular emphasis on the effects of the Mongol conquest on the transfer of central Asians to China, the establishment of stable immigrant communities in the Ming dynasty and the devastating insurrections against the Qing state during the nineteenth century. Sufi and other Islamic orders such as the Ikhwani have played a key role in establishing the identity of the Hui, especially in north-western China, and these are examined in detail as is the growth of religious education and organisation and the use of the Arabic and Persian languages. The relationship between the Chinese Communist Party and the Hui as an officially designated nationality and the social and religious life of Hui people in contemporary China are also discussed.
Time correlations in KPZ models with diffusive initial conditions

Temporal correlation for randomly growing interfaces in the KPZ universality class is a topic of recent interest. Most of the works so far have been concentrated on the zero temperature model of exponential last passage percolation, and three special initial conditions, namely droplet, flat and stationary. We focus on studying the time correlation problem for generic random initial conditions with diffusive growth. We formulate our results in terms of the positive temperature exactly solvable model of the inverse-gamma polymer and obtain up to constant upper and lower bounds for the correlation between the free energy of two polymers whose endpoints are close together or far apart. Our proofs apply almost verbatim to the zero temperature set-up of exponential LPP and are valid for a broad class of initial conditions. Our work complements and completes the partial results obtained in (Ferrari-Occelli'19), following the conjectures of (Ferrari-Spohn'16). Moreover, our arguments rely on the one-point moderate deviation estimates which have recently been obtained using stationary polymer techniques and thus do not depend on complicated exact formulae.
A Revised Correlation of Silurian Rocks in the British Isles

A discussion of Silurian stratigraphical classification is followed by detailed comments upon the correlation of Llandovery, Wenlock, Ludlow and Přidoli rocks throughout the British Isles. Correlation charts show selected successions in Wales, the Welsh Borderland, Northwest England, Scotland and Ireland. The concealed Silurian rocks of Eastern and Southern England are considered relatively briefly, as are the enigmatic records from Cornwall. Finally, a chart and short commentary serve to correlate the Silurian successions of New York, Anticosti Island, Oslo, Gotland, Estonia, Thuringia, Bohemia, Podolia and Kazakhstan with the international standard employed here for the British Isles. There is an extensive bibliography.