Miracle-dz/UniFAR-FTUs huggingface dataset:
How can a chemical system act purposefully? Bridging between life and non-life

One of life's most striking characteristics is its purposeful (teleonomic) character, a character already evident at the simplest level of life – a bacterial cell. But how can a bacterial cell, effectively an aqueous solution of an assembly of biomolecules and molecular aggregates within a membrane (that is itself a macromolecular aggregate), act purposefully? In this review, we discuss this fundamental question by showing that the somewhat vague concept of purpose can be given precise physicochemical characterization, and can be shown to derive directly from the powerful kinetic character of the replication reaction. At the heart of our kinetic model is the idea that the stability that governs replicating systems is a dynamic kinetic stability, one that is distinctly different to the thermodynamic stability that dominates the inanimate world. Accordingly, living systems constitute a kinetic state of matter as opposed to the thermodynamic states that dominate the inanimate world. Thus, the model is able to unite animate and inanimate within a single conceptual framework, yet is able to account for life's unique characteristics, amongst them its purposeful character. As part of that unification, it is demonstrated that key Darwinian concepts are special examples of more general chemical concepts. Implications of the model with regard to the possible synthesis of living systems are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Adsorption Equilibria of Water Vapor on Activated Carbon and DAY Zeolite

The adsorption equilibria of water vapor on activated carbon and DAY zeolite were measured by a static volumetric method. The equilibrium experiments were conducted at (293, 313, 333, 353, and 373) K and pressures up to 3.4 kPa for activated carbon and 1.9 kPa for DAY zeolite. According to the classification of isotherms, the experimental data are correlated by the Dubinin−Serpinsky and Sips models for activated carbon as well as the Toth, UNILAN, and Sips models for DAY zeolite.
Role of comorbidities on therapeutic persistence of biological agents in rheumatoid arthritis: results from the RECord-linkage On Rheumatic Disease study on administrative healthcare databases

Objectives: This study aimed to evaluate the impact of different comorbidities on thereflecting its safety profile persistence of biological disease-modifying anti-rheumatic drugs (bDMARDs) in rheumatoid arthritis (RA), taking advantage of a retrospective analysis of administrative healthcare databases (AHDs). Method: A retrospective observational study was conducted on AHDs of the Lombardy region, Italy (2004–2013). Among RA patients treated with bDMARDs, drug survival was estimated using Cox proportional hazard models [hazard ratio (HR), 95% confidence interval (CI)], crude and adjusted for prespecified confounders (gender, age, disease duration, concomitant use of non-steroidal anti-inflammatory drugs, glucocorticoids, conventional DMARDs, specific bDMARDs), in first-line and subsequent lines of treatment. The role of comorbidities in administration of specific bDMARDs was analysed through multinomial logistic models. Results: The study included 4657 RA patients. In the first-line treatment strategy, the Charlson Comorbidity Index (CCI) (RA excluded) was significantly associated with an increased rate of bDMARD failure (CCI = 1: HR 1.28, 95% CI 1.13–1.46; CCI ≥ 2: HR 1.26, 95% CI 1.03–1.53). Among selected comorbidities, chronic obstructive pulmonary disease (HR 1.38, 95% CI 1.01–1.91), diabetes (HR 1.18, 95% CI 1.01–1.37), and previous-year bacterial infections (HR 1.18, 95% CI 1.07–1.30) were slightly associated with risk of bDMARD failure, while acute myocardial infarction (HR 1.30, 95% CI 0.97–1.75), mild liver disease (HR 1.21, 95% CI 0.91–1.60), and solid tumours (HR 1.19, 95% CI 0.93–1.53) were not. In the following treatment lines, neoplasms were associated with reduced risk of failure (HR 0.64, 95% CI 0.41–0.99). Multiple comorbidities were associated with first-line abatacept and rituximab administration. Conclusions: Comorbidities affect treatment decisions in RA and influence bDMARD failure, and should be considered when analysing the persistence of biological therapy.
Adenomyosis and in vitro fertilization impacts - A literature review

Adenomyosis is a gynecological condition, which is characterized by stromal and glandular endometrial tissue infiltration inti the myometrium, resulting in an increase of uterine volume. The etiology of adenomyosis is presently unknown, but some theories assist us in understanding its pathogenesis and natural history. Clinical manifestations are increased menstrual flow and dysmenorrhea, abnormal uterine bleeding, chronic pelvic pain, and dyspareunia. The signs and symptoms suggestive of adenomyosis are complemented by diagnostic methods such as transvaginal ultrasound (TVUS), ideally with intestinal preparation, magnetic resonance imaging (MRI) and surgery; although currently, there are no precise criteria for the classification of findings on imaging studies. The clinical and surgical therapeutic approach must be individualized, taking into account the patient’s characteristics, for instance, age, parity, depth and number of adenomyotic foci, uterine volume and, mainly, clinical manifestations. A causal relation between adenomyosis and infertility has been repeatedly suggested, mostly due to the anatomo-physiopathological conditions originated by the adenomyosis on the female genital tract; however, definitive conclusions are still lacking. This pathology is found in approximately 25% of infertile women, especially those who have had recurrent pregnancy loss (RPL), recurrent implantation failure, older women seeking In Vitro fertilization (IVF) treatment, and those with concomitant endometriosis. To determine whether adenomyosis per se affects fertility, several researchers have focused on women who are affected by the condition and underwent IVF/intracytoplasmic sperm injection (ICSI); for this model provides more accurate data about the influence of adenomyosis on embryo implantation. Therefore, our objective was to analyze, through a systematic literature review, the effect of uterine adenomyosis on the probability of pregnancy by IVF / ICSI, as well as trying to point out the main difficulties and gaps to establish a standard protocol for the management of these patients, since most of the patients with adenomyosis have other associated gynecological pathologies, mostly endometriosis; in addition to the heterogeneity of the studies still remaining as an obstacle to precise conclusions.
iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

Abstract Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins. Rapid accumulation of sequences requires equally pervasive development of new predictive models, which depends on the availability of effective tools that support these efforts. We introduce iLearnPlus, the first machine-learning platform with graphical- and web-based interfaces for the construction of machine-learning pipelines for analysis and predictions using nucleic acid and protein sequences. iLearnPlus provides a comprehensive set of algorithms and automates sequence-based feature extraction and analysis, construction and deployment of models, assessment of predictive performance, statistical analysis, and data visualization; all without programming. iLearnPlus includes a wide range of feature sets which encode information from the input sequences and over twenty machine-learning algorithms that cover several deep-learning approaches, outnumbering the current solutions by a wide margin. Our solution caters to experienced bioinformaticians, given the broad range of options, and biologists with no programming background, given the point-and-click interface and easy-to-follow design process. We showcase iLearnPlus with two case studies concerning prediction of long noncoding RNAs (lncRNAs) from RNA transcripts and prediction of crotonylation sites in protein chains. iLearnPlus is an open-source platform available at https://github.com/Superzchen/iLearnPlus/ with the webserver at http://ilearnplus.erc. monash.edu/.
A protocol for mitigating safety events in a sleep lab.

STUDY OBJECTIVES Polysomnography is a common outpatient procedure and the rate of adverse events is considered low. Due to the emergence and use of home sleep testing, the patient population presenting for in-lab testing may have greater medical complexity, suggesting greater risk for in-lab adverse events. We believe that there is a greater need for standardized protocols to triage medically vulnerable populations and for formalized training of sleep technicians to respond to safety events. METHODS The sleep laboratories affiliated with the Beth Israel Deaconess Medical Center system developed a referral triage protocol for patients undergoing PSG and a training protocol for sleep technicians with a formalized response to medical incidents. Safety events occurring from January 2016-January 2020 were documented and patient demographics, referral characteristics, event characteristics, and outcomes were analyzed. RESULTS 65 safety events occurred over this period, with a rate of 1:147 studies. The most common events were chest pain (20/65, 31%), shortness of breath (13/65, 20%), and vital sign abnormalities (12/65, 18%). Patients experiencing events were 49% (32/65) female, median age of 57 (range 19-91) years, 60/65 (92%) had documented medical comorbidities, with a median of 3 documented medical or psychiatric comorbidities (range 0-9). With the formalized response protocol, the time from incident identification to activation of the appropriate response was a median of 3 minutes (range 0-47 minutes). CONCLUSIONS The incidence of in-lab safety events may be greater than previously described due to the widespread use of home sleep testing. Implementation of formalized response protocols and sleep technician training may be necessary to meet the needs of an increasingly medically complex population.
Red blood cells from patients with pre-eclampsia induce endothelial dysfunction

Supplemental Digital Content is available in the text Rationale: Pre-eclampsia is a multisystem disorder associated with systemic vascular dysfunction and decreased nitric oxide (NO) bioactivity. Arginase competes with NO synthase (NOS) for l-arginine, and its upregulation may reduce NOS-derived NO formation or induce production of reactive oxygen species (ROS) via uncoupling of NOS, resulting in endothelial dysfunction. Red blood cells (RBCs) have emerged as key players in NO homeostasis via their interactions with the endothelium. Studies have demonstrated that abnormal RBC arginase function in patients with diabetes contributes to oxidative stress and endothelial dysfunction. Aim: The aim of the study was to investigate if reduced NO bioavailability and increased ROS in pre-eclampsia is mediated via RBC-dependent mechanisms. Methods: In this translational study, plasma and RBCs were isolated from gestationally matched pre-eclamptic and healthy pregnant women and co-incubated overnight with mouse aortas for vascular reactivity studies. NO bioactivity, that is, nitrate, nitrite and cGMP, was assessed in plasma. Arginase activity and expression were analysed in RBCs. Results: Plasma markers of NO homeostasis and signalling were decreased in pre-eclamptic women vs. healthy pregnant women. Co-incubation of aorta with pre-eclamptic RBCs, but not healthy pregnant RBCs, induced endothelial dysfunction, which was ameliorated by pharmacological inhibition of arginase, scavenging of ROS, and by nitrite treatment. This pathological vascular phenotype was not observed following incubation with pre-eclamptic plasma. Arginase expression and activity in RBCs were increased in pre-eclamptic vs. healthy pregnant women and was associated with pre-eclampsia severity. Pre-eclamptic RBC-induced endothelial dysfunction was not because of increased haemolysis/cell-free haemoglobin. Conclusion: This study demonstrates a novel role of the RBC in mediating the endothelial dysfunction associated with pre-eclampsia through arginase-dependent and oxidative stress-dependent mechanisms. Targeting of RBC arginase may provide a novel treatment modality for pre-eclampsia.
Reversible thermal gating of the photochromic properties of 3-methyl-2-(2',4'-dinitrobenzyl)pyridine in a single crystal

By cooperative twisting of alternating molecules from the adjacent columns, the structure and reaction kinetics of the photochromic compound 3-methyl-2-(2‘,4‘-dinitrobenzyl)pyridine can be reversibly gated in a single crystal over a hysteresis gap of 10−11 K close to ambient temperature.
Living Radical Polymerization with Reversible Addition−Fragmentation Chain Transfer (RAFT Polymerization) Using Dithiocarbamates as Chain Transfer Agents

Living radical polymerization with reversible addition−fragmentation chain transfer (RAFT polymerization) can be achieved with the use of dithiocarbamate derivatives that have the nonbonded electron pair of the nitrogen included as part of an aromatic system. These compounds have been shown to be highly effective in RAFT polymerization of styrene and (meth)acrylate esters to produce polymers of predetermined molecular weight and narrow polydispersity (usually <1.2). By contrast, simple N,N-dialkyl dithiocarbamates (those compounds previously described as “photoiniferters”) are ineffective as RAFT agents. The reasons for the different behavior are discussed.
Surface Functionalization of 2D MXenes: Trends in Distribution, Composition, and Electronic Properties

Using a multiscale computational scheme, we study the trends in distribution and composition of the surface functional groups −O, −OH, and −F on two-dimensional (2D) transition metal carbides and nitrides (MXenes). We consider Ti2N, Ti4N3, Nb2C, Nb4C3, Ti2C, and Ti3C2 to explore MXenes with different chemistry and different number of atomic layers. Using a combination of cluster expansion, Monte Carlo, and density functional theory methods, we study the distribution and composition of functional groups at experimentally relevant conditions. We show that mixtures of functional groups are favorable on all studied MXene surfaces. The distribution of functional groups appears to be largely independent of the type of metal, carbon, or nitrogen species and/or number of atomic layers in the MXene. We further show that some properties (e.g., the work function) strongly depend on the surface composition, while others, for example, the electric conductivity, exhibit only a weak dependence.
Safe use of right lobe living donor livers with moderate steatosis in adult‐to‐adult living donor liver transplantation: a retrospective study

Hepatic steatosis (HS) beyond a certain degree can jeopardize living donor (LD) safety, particularly in right lobe (RL) donors, making it a major obstacle for donor pool expansion in adult‐to‐adult living donor liver transplantation (ALDLT). From July 2004 to June 2016, 58 LDs donated their RLs despite having moderate HS (30%‐50% steatosis) determined by intraoperative biopsy at a single center. We performed greedy matching to compare the outcomes of the donors and recipients of this group with those of LDs with no HS. The mean left lobe (LL) HS value in the 58 cases was 20.9 ± 12.4%, which was significantly lower than the mean RL HS value (38.8 ± 6.7%, P < 0.001). The mean ratio of the remnant LL to the total liver volume was 37.8 ± 2.2. No differences were observed in the postoperative liver function and donor and recipient morbidity and mortality rates. The liver regeneration rates in recipients and donors at 1 month, 6 months, and 1 year postoperatively did not differ significantly. The patient and graft survival rates of the recipients showed no differences. The use of well‐selected RL grafts with moderate steatosis does not impair graft function, recipient outcomes, or donor safety.
Whole-body vibration therapy does not improve the peripheral nerve regeneration in experimental model

Objectives: Whole-body vibration (WBV) is commonly used to improve motor function, balance and functional performance, but its effects on the body are not fully understood. The main objective was to evaluate the morphometric and functional effects of WBV in an experimental nerve regeneration model. Methods: Wistar rats were submitted to unilateral sciatic nerve crush and treated with WBV (4-5 weeks), started at 3 or 10 days after injury. Functional performances were weekly assessed by sciatic functional index, horizontal ladder rung walking and narrow beam tests. Nerve histomorphometry analysis was assessed at the end of the protocol. Results: Injured groups, sedentary and WBV started at 3 days, had similar functional deficits. WBV, regardless of the start time, did not alter the histomorphometry parameters in the regeneration process. Conclusions: The earlier therapy did not change the expected and natural recovery after the nerve lesion, but when the WBV starts later it seems to impair function parameter of recovery.
Early Surgical Treatment of Both Tumor and Fracture in Patients With Enchondroma of the Hand Combined With Pathologic Fracture

Purpose The aims of this study were to evaluate the degree of cortical thinning and the tumor area in simple radiographs in patients with enchondroma of the hand combined with pathologic fracture and to determine the surgical outcome of simultaneous tumor curettage and internal fixation of fracture. Methods We enrolled 23 bone lesions of 21 patients diagnosed with enchondroma of the hand. Of them, 9 bone lesions of 8 patients had pathologic fracture. We evaluated the degree of cortical thinning and tumor area in simple radiographs and compared them between patients with and without pathologic fracture. For patients with pathologic fracture, we performed curettage of the tumor through the fracture site and fixed the fracture using K-wires. We then evaluated the clinical outcome of these patients using the visual analog scale to measure pain intensity and Takigawa's criteria 1 year after surgery. Results There was a significant difference in the degree of cortical thinning between the 2 groups (P < 0.001); however, there was no significant difference in the percentage of tumor area (P = 0.259). The average time from surgery to bony union was 8.5 weeks in patients with pathologic fracture. The patients reported that they could return to their previous activities of daily living within 12 weeks of surgery. The average visual analog scale score was 0.6 at 1 year after surgery, and 6 patients were graded as excellent and 2 as good according to Takigawa's criteria. Conclusions Cortical thinning seems to be related to pathologic fracture. Our scoring system for cortical thinning may be helpful in evaluating the risk for pathologic fracture. Early 1-stage surgical treatment for pathologic hand fracture with enchondroma is a very useful method with satisfactory outcomes that could shorten the treatment period.
Generalized Multiresolution Decomposition Frameworks for the Analysis of Industrial Data with Uncertainty and Missing Values

In this paper, we address the problem of extending the multiscale decomposition framework based upon the wavelet transform to situations where datasets contain any type of missing data patterns (e.g., random, multirate). Furthermore, the proposed approaches explicitly integrate data uncertainty information into their algorithms, to explore all knowledge available about data during the decomposition stage, as well as to enable its posterior use in subsequent data-analysis tasks. Beside their role in the multiscale decomposition of complex datasets, these frameworks, called generalized multiresolution decomposition frameworks (GMRD), also lead to new developments in data-analysis tools based upon the information they provide, namely, in the selection of relevant scales for data analysis and in the improvement of signal-denoising procedures. Guidelines are presented regarding their adequate use and how they can be combined into an integrated multiscale data analysis framework. The pertinence of the proposed .
Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study

Background Novel wearable biosensors, ubiquitous smartphone ownership, and telemedicine are converging to enable new paradigms of clinical research. A new generation of continuous glucose monitoring (CGM) devices provides access to clinical-grade measurement of interstitial glucose levels. Adoption of these sensors has become widespread for the management of type 1 diabetes and is accelerating in type 2 diabetes. In parallel, individuals are adopting health-related smartphone-based apps to monitor and manage care. Objective We conducted a proof-of-concept study to investigate the potential of collecting robust, annotated, real-time clinical study measures of glucose levels without clinic visits. Methods Self-administered meal-tolerance tests were conducted to assess the impact of a proprietary synbiotic medical food on glucose control in a 6-week, double-blind, placebo-controlled, 2×2 cross-over pilot study (n=6). The primary endpoint was incremental glucose measured using Abbott Freestyle Libre CGM devices associated with a smartphone app that provided a visual diet log. Results All subjects completed the study and mastered CGM device usage. Over 40 days, 3000 data points on average per subject were collected across three sensors. No adverse events were recorded, and subjects reported general satisfaction with sensor management, the study product, and the smartphone app, with an average self-reported satisfaction score of 8.25/10. Despite a lack of sufficient power to achieve statistical significance, we demonstrated that we can detect meaningful changes in the postprandial glucose response in real-world settings, pointing to the merits of larger studies in the future. Conclusions We have shown that CGM devices can provide a comprehensive picture of glucose control without clinic visits. CGM device usage in conjunction with our custom smartphone app can lower the participation burden for subjects while reducing study costs, and allows for robust integration of multiple valuable data types with glucose levels remotely. Trial Registration ClinicalTrials.gov NCT04424888; http://clinicaltrials.gov/ct2/show/NCT04424888.