Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size

Nanoparticle biological activity, biocompatibility and fate can be directly affected by layers of readily adsorbed host proteins in biofluids. Here, we report a study on the interactions between human blood plasma proteins and nanoparticles with a controlled systematic variation of properties using 18O‐labeling and LC‐MS‐based quantitative proteomics. We developed a novel protocol to both simplify isolation of nanoparticle bound proteins and improve reproducibility. LC‐MS analysis identified and quantified 88 human plasma proteins associated with polystyrene nanoparticles consisting of three different surface chemistries and two sizes, as well as, for four different exposure times (for a total of 24 different samples). Quantitative comparison of relative protein abundances was achieved by spiking an 18O‐labeled “universal” reference into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label‐free and isotopic labeling quantification across the entire sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive patterns that classified the nanoparticles based on their surface properties and size. In addition, temporal data indicated that the formation of the stable protein corona was at equilibrium within 5 min. The comprehensive quantitative proteomics results obtained in this study provide rich data for computational modeling and have potential implications towards predicting nanoparticle biocompatibility.
Revision Cochlear Implant Surgery in Patients With Suspected Soft Failures

Objective: To review our patient series who underwent revision cochlear implantation surgery, with special emphasis on the "soft failure" group. Study Design: Retrospective chart review of cochlear implant revision surgeries from 1979 to 2008. An extensive review of these patients' medical, audiologic, and radiographic histories was performed. Setting: Two tertiary care hospitals and 1 academic cochlear implant center. Intervention: Explantation and reimplantation of cochlear implant, explanted device analysis, speech perception testing. Main Outcome Measures: Postoperative speech performance. Results: Approximately 1,500 cochlear implant surgeries were performed from 1979 to 2008. Of these, 113 (7.53%) procedures in 98 patients were revision cases. The underlying reason for revision surgery was divided into 4 categories: 26 hard failures (23%), 31 medical failures (27.4%), 14 soft failures (12.4%), and 42 (37.2%) not classified/ambiguous cases. The last group was not categorized because of lack of available medical documentation or because of an ambiguous device failure analysis. The top 3 most common causes of hard failure were loss of hermiticity (8 patients [30.8%]), Vendor B defects (7 patients [26.9%]), and cracked casing (4 patients [15.4%]). The most common cause of medical failure was device extrusion (11 patients [35.5%]) followed by head trauma to the site of implantation (11 patients [35.5%]), and wound infection (5 patients [16.1%]). Fourteen patients (14.2%) were categorized as soft failures. All soft failure patients demonstrated a deterioration in pure-tone average and speech perception. Of the soft failure group, time to revision surgery was 4.7 years in contrast to 4.2 years for the hard failure group and 4.3 years for all revisions. An extensive review of patients' medical histories showed that 4 (28.5%) of the 14 patients had a previous diagnosis of meningitis. Two patients (14.3%) had evidence of inner ear malformations, and 2 patients (14.3%) had history of asthma. Conclusion Our cochlear revision series are comparable to what is reported in the literature. However, an unexpected relationship between meningitis was identified among our soft failure group. More than one-quarter carried a history of meningitis. Moreover, nearly one-half of all soft failures had some form of inflammatory derangement. We used the soft failure criteria established by the 2005 Consensus Development Conference for our population analysis. Although we agree that audiologic data often are essential for defining soft failure, multiple patients in our series experienced pain that was severe enough to prevent a complete audiometric evaluation, therefore not rigorously fulfilling the criteria set forth by the 2005 Consensus. However, because their symptoms resolved after reimplantation, and their speech performance restored, we propose modifications of the current definition of "soft failure" to include these patients.
Natural history of uremic polyneuropathy and effects of dialysis.

THE advent of long-term hemodialysis and renal transplantation has focused attention upon the peripheral neuropathy associated with chronic renal insufficiency.1 2 3 4 Although the initial clinical manifestations of this generally symmetrical neuropathy usually consist in painful paresthesia of the feet, progression of the neuropathy may lead to sensory deficit, loss of deep tendon reflexes and severe muscular weakness. The pathophysiology of this neuropathy is unknown; however, histologic studies have shown destruction of myelin and axon cylinders, predominantly in the distal segments of the peripheral nerve trunks.2 Prevalence of clinical neuropathy among patients managed conservatively (excluding dialysis and transplantation) has been reported as .
Quality of life and outcomes after pancreaticoduodenectomy.

OBJECTIVE To assess the quality of life (QOL) and functional outcome of patients after pancreaticoduodenectomy. SUMMARY BACKGROUND DATA Pancreaticoduodenectomy is gaining acceptance and is being performed in increasing numbers for various malignant and benign diseases of the pancreas and periampullary region. There is a general impression that pancreaticoduodenectomy can severely impair QOL and alter normal activities. Only a few small studies have evaluated QOL after pancreaticoduodenectomy. METHODS A standard QOL questionnaire was sent to 323 patients surviving pancreaticoduodenectomy who had undergone surgery at The Johns Hopkins Hospital between 1981 and 1997. Thirty items on a visual analog scale were categorized into three domains: physical (15 items), psychological (10 items), and social (5 items). Scores are reported as a percentile, with 100% being the highest possible score. The same QOL questionnaire was also sent to laparoscopic cholecystectomy patients and healthy controls. A separate component of the questionnaire asked about functional outcomes and disabilities. RESULTS Overall QOL scores for the 192 responding pancreaticoduodenectomy patients in the three domains (physical, psychological, social) were 78%, 79%, and 81%, respectively. These QOL scores were comparable to those of the 37 laparoscopic cholecystectomy patients and the 31 healthy controls. The pancreaticoduodenectomy patients were subgrouped into chronic pancreatitis, other benign disease, pancreatic adenocarcinoma, and other cancers. Patients who underwent resection for chronic pancreatitis and pancreatic adenocarcinoma had significantly lower QOL scores in the physical and psychological domains compared with the laparoscopic cholecystectomy patients and the healthy controls. Common problems after pancreaticoduodenectomy were weight loss, abdominal pain, fatigue, foul stools, and diabetes. CONCLUSIONS This is the largest single-institution experience assessing QOL after pancreaticoduodenectomy. These data demonstrate that as a group, patients who survive pancreaticoduodenectomy have near-normal QOL scores. Many patients report weight loss and symptoms consistent with pancreatic exocrine and endocrine insufficiency. Most patients have QOL scores comparable to those of control patients and can function independently in daily activities.
Can people with nonsevere major depression benefit from antidepressant medication?

BACKGROUND Several meta- or mega-analyses suggest antidepressant medications should be given only to severely depressed patients. In our experience, mild depression benefits from medication. We reanalyzed 1 clinic's randomized placebo-controlled antidepressant studies, limiting analyses to patients with major depressive disorder (MDD) without severe illness, to determine whether nonsevere depression responds to antidepressant medication. DATA SOURCES Archives of the Depression Evaluation Service outpatient clinic of the New York State Psychiatric Institute were searched for randomized, placebo-controlled antidepressant studies that were conducted between 1977 and 2009 and included patients having MDD and pretreatment Hamilton Depression Rating Scale (HDRS) scores < 23. STUDY SELECTION Six placebo-controlled studies were found, including 8 active treatment arms and 1,440 patients. 825 patients were randomized and had MDD and an HDRS score < 23. DSM-III, DSM-III-R, or DSM-IV diagnostic criteria contemporary to each study were employed. DATA EXTRACTION Treatments were compared within study and via a patient-level meta-analysis using analysis of covariance (ANCOVA) of HDRS end point scores adjusted for pretreatment score. The number needed to treat (NNT) was calculated from remission rates (HDRS end point score ≤ 7), which were compared by χ². Effect sizes were calculated from change in HDRS scores. Secondary analyses investigated the effect of chronicity and atypical features on treatment response. DATA SYNTHESIS Three of 6 studies showed significant (P < .001) treatment effects by ANCOVA, and 4 of 6 studies showed significant (P < .04) differences in remission. The NNT ranged from 3 to 8. Effect sizes ranged from -0.04 to 0.8, with 4 of 8 greater than 0.4. The patient-level meta-analysis confirmed these results; neither chronicity nor atypical features significantly affected outcome. Secondary analyses utilizing global ratings and self-report mimicked the main findings. CONCLUSIONS Several studies demonstrated significant antidepressant efficacy for patients having nonsevere MDD. Efficacy was not trivial, as NNT ranged from 3 to 8, a range accepted by researchers as sufficiently robust to recommend treatment. These findings suggest mild-moderate MDD can benefit from antidepressants, contrary to findings by several other meta- or mega-analyses.
Model predictive coordinating control of dynamically interacting systems with stochastic disturbances

A computationally-efficient, model-predictive-control (MPC)-based coordinated control scheme is explored for a large-scale system with dynamically coupled subsystems. Considering a class of coordinated control problems involving consensus, the proposed formulation presents the control problem as a distributed optimization problem with sets of local and global decision variables which can be optimized online. The formulation comprises dynamic-policy-based local MPC laws whose dynamics together with the decoupled feasible sets for the subsystem decision variables are computed off-line in order to simplify the on-line computation of the local MPC moves. The overall distributed MPC optimization problem is solved using a dual-averaging-based iterative algorithm in real time. The performance of the proposed scheme is illustrated with a simulation example.
Improving transient performance of adaptive control via a modified reference model and novel adaptation

This paper presents a new model reference adaptive control (MRAC) framework for a class of nonlinear systems to address the improvement of transient performance. The main idea is to introduce a nonlinear compensator to reshape the closed‐loop system transient, and to suggest a new adaptive law with guaranteed convergence. The compensator captures the unknown system dynamics and modifies the given nominal reference model and the control action. This modified controlled system can approach the response of the ideal reference model. The transient is easily tuned by a new design parameter of this compensator. The nominal adaptive law is augmented by new leakage terms containing the parameter estimation errors. This allows for fast, smooth and exponential convergence of both the tracking error and parameter estimation, which again improves overall reference model following. We also show that the required excitation condition for the estimation convergence is equivalent to the classical persistent excitation (PE) condition. In this respect, this paper provides an intuitive and numerically feasible approach to online validate the PE condition. The salient feature of the suggested methodology is that the rapid suppression of uncertainties in the controlled system can be achieved without using a large, high‐gain induced, learning rate in the adaptive laws. Extensive simulations are given to show the effectiveness and the improved response of the proposed schemes. Copyright © 2016 John Wiley & Sons, Ltd.
The reliability of arousal threshold during sleep.

Thirty-five subjects from two independent studies were awakened at EEG-defined periods during the night with 1000 Hz ascending tone series. Awakenings were made five to eight times per night during stage 2, stage 4, or REM sleep over a series of nights in good and poor sleepers. Reliability was assessed within stage, within night, between stages, and between nights. Good and poor sleepers did not differ in either depth of sleep or reliability of arousal threshold and were thus pooled in the analyses. From night to night, the most consistency was seen in stage 4 (r=.74), although REM reliability (r1= .49) and stage 2 reliability (r1= .50 and r1= .69 in the two respective studies) estimates were also greater than zero. Early sleep onset and morning arousals were more variable. Reliability estimates on arousal thresholds taken within the same night for stage 2 were r= . 64 and r1= . 77 for the two studies and r= . 96 for REM. The depth of sleep was not correlated with awake auditory threshold. It was concluded that five or six carefully placed arousals could give a good estimate of an individual's usual arousal threshold.
Extending the model of ObjectTeams/Java programming language to distributed environments

ObjectTeams/Java realizes the Object Teams Model, a flexible and rigorous programming language model that combines aspect-oriented and collaboration-based concepts and integrates them with the object orientation model. OT/J establishes strong bonds through playedBy relationships between players and roles within a team (collaborations). OT/J has proved to be a strong programming model that allows adaptation of objects interacting within a collaboration in a single JVM. We believe that extending the OT model to distributed environments will allow the creation of a rigorous model for adapting distributed objects and developing adaptable distributed applications. This paper presents Distributed ObjectTeams/Java (DOT/J) as a distributed model that extends the OT model to distributed environments.
Recommendation

An important task in recommender systems is suggesting relevant venues in a city to a user. These suggestions are usually created by exploiting the user’s history of preferences, which are, for example, collected in previously visited cities. In this paper, we ﬁrst introduce a user model based on venues’ categories and their descriptive keywords extracted from Foursquare tips. Then, we propose an enriched user model which leverages the users’ reviews from Yelp. Our participation in the TREC 2015 Contextual Suggestion track, conﬁrmed that our model out-performs other approaches by a signiﬁcant margin.
Demonstration of a somatotopically arranged cortico‐rubral projection in the cat. An experimental study with silver methods

Based on experiments in kittens where the spinal cord was sectioned at various levels, and the retrograde cellular changes studied in the red nucleus, Pompeiano and Brodal ('57) have shown that a clearcut somatotopical principle exists in the organization of the rubro-spinal tract. The ventral part of the nucleus projects to the lumbar, the dorsal part to the cervical region of the cord. In addition the part intermediate to what may be called the "fore-" and "hindlimb" regions, respectively, sends its fibers to the thoracic region of the spinal cord. Physiological observations by Pompeiano ('57) are in agreement with these anatomical findings. The present study was prompted by these observations which raised the question whether, like the rubro-spinal, also the cortico-rubral projection system in the cat is somatotopically organized. As will be seen, this indeed turned out to be the case. A perusal of the relevant literature shows that the existence of a direct corticorubral projection system has been a matter of dispute and controversy. While the presence of such a tract has been denied by Lewandowsky ('04), Cajal ('11) and Verhaart and Kennard ('40), other authors have produced evidence for its existence in animals and man (Dkjerine et Dkjerine, 1895; Ddjerine, '01; von Monakow, '09-'10; Archambault, '1 4-2 5 ; Minkow ski, '23-'24 ; Hirasawa and Kariya, '36; Levin, '36; Mettler, '47; Kanki and Ban, '52). Some of the authors mentioned studied the secondary atrophy in the red nucleus following cortical lesions, while others used the Marchi method in order to trace the degenerating myelinated nerve fibers. However, only studies where the axon itself is impregnated can be used in order to study the exact site of termination of degenerating cortico-rubral fibers and to visualize unmyelinated fibers, possibly present. As far as we know, no such systematical investigations have been undertaken, although a few authors have observed cortico-rubral fibers in silver impregnated sections. Thus Szentggothai and Rajkovits ('SS), in a paper on the corticofugal connections in the cat in a footnote mention that they could trace degenerating fibers to the red nuclei. Pearce ('59) made similar findings.
RanBP3 Contains an Unusual Nuclear Localization Signal That Is Imported Preferentially by Importin-α3

ABSTRACT The full range of sequences that constitute nuclear localization signals (NLSs) remains to be established. Even though the sequence of the classical NLS contains polybasic residues that are recognized by importin-α, this import receptor can also bind cargo that contains no recognizable signal, such as STAT1. The situation is further complicated by the existence of six mammalian importin-α family members. We report the identification of an unusual type of NLS in human Ran binding protein 3 (RanBP3) that binds preferentially to importin-α3. RanBP3 contains a variant Ran binding domain most similar to that found in the yeast protein Yrb2p. Anti-RanBP3 immunofluorescence is predominantly nuclear. Microinjection of glutathione S-transferase–green fluorescent protein–RanBP3 fusions demonstrated that a region at the N terminus is essential and sufficient for nuclear localization. Deletion analysis further mapped the signal sequence to residues 40 to 57. This signal resembles the NLSs of c-Myc and Pho4p. However, several residues essential for import via the c-Myc NLS are unnecessary in the RanBP3 NLS. RanBP3 NLS-mediated import was blocked by competitive inhibitors of importin-α or importin-β or by the absence of importin-α. Binding assays using recombinant importin-α1, -α3, -α4, -α5, and -α7 revealed a preferential interaction of the RanBP3 NLS with importin-α3 and -α4, in contrast to the simian virus 40 T-antigen NLS, which interacted to similar extents with all of the isoforms. Nuclear import of the RanBP3 NLS was most efficient in the presence of importin-α3. These results demonstrate that members of the importin-α family possess distinct preferences for certain NLS sequences and that the NLS consensus sequence is broader than was hitherto suspected.
Long-Term Outcomes of an Antimicrobial Stewardship Program Implemented in a Hospital with Low Baseline Antibiotic Use

OBJECTIVE To evaluate the long-term outcomes of an antimicrobial stewardship program (ASP) implemented in a hospital with low baseline antibiotic use. DESIGN Quasi-experimental, interrupted time-series study. SETTING Public safety net hospital with 525 beds. INTERVENTION Implementation of a formal ASP in July 2008. METHODS We conducted a time-series analysis to evaluate the impact of the ASP over a 6.25-year period (July 1, 2008–September 30, 2014) while controlling for trends during a 3-year preintervention period (July 1, 2005–June 30, 2008). The primary outcome measures were total antibacterial and antipseudomonal use in days of therapy (DOT) per 1,000 patient-days (PD). Secondary outcomes included antimicrobial costs and resistance, hospital-onset Clostridium difficile infection, and other patient-centered measures. RESULTS During the preintervention period, total antibacterial and antipseudomonal use were declining (−9.2 and −5.5 DOT/1,000 PD per quarter, respectively). During the stewardship period, both continued to decline, although at lower rates (−3.7 and −2.2 DOT/1,000 PD, respectively), resulting in a slope change of 5.5 DOT/1,000 PD per quarter for total antibacterial use (P=.10) and 3.3 DOT/1,000 PD per quarter for antipseudomonal use (P=.01). Antibiotic expenditures declined markedly during the stewardship period (−$295.42/1,000 PD per quarter, P=.002). There were variable changes in antimicrobial resistance and few apparent changes in C. difficile infection and other patient-centered outcomes. CONCLUSION In a hospital with low baseline antibiotic use, implementation of an ASP was associated with sustained reductions in total antibacterial and antipseudomonal use and declining antibiotic expenditures. Common ASP outcome measures have limitations. Infect Control Hosp Epidemiol 2015;00(0): 1–9
A Dipole Pattern of Summertime Rainfall across the Indian Subcontinent and the Tibetan Plateau

AbstractThe Tibetan Plateau (TP) has long been regarded as a key driver for the formation and variations of the Indian summer monsoon (ISM). Recent studies, however, have indicated that the ISM also exerts a considerable impact on rainfall variations in the TP, suggesting that the ISM and the TP should be considered as an interactive system. From this perspective, the covariability of the July–August mean rainfall across the Indian subcontinent (IS) and the TP is investigated. It is found that the interannual variation of IS and TP rainfall exhibits a dipole pattern in which rainfall in the central and northern IS tends to be out of phase with that in the southeastern TP. This dipole pattern is associated with significant anomalies in rainfall, atmospheric circulation, and water vapor transport over the Asian continent and nearby oceans. Rainfall anomalies and the associated latent heating in the central and northern IS tend to induce changes in regional circulation that suppress rainfall in the southeast.