Miracle-dz/UniFAR-FTUs huggingface dataset:
MUC1 and Polarity Markers INADL and SCRIB Identify Salivary Ductal Cells

Current treatments for xerostomia/dry mouth are palliative and largely ineffective. A permanent clinical resolution is being developed to correct hyposalivation using implanted hydrogel-encapsulated salivary human stem/progenitor cells (hS/PCs) to restore functional salivary components and increase salivary flow. Pluripotent epithelial cell populations derived from hS/PCs, representing a basal stem cell population in tissue, can differentiate along either secretory acinar or fluid-transporting ductal lineages. To develop tissue-engineered salivary gland replacement tissues, it is critical to reliably identify cells in tissue and as they enter these alternative lineages. The secreted protein α-amylase, the transcription factor MIST1, and aquaporin-5 are typical markers for acinar cells, and K19 is the classical ductal marker in salivary tissue. We found that early ductal progenitors derived from hS/PCs do not express K19, and thus earlier markers were needed to distinguish these cells from acinar progenitors. Salivary ductal cells express distinct polarity complex proteins that we hypothesized could serve as lineage biomarkers to distinguish ductal cells from acinar cells in differentiating hS/PC populations. Based on our studies of primary salivary tissue, both parotid and submandibular glands, and differentiating hS/PCs, we conclude that the apical marker MUC1 along with the polarity markers INADL/PATJ and SCRIB reliably can identify ductal cells in salivary glands and in ductal progenitor populations of hS/PCs being used for salivary tissue engineering. Other markers of epithelial maturation, including E-cadherin, ZO-1, and partition complex component PAR3, are present in both ductal and acinar cells, where they can serve as general markers of differentiation but not lineage markers.
Modification of polyetheretherketone (PEEK) physical features to improve osteointegration

Polyetheretherketone (PEEK) has been widely applied in orthopedics because of its excellent mechanical properties, radiolucency, and biocompatibility. However, the bioinertness and poor osteointegration of PEEK have greatly limited its further application. Growing evidence proves that physical factors of implants, including their architecture, surface morphology, stiffness, and mechanical stimulation, matter as much as the composition of their surface chemistry. This review focuses on the multiple strategies for the physical modification of PEEK implants through adjusting their architecture, surface morphology, and stiffness. Many research findings show that transforming the architecture and incorporating reinforcing fillers into PEEK can affect both its mechanical strength and cellular responses. Modified PEEK surfaces at the macro scale and micro/nano scale have positive effects on cell—substrate interactions. More investigations are necessary to reach consensus on the optimal design of PEEK implants and to explore the efficiency of various functional implant surfaces. Soft-tissue integration has been ignored, though evidence shows that physical modifications also improve the adhesion of soft tissue. In the future, ideal PEEK implants should have a desirable topological structure with better surface hydrophilicity and optimum surface chemistry.
Self-organized rod undulations on pre-stretched textiles

Textile technology is a traditional approach to additive manufacturing based on one-dimensional yarn. Printing solid rods onto pre-stretched textiles creates internal stresses upon relaxation of the pre-stretch, which leads to buckling-induced out-of-plane deformation of the textile. Similar behaviours are well known to occur also in biological systems where differential growth leads to internal stresses that are responsible for the folding or wrinkling of leaves, for example. Our goal was to get a quantitative understanding of this wrinkling by a systematic experimental and numerical investigation of parallel rods printed onto a pre-stretched textile. We vary rod thickness and spacing to obtain wavelength and phase coherence of the wrinkles as a function of these parameters. We also derive a simple analytical description to rationalize these observations. The result is a simple analytical estimate for the phase diagram of behaviours that may be used for design purposes or to describe wrinkling phenomena in biological or bioinspired systems.
Remote Assessments of Hand Function in Neurological Disorders: Systematic Review

Background Loss of fine motor skills is observed in many neurological diseases, and remote monitoring assessments can aid in early diagnosis and intervention. Hand function can be regularly assessed to monitor loss of fine motor skills in people with central nervous system disorders; however, there are challenges to in-clinic assessments. Remotely assessing hand function could facilitate monitoring and supporting of early diagnosis and intervention when warranted. Objective Remote assessments can facilitate the tracking of limitations, aiding in early diagnosis and intervention. This study aims to systematically review existing evidence regarding the remote assessment of hand function in populations with chronic neurological dysfunction. Methods PubMed and MEDLINE, CINAHL, Web of Science, and Embase were searched for studies that reported remote assessment of hand function (ie, outside of traditional in-person clinical settings) in adults with chronic central nervous system disorders. We excluded studies that included participants with orthopedic upper limb dysfunction or used tools for intervention and treatment. We extracted data on the evaluated hand function domains, validity and reliability, feasibility, and stage of development. Results In total, 74 studies met the inclusion criteria for Parkinson disease (n=57, 77% studies), stroke (n=9, 12%), multiple sclerosis (n=6, 8%), spinal cord injury (n=1, 1%), and amyotrophic lateral sclerosis (n=1, 1%). Three assessment modalities were identified: external device (eg, wrist-worn accelerometer), smartphone or tablet, and telerehabilitation. The feasibility and overall participant acceptability were high. The most common hand function domains assessed included finger tapping speed (fine motor control and rigidity), hand tremor (pharmacological and rehabilitation efficacy), and finger dexterity (manipulation of small objects required for daily tasks) and handwriting (coordination). Although validity and reliability data were heterogeneous across studies, statistically significant correlations with traditional in-clinic metrics were most commonly reported for telerehabilitation and smartphone or tablet apps. The most readily implementable assessments were smartphone or tablet-based. Conclusions The findings show that remote assessment of hand function is feasible in neurological disorders. Although varied, the assessments allow clinicians to objectively record performance in multiple hand function domains, improving the reliability of traditional in-clinic assessments. Remote assessments, particularly via telerehabilitation and smartphone- or tablet-based apps that align with in-clinic metrics, facilitate clinic to home transitions, have few barriers to implementation, and prompt remote identification and treatment of hand function impairments.
ImmuneData: an integrated data discovery system for immunology data repositories

To meet the increasing demand for data sharing, data reuse and meta-analysis in the immunology research community, we have developed the data discovery system ImmuneData. The system provides integrated access to five immunology data repositories funded by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology and Transplantation, including ImmPort, ImmuneSpace, ITN TrialShare, ImmGen and IEDB. ImmuneData restructures the data repositories' metadata into a uniform schema using domain experts' knowledge and state-of-the-art Natural Language Processing (NLP) technologies. It comes with a user-friendly web interface, accessible at http://www.immunedata. org/, and a Google-like search engine for biological researchers to find and access data easily. The vast quantity of synonyms used in biomedical research increase the likelihood of incomplete search results. Thus, our search engine converts queries submitted by users into ontology terms, which are then expended by NLP technologies to ensure that the search results will include all synonyms for a particular concept. The system also includes an advanced search function to build customized queries to meet higher-level users' needs. ImmuneData ensures the FAIR principle (Findability, Accessibility, Interoperability and Reusability) of the five data repositories to benefit data reuse in the immunology research community. The data pipeline constructing our system can be extended to other data repositories to build a more comprehensive biological data discovery system. DATABASE URL http://www.immunedata. org/.
Combination cancer immunotherapy targeting TNFR2 and PD-1/PD-L1 signaling reduces immunosuppressive effects in the microenvironment of pancreatic tumors

Backgrounds In advanced pancreatic ductal adenocarcinoma (PDAC), immune therapy, including immune checkpoint inhibitors, has limited efficacy, encouraging the study of combination therapy. Methods Tumor necrosis factor receptor 2 (TNFR2) was analyzed via immunohistochemistry, immunofluorescence, western blotting, and ELISAs. The in vitro mechanism that TNFR2 regulates programmed cell death 1 ligand 1 (PD-L1) was investigated using immunofluorescence, immunohistochemistry, flow cytometry, western blotting, and chromatin immunoprecipitation (ChIP). In vivo efficacy and mechanistic studies, using C57BL/6 mice and nude mice with KPC cell-derived subcutaneous and orthotopic tumors, employed antibodies against TNFR2 and PD-L1. Survival curves were constructed for the orthotopic model and a genetically engineered PDAC model (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre). Mass cytometry, immunohistochemistry, and flow cytometry analyzed local and systemic alterations in the immunophenotype. Results TNFR2 showed high expression and is a prognostic factor in CD8+ T cell-enriched pancreatic cancer. TNFR2 promotes tumorigenesis and progression of pancreatic cancer via dual effect: suppressing cancer immunogenicity and partially accelerating tumor growth. TNFR2 positivity correlated with PD-L1, and in vitro and in vivo, it could regulate the expression of PDL1 at the transcription level via the p65 NF-κB pathway. Combining anti-TNFR2 and PD-L1 antibodies eradicated tumors, prolonged overall survival in pancreatic cancer, and induced strong antitumor immune memory and secondary prevention by reducing the infiltration of Tregs and tumor-associated macrophages and inducing CD8+ T cell activation in the PDAC microenvironment. Finally, the antitumor immune response derived from combination therapy is mainly dependent on CD8+ T cells, partially dependent on CD4+ T cells, and independent of natural killer cells. Conclusions Anti-TNFR2 and anti-PD-L1 combination therapy eradicated tumors by inhibiting their growth, relieving tumor immunosuppression, and generating robust memory recall.
Generation and analysis of graphical codes using textured patterns for printed document authentication

Due to the development and availability of printing and scanning devices, the number of forged/counterfeited valuable documents and product packages is increasing. Therefore, different security elements (holograms, inks, papers) have been suggested to prevent these illegal actions. In this thesis, we focus on printed security elements that give access to a high security level with an easy implementation and integration. We present how to generate several novel security elements that aim to protect valuable documents and packaging against unauthorized copying process. Moreover, these security elements allow us to store a huge amount of hidden information. The main characteristic of these security elements is their sensitivity to the print-and-scan process. This sensitivity stems from the use of specific textured patterns. These patterns, which are binary images, have a structure that changes during the printing, scanning and copying processes. We define new specific criteria that ensures the chosen textured patterns to have the appropriate property. The amount of additional information encoded in the patterns increases with the number of patterns used. Additionally, we propose a new weighted mean squared error measure to improve the robustness of module detection for any high density barcodes. Thanks to this measure, the recognition rate of modules used in standard high density barcodes after print-and-scan process can be significantly increased. Finally, we experimentally study several effects: the physical print-and-scan process, separation of scanner noise from printer noise and changes of colors after print-and-scan process. We conclude, from these experimental results, that the print-and-scan process cannot be considered as being a Gaussian process. It has been also highlighted that this process is neither white nor ergodic in the wide sense.
UAV‐assisted real‐time evidence detection in outdoor crime scene investigations

Nowadays, a plethora of unmanned aerial vehicles (UAVs) designs that significantly vary in size, shape, operating flight altitude, and flight range have been developed to provide multidimensional capabilities across a wide range of military and civil applications. In the field of forensic and police applications, drones are becoming increasingly used instead of helicopters to assist field officers to search for vulnerable missing persons or to target criminals in crime hotspots, and also to provide high‐quality data for the documentation and reconstruction of the forensic scene or to facilitate evidence detection. This paper aims to examine the contribution of UAVs in real‐time evidence detection in outdoor crime scene investigations. It should be highlighted that the project innovates by providing a quantitative comparative analysis of UAV‐based and traditional search methods through the simulation of a crime scene investigation for evidence detection. The first experimental phase tested the usefulness of UAVs as a forensic detection tool by posing the dilemma of humans or drones. The second phase examined the ability of the drone to reproduce the obtained performance results in different terrains, while the third phase tested the accuracy in detection by subjecting the drone‐recorded videos to computer vision techniques. The experimental results indicate that drone deployment in evidence detection can provide increased accuracy and speed of detection over a range of terrain types. Additionally, it was found that real‐time object detection based on computer vision techniques could be the key enabler of drone‐based investigations if interoperability between drones and these techniques is achieved.
Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue

ABSTRACT Background The purpose of the study is to assess the etiology detection ability of Metagenomic Next-Generation Sequencing (mNGS) on formalin fixation and paraffin embedding (FFPE) tissue from postoperative biopsy specimens. Methods We prospectively enrolled specimens from patients undergone surgery biopsy due to undefinite diagnosis and pathologically indicated granulomatous lesions. FFPE tissues were tested by mNGS and histopathology. The etiology detection rate of mNGS was calculated and compared with histopathology. Results Among the 69 cases eventually included, 41 (59.42%) were diagnosed with infectious granuloma. The overall fungi and mycobacteria etiology detection rates of mNGS in granuloma lesions was 87.80% (36/41). The mNGS increased the detection rate by 68.29% (28/41) compared with histopathology, the difference was statistically significant (χ2 = 28.97, P = 0.00). The detection rates of mNGS in fungal infections (12/12,100%) and in mycobacterium infections (22/27, 81.48%) were significant higher than those of histopathology (8/12, 66.67% and 0/27, 0.00%; both P = 0.00). Two (2/2.100%) cases of co-infection were detected at one time by mNGS. All mNGS-based clinical decisions were made within 2 days. Conclusions The mNGS could accurately and quickly detect fungi and mycobacteria in FFPE specimens from postoperative granuloma specimens and identify the pathogens to the species level. Clinical Trials Registration China Clinical Trial Registry ChiCTR2000035464
Strategies for creating effective industrial development corporations : three Massachusetts case studies

Many towns and cities are faced with unemployment or underemployment, underutilized or blighted areas, and tax bases not expanding as quickly as servite needs. These challenges have led many municipalities to create Industrial Development Corporations. To achieve the desired goals of job creation and retention, expansion of the tax base, and an improved use of underutilized or blighted areas requires a successful implementation strategy by this organization. An effective implementation strategy is influenced by three main factors: the initial conditions and resources, the tools empowered to the Industrial Development Corporation, and organizational factors. Three Massachusetts case studies, Boston, Lynn, and Wareham, were examined to determine the important elements of each of these three factors. While the powers an Industrial Development Corporation has and the organizational factors it requires are similar for each town or city, each has its own unique set of circumstances and environment. Because of this, each municipality requires a tailor-made implementation strategy. The important environmental elements that differentiate the strategies include: size, location, access, industrial base, macro-economic trends, land availability, and stage of growth of the Industrial Development Corporation. Thesis Supervisor: Lynne B. Sagalyn Title: Associate Professor of Planning and Real Estate Development
Quality and Safety in Health Care, Part XCV

Abstract Many times in high reliability organizations, there is uncertainty about the meaning of various happenings or circumstances. Unfortunately, in an emergency, there is often no time to fully investigate events or what is going on in the environment before action must be taken to avoid unfortunate results or disaster. In groups, sensemaking refers to the process of interrelating with others so that a shared understanding may be reached, taking advantage of the differing observations, expertise, and opinions of the people involved, and then taking appropriate action.
Degeneration of retinal ganglion cells in hypoxic responses: hypoxia-inducible factor inhibition, a new therapeutic insight

Degeneration of retinal ganglion cells (RGCs) is one of the hallmarks of common optic neuropathies (Weinreb et al., 2014). G l a u co m a , t h e m o st co m m o n o p t i c neuropathy, is characterized by degeneration of RGCs. Acute angle-closure glaucoma is a serious ocular condition caused by a rapid increase in intraocular pressure (IOP) (Emanuel et al., 2014). One of the experimental models which could mimic this condition is a murine model of retinal ischemia/reperfusion (I/R) injury (Johnson and Tomarev, 2010). Retinal I/R injury can induce a rapid and transient elevation of IOP, which contributes to the degeneration of RGCs. Although understanding the pathophysiology of the degeneration of RGCs was considerably attempted, the major contributing pathways have not been yet elucidated (Calkins and Horner, 2012).
Ustekinumab and Vedolizumab Are Not Associated With Subsequent Cancer in IBD Patients with Prior Malignancy.

BACKGROUND There is little data regarding the risk of new or recurrent cancer in patients with inflammatory bowel disease (IBD) and a prior history of cancer who are exposed to ustekinumab or vedolizumab. We assessed the risk of subsequent cancer in patients exposed to these agents. METHODS We performed a retrospective cohort study of patients with IBD and a history of cancer at an academic medical center between January 2013 and December 2020. We collected data on demographics, IBD and cancer disease characteristics, and drug exposures. The primary exposure was immunosuppressive therapy after diagnosis of cancer. The primary outcome was interval development of new or recurrent cancer. RESULTS Of 390 patients with IBD and a previous history of cancer, 37 were exposed to vedolizumab, 14 ustekinumab, 41 antitumor necrosis factor (anti-TNF), and 31 immunomodulator; and 267 were not exposed to immunosuppression following cancer diagnosis. During a total median follow-up time of 52 months, 81 (20%) patients developed subsequent cancer: 6 (16%) were exposed to vedolizumab, 2 (14%) to ustekinumab, 3 (10%) to immunomodulators, 12 (29%) to anti-TNF, and 56 (21%) with no immunosuppression (P = .41). In a multivariable Cox model adjusting for age, IBD subtype, smoking, cancer recurrence risk, and cancer stage, there was no increase in subsequent cancer with vedolizumab (adjusted hazard ratio, 1.36; 95% CI, 0.27-7.01) or ustekinumab (adjusted hazard ratio, 0.96; 95% CI, 0.17-5.41). Patients with more than 1 biologic exposure also did not have an increased risk of subsequent cancer. CONCLUSIONS Exposure to ustekinumab or vedolizumab in patients with IBD and a prior history of cancer does not appear to be associated with an increased risk of subsequent new or recurrent cancer.
Do learners implement what they learn? Commitment-to-change following an interprofessional palliative care course

Background: Palliative care educators should incorporate strategies that enhance application into practice by learners. Commitment-to-change is an approach to reinforce learning and encourage application into practice; immediately post-course learners commit to making changes in their practices as a result of participating in the course (“statements”) and then several weeks or months later are prompted to reflect on their commitments (“reflections”). Aim: Explore if and how learners implemented into practice what they learned in a palliative care course, using commitment-to-change reflections. Design: Secondary analysis of post-course commitment statements and 4-months post-course commitment reflections submitted online by learners who participated in Pallium Canada’s interprofessional, 2-day, Learning Essential Approaches to Palliative Care (LEAP) Core courses. Setting/participants: Primary care providers from across Canada and different profession who attended LEAP Core courses from 1 April 2015 to 31 March 2017. Results: About 1063 of 4636 learners (22.9%) who participated in the 244 courses delivered during the study period submitted a total of 4250 reflections 4 months post-course. Of these commitments, 3081 (72.5%) were implemented. The most common implemented commitments related to initiating palliative care early across diseases, pain and symptom management, use of clinical instruments, advance care planning, and interprofessional collaboration. Impact extended to patients, services, and colleagues. Barriers to implementation into practice included lack of time, and system-level factors such as lack of support by managers and untrained colleagues. Conclusions: Examples of benefits to patients, families, services, colleagues, and themselves were described as a result of participating in the courses.