Miracle-dz/UniFAR-FTUs huggingface dataset:
H-EMD: A Hierarchical Earth Mover’s Distance Method for Instance Segmentation

Deep learning (DL) based semantic segmentation methods have achieved excellent performance in biomedical image segmentation, producing high quality probability maps to allow extraction of rich instance information to facilitate good instance segmentation. While numerous efforts were put into developing new DL semantic segmentation models, less attention was paid to a key issue of how to effectively explore their probability maps to attain the best possible instance segmentation. We observe that probability maps by DL semantic segmentation models can be used to generate many possible instance candidates, and accurate instance segmentation can be achieved by selecting from them a set of “optimized” candidates as output instances. Further, the generated instance candidates form a well-behaved hierarchical structure (a forest), which allows selecting instances in an optimized manner. Hence, we propose a novel framework, called hierarchical earth mover’s distance (H-EMD), for instance segmentation in biomedical 2D+time videos and 3D images, which judiciously incorporates consistent instance selection with semantic-segmentation-generated probability maps. H-EMD contains two main stages: (1) instance candidate generation: capturing instance-structured information in probability maps by generating many instance candidates in a forest structure; (2) instance candidate selection: selecting instances from the candidate set for final instance segmentation. We formulate a key instance selection problem on the instance candidate forest as an optimization problem based on the earth mover’s distance (EMD), and solve it by integer linear programming. Extensive experiments on eight biomedical video or 3D datasets demonstrate that H-EMD consistently boosts DL semantic segmentation models and is highly competitive with state-of-the-art methods.
The need for socket preservation: a systematic review

The aim of this study was to evaluate the clinical need and impact of socket preservation to protect the bone for future dental implant placement. Moreover, we aimed to list down various methods of socket preservation by going through randomized clinical trials. We searched PubMed, Google Scholar, and Cochrane databases for all relevant publications, where researchers compared various methods and tools for socket preservation. All eight randomized controlled trials mentioned several methods that are helpful in preserving bone levels both horizontally and vertically. The studies included in this systematic review demonstrate that each material has certain efficacy in preserving the socket after tooth extraction for future implant placement. Socket preservation methods and materials are effective in preparing patients for future prostheses.
The Association Between Payer Source and Traumatic Brain Injury Rehabilitation Outcomes: A TBI Model Systems Study

Objective: To examine the relationship between payer source for acute rehabilitation, residential median household income (MHI), and outcomes at rehabilitation discharge after traumatic brain injury (TBI). Setting: Acute inpatient rehabilitation facilities. Participants: In total, 8558 individuals enrolled in the Traumatic Brain Injury Model Systems (TBIMS) National Database who were admitted to inpatient rehabilitation between 2006 and 2019 and were younger than 64 years. Design: Secondary data analysis from a multicenter longitudinal cohort study. Main Measures: Payer source was divided into 4 categories: uninsured, public insurance, private insurance, and workers' compensation/auto. Relationships between payer source with residential MHI, rehabilitation length of stay (RLOS), and the FIM Instrument at discharge were examined. Covariates included age, injury severity, FIM at admission, and a number of sociodemographic characteristics including minority status, preinjury limitations, education level, and employment status. Results: Individuals with workers' compensation/auto or private insurance had longer RLOS than uninsured individuals or those with public insurance after controlling for demographics and injury characteristics. An adjusted model controlling for demographics and injury characteristics showed a significant main effect of payer source on FIM scores at discharge, with the highest scores noted among those with workers' compensation/auto insurance. The main effect of payer source on FIM at discharge became nonsignificant after RLOS was added to the model as a covariate, suggesting a mediating effect of RLOS. Conclusion: Payer source was associated with preinjury residential MHI and predicted RLOS. While prior studies have demonstrated the effect of payer source on long-term outcomes due to lack of inpatient rehabilitation or quality follow-up care, this study demonstrated that individuals with TBI who are uninsured or have public insurance may be at risk for poorer functional status at the point of rehabilitation discharge than those with private insurance, particularly compared with those with workers' compensation/auto insurance. This effect may be largely driven by having a shorter length of stay in acute rehabilitation.
Multivariable prognostic model for heart failure in Chinese Han population‐based setting

The prognosis of heart failure (HF) depends on genetic predisposition, and recent studies have shown that impaired autophagy is involved in HF. This study was aimed to construct a prognostic model combining polygenetic background based on the autophagy pathway and other traditional risk factors (TRF) of HF prognosis.
Predictors of adverse events after endoscopic ultrasound-guided through-the-needle biopsy of pancreatic cysts: a recursive partitioning analysis

Background and study aims Endoscopic ultrasound-guided through-the-needle biopsy (TTNB) of pancreatic cystic lesions (PCLs) is associated with a non-negligible risk for adverse events (AEs). We aimed to identify the hierarchic interaction among independent predictors for TTNB-related AEs and to generate a prognostic model using recursive partitioning analysis (RPA). Patients and methods Multicenter retrospective analysis of 506 patients with PCLs who underwent TTNB. RPA of predictors for AEs was performed and the model was validated by means of bootstrap resampling. Results Mean cysts size was 36.7mm. Most common diagnoses were intraductal papillary mucinous neoplasm (IPMN, 45%), serous cystadenoma (18.8%), and mucinous cystadenoma (12.8%). Fifty-eight (11.5%) AEs were observed. At multivariate analysis, age (odds ratio [OR] 1.32, 1.09-2.14; p=0.05), number of TTNB passes (OR from 2.17, 1.32-4.34 to OR 3.16, 2.03-6.34 with the increase of the number of passes), complete aspiration of the cyst (OR 0.56, 0.31-0.95; p=0.02), and diagnosis of IPMN (OR 4.16, 2.27-7.69; p<0.001) were found to be independent predictors of AEs, as confirmed by logistic regression and random forest analyses. RPA identified three risk classes: high-risk (IPMN sampled with multiple microforceps passes, 28% AEs rate), low-risk (1.4% AE rate, including patients <64 years with other-than-IPMN diagnosis sampled with ≤2 microforceps passes and with complete aspiration of the cyst) and middle-risk class (6.1% AEs rate, including the remaining patients). Conclusion TTNB should be selectively used in the evaluation of patients with IPMN. The present model could be applied during patient selection as to optimize the benefit/risk of TTNB.
Demonstration of a compact deep UV Raman spatial heterodyne spectrometer for biologics analysis

Monoclonal antibodies and antibody fragments are increasingly important classes of biotherapeutics. However, these products are both challenging and expensive to manufacture. New process analytical technologies used to monitor these products during their manufacture are of significant interest. Deep UV Raman spectroscopy promises to provide the required specificity and accuracy, however instruments, have historically been large and complex. In this paper, a new deep UV Raman instrument is described using a solid‐state laser and a spatial heterodyne spectrometer. The instrument overcomes practical limitations of the technique and could readily be used for online measurement. A series of observations have been made of biopharmaceutical products, including immunoglobulin G and domain antibodies. Where high levels of both specificity and linearity when measuring samples of different concentration with a precision of better than 0.05 mg/mL has been demonstrated.
Power and Obstacle Aware 3D Clock Tree Synthesis

Clock Network Design (CDN) is a critical step while designing any Integrated-Circuits (ICs). It holds vital importance in the performance of entire circuit. Due to continuous scaling, 3D ICs stacked with TSV are gaining importance, with an objective to continue with the Moore's law. Through-SiliconVia (TSV) provides the vertical interconnection between two die, which allows the electrical signal to flow through it. 3D ICs has many advantages over conventional 2D planar ICs like reduced power, area, cost, wire-length etc. The proposed work is mainly focused on power reduction and obstacle avoidance for 3D ICs. Various techniques have already been introduced for minimizing clock power within specified clock constraints of the 3D CND network. Proposed 3D Clock Tree Synthesis (CTS) is a combination of various algorithms with an objective to meet reduction in power as well as avoidance of obstacle or blockages while routing the clock signal from one sink to other sink. These blockages like RAM, ROM, PLL etc. are fixed during the placement process. The work is carried out mainly in three stepsfirst is Generation of 3D Clock tree avoiding the blockages, then Buffering and Embedding and finally validating the results by SPICE simulation. The experimental result shows that our CTS approach results in significant 9% reduction in power as compare to the existing work.
Sudden Change of Joint Velocity During Fault Tolerant Operations for Redundant Manipulators

In order to reduce the sudden change,improve the motion stability of the manipulator and increase its operational accuracy in fault tolerance,this paper defines the sudden change in joint velocity as an index and a corresponding fault tolerant planning algorithm based on this index is proposed.Then an experiment platform is built up with a PowerCube manipulator and an Optotrak motion measurement system.And the trajectory error of the manipulator's end-effector caused by the sudden change is detected with this platform. Simulation results show that the sudden change in joint velocity does occur when a redundant manipulator per- form a fault olerant operation for locked joint failures.The algorithm proposed here can effectively minimize the sudden change.
Rehabilitation of Worn Dentition with Direct Resin Composite Restorations: A Case Report

The incidence of tooth wear has steadily increased in all Western populations during the past decades. A through-care strategy, extendable for a lifetime, has become crucial to prevent the extensive loss of sound dental structure and to make an eventual retreatment affordable in the long term. An interceptive treatment using resin composite materials and no-preparation approaches meets these requirements. Moreover, continual developments in digital dentistry makes possible to predict the treatment plan for the restorative rehabilitation of the mouth. The availability of digital resources allows clinicians to increase predictability for excellent esthetics and good functional results. This article provides a step-by-step description of a full-mouth additive rehabilitation achieved by employing digital workflows and direct resin composite restorations. A comprehensive functional and esthetic evaluation of the treatment is proposed and discussed.
Participation architectures for free and open-source software innovation

Free, Open-Source Software (FOSS) communities are centered on software product innovation. But the social organization of FOSS communities of practice and inappropriate technology platform design can discourage product users from engaging with FOSS communities. The process of suggesting, exploring, and gaining acceptance for new software features can be daunting. We study trajectories of userparticipation and social network structures in a vertically-integrated FOSS community to explore what distinguishes successful from unsuccessful participation architecture. We identify socio-cultural and IT platform design (instrumental) barriers to new feature acceptance, to suggest socio-technical affordances for FOSS participation architectures.
Comparison between second-look ultrasound and second-look digital breast tomosynthesis in the detection of additional lesions with presurgical CESM.

OBJECTIVES To compare second-look US with second-look DBT in the detection of additional lesions (ALs) with presurgical CESM. METHODS We retrospectively included 121 women with 128 ALs from patients who underwent CESM for presurgical staging at our centre from September 2016 to December 2018. These ALs underwent SL-US and a retrospective review of DBT (SL-DBT) performed 1-3 weeks prior to CESM to evaluate the performance of each technique individually and in combination. ALs in CESM images were evaluated according to enhancement type (focus, mass, or non-mass), size (<10 mm or >10 mm) and level of suspicion (BI-RADS 2, 3, four or 5). Our gold standard was post-biopsy histology, post-surgical specimen or >24 month negative follow-up. McNemar's test was used for the statistical analysis. RESULTS Out of the 128 Als, an imaging correlate was found for 71 (55.5 %,) with US, 79 (61.7%) with DBT, 53 (41.4 %) with DBT and US, and 97 (75.8%) with US and/or DBT. SL-DBT demonstrated a higher detection rate vs SL-US in non-mass enhancement (NME) pattern (p:0.0325) and DCIS histological type (p:0.0081). Adding SL-DBT improved the performance vs SL-US alone in the overall sample (p:<0.0001) and in every subcategory identified; adding SL-US to SL-DBT improved the detectability of ALs in the overall sample and in every category except for NME (p:0.0833), foci (p:0.0833) and B3 lesions (p:0.3173). CONCLUSIONS Combined second-look imaging (SL-DBT +SL US) for CESM ALs is superior to SL-DBT alone and SL-US alone. In B3 lesions, NME, and foci, the analysis of a larger sample could determine whether adding SL-US to SL-DBT is necessary or not. ADVANCES IN KNOWLEDGE Thanks to its high sensitivity, CESM is a useful tool in presurgical staging to detect the extent of the disease burden and identify ALs not detected with conventional imaging. Since CESM-guided biopsy systems are still scarcely available in clinical practice, it is necessary to look for other approaches to histologically characterize ALs detected with CESM. In our study, combined second-look imaging (SL-DBT +SL US) showed better performance in terms of detectability of ALs, than either SL-DBT or SL-US alone, and allowed us to identify 91.2% of ALs that turned out to be malignant at final histology; for the remaining 8.8% it was still necessary to perform MRI or MRI-guided biopsy. However, this issue could be solved once CESM-guided biopsies spread in clinical practice. SL-DBT demonstrated a higher detection rate than SL-US in NME and DCIS histology.
A Restorative Justice Intervention in United States Prisons: Implications of Intervention Timing, Age, and Gender on Recidivism

Restorative justice seeks to balance the needs of the victim, offender, and community by repairing the harm caused by crime and wrongdoing and improving the prosocial competencies and accountability of the offender in response to an offense. Restorative justice interventions (RJIs) offer an alternative method to reduce harm and short- and long-term recidivism. However, empirical validation of mechanisms and moderating factors warrant additional inquiry within jail and prison settings. Thus, the authors sought to examine RJI delivery timing on recidivism outcomes with age and gender as moderators. A final sample of 1,316 individuals (49.8% female) incarcerated in several United States prisons received an RJI between 2001 and 2017. RJI timing did not relate to binary recidivism. However, women recidivated less than men and older individual recidivated less than younger individuals. For the subsample of reoffenders (n = 283), RJIs delivered closer to release increased the amount of time before recidivism. Delivering RJIs closer to release from prison may allow for other community programs to intervene and reduce recidivism even further.
Method development and optimization for measuring chymotrypsin and chymotrypsin inhibitor activities.

Protease inhibitors of protein nature are rich in seeds of legume crops. There are two common types: Kunitz inhibitor, which mainly inhibits trypsin, and Bowman-Birk inhibitor, which inhibits both trypsin and chymotrypsin. Historically, trypsin inhibitor activity in legume products has been of primary interest for measurement. However, as plant proteins are increasingly used for food or feed in recent years, there is a growing interest in monitoring chymotrypsin inhibitor activity (CIA) in these products as well. Reported methods for CIA assay vary greatly and are incompletely described. No standardized or official method is available. The present study focused on developing a robust method for accurately measuring CIA, using N-benzoyl-L-tyrosine p-nitroanilide (BTpNA) as a substrate. Since BTpNA is not water soluble, a water-miscible organic solvent must be present. After investigating the effects of several factors, such as absorption spectra, organic solvent type and concentration, substrate and enzyme concentrations, inhibitor levels (which affected % chymotrypsin inhibition), the sequence of adding reagents, extractant and extraction time, and so forth, an optimized method for CIA measurement was finally developed. It features dimethylformamide as the organic solvent, the enzyme-last sequence, 5 ml total assay volume, and calculation of the inhibitor activity based on 40% chymotrypsin inhibition. The method can also be slightly modified for measuring chymotrypsin activity. The robust performance of the method was verified by measuring 11 assorted protein products, paving a way for standardization. PRACTICAL APPLICATION: With an increasing use of plant proteins, there is an urgent need to measure chymotrypsin inhibitor activity in various protein products with accuracy. After thoroughly investigating several factors, an optimized method for measuring chymotrypsin inhibitor activity in various protein products was developed. The proposed method is sensitive and robust, providing a basis for standardization. It can also be used for measuring chymotrypsin activity.
Managing idiopathic intracranial hypertension in pregnancy: practical advice

Idiopathic intracranial hypertension (IIH) is more common in women of reproductive age who have obesity, yet there is little information on its management specifically in pregnancy. Women with IIH should plan their pregnancy including discussing contraception before pregnancy, recognising that hormonal contraceptives are not contraindicated. Potentially teratogenic medications including acetazolamide and topiramate are not recommended during pregnancy or in those with immediate plans to conceive; prescribing acetazolamide in pregnancy must only follow discussion with the patient and their obstetrician. Ideally, patients should aim to achieve disease remission or control before pregnancy, through optimising their weight. Although weight gain is expected in pregnancy, excessive weight gain may exacerbate IIH and increase maternal and fetal complications; evidence-based recommendations for non-IIH pregnancies may help in guiding optimal gestational weight gain. The vast majority of women with IIH can have a normal vaginal delivery, with spinal or epidural anaesthesia if needed, provided the papilloedema is stable or the IIH is in remission.
Autoantibodies against specific post-translationally modified proteins are present in patients with lupus and associate with major neuropsychiatric manifestations

Background Although autoantibodies are an important hallmark of systemic lupus erythematosus (SLE), most are not specific for SLE or any of its clinical manifestations. Autoantibodies against post-translationally modified (PTM) proteins have been studied extensively in rheumatoid arthritis and associate with disease progression. While PTMs have also been detected in patients with SLE, studies on anti-PTM antibodies remain scarce. We studied the presence of anti-PTM antibodies in SLE and neuropsychiatric SLE (NPSLE), a manifestation that lacks serological markers. Methods IgG antibody responses against six PTMs (malondialdehyde–acetaldehyde adducts (MAA), advanced glycation end-products (AGE), carbamylation (CarP), citrullination, acetylation and nitration) were tested using ELISA in sera of 349 patients with SLE (mean age 44±13 years; 87% female) and compared with 108 healthy controls. Levels and positivity were correlated with clinical features and SLE manifestations. Results Anti-MAA, anti-AGE and anti-CarP antibodies were more prevalent in SLE compared with controls (MAA: 29% vs 3%, AGE: 18% vs 4%, CarP: 14% vs 5%, all p≤0.0001). Anti-MAA and anti-AGE antibodies correlated with clinical manifestations and serological inflammatory markers. Patients with major NPSLE showed higher positivity of anti-MAA (39% vs 24%, p=0.01) and anti-CarP antibodies (20% vs 11%, p=0.04) than patients without major NPSLE. In addition, anti-PTM antibody levels correlated with brain volumes, an objective measure of nervous system involvement. Conclusions In our NPSLE cohort, a subset of patients with SLE have anti-PTM antibodies against MAA, AGE and CarP modified proteins. Interestingly, anti-MAA and anti-CarP were more prevalent in NPSLE, a manifestation for which no biomarkers exist.
Prioritising Responses Of Nurses To deteriorating patient Observations (PRONTO): a pragmatic cluster randomised controlled trial evaluating the effectiveness of a facilitation intervention on recognition and response to clinical deterioration

Background Most hospitals use physiological signs to trigger an urgent clinical review. We investigated whether facilitation could improve nurses’ vital sign measurement, interpretation, treatment and escalation of care for deteriorating patients. Methods In a pragmatic cluster randomised controlled trial, we randomised 36 inpatient wards at four acute hospitals to receive standard clinical practice guideline (CPG) dissemination to ward staff (n=18) or facilitated implementation for 6 months following standard dissemination (n=18). Expert, hospital and ward facilitators tailored facilitation techniques to promote nurses’ CPG adherence. Patient records were audited pre-intervention, 6 and 12 months post-intervention on randomly selected days. Escalation of care as per hospital policy was the primary outcome at 6 and 12 months after implementation. Patients, nurses and assessors were blinded to group assignment. Analysis was by intention-to-treat. Results From 10 383 audits, improved escalation as per hospital policy was evident in the intervention group at 6 months (OR 1.47, 95% CI (1.06 to 2.04)) with a complete set of vital sign measurements sustained at 12 months (OR 1.22, 95% CI (1.02 to 1.47)). There were no significant differences in escalation of care as per hospital policy between study groups at 6 or 12 months post-intervention. After adjusting for patient and hospital characteristics, a significant change from T0 in mean length of stay between groups at 12 months favoured the intervention group (−2.18 days, 95% CI (−3.53 to –0.82)). Conclusion Multi-level facilitation significantly improved escalation as per hospital policy at 6 months in the intervention group that was not sustained at 12 months. The intervention group had increased vital sign measurement by nurses, as well as shorter lengths of stay for patients at 12 months. Further research is required to understand the dose of facilitation required to impact clinical practice behaviours and patient outcomes. Trial registration number ACTRN12616000544471p