LLukas22/scidocs huggingface dataset:
The Next Era: Deep Learning in Pharmaceutical Research

Over the past decade we have witnessed the increasing sophistication of machine learning algorithms applied in daily use from internet searches, voice recognition, social network software to machine vision software in cameras, phones, robots and self-driving cars. Pharmaceutical research has also seen its fair share of machine learning developments. For example, applying such methods to mine the growing datasets that are created in drug discovery not only enables us to learn from the past but to predict a molecule’s properties and behavior in future. The latest machine learning algorithm garnering significant attention is deep learning, which is an artificial neural network with multiple hidden layers. Publications over the last 3 years suggest that this algorithm may have advantages over previous machine learning methods and offer a slight but discernable edge in predictive performance. The time has come for a balanced review of this technique but also to apply machine learning methods such as deep learning across a wider array of endpoints relevant to pharmaceutical research for which the datasets are growing such as physicochemical property prediction, formulation prediction, absorption, distribution, metabolism, excretion and toxicity (ADME/Tox), target prediction and skin permeation, etc. We also show that there are many potential applications of deep learning beyond cheminformatics. It will be important to perform prospective testing (which has been carried out rarely to date) in order to convince skeptics that there will be benefits from investing in this technique.
Lopinavir tablet pharmacokinetics with an increased dose during pregnancy.

OBJECTIVE
Reduced lopinavir concentrations have been demonstrated with use of the capsule formulation during the third trimester of pregnancy. This study determined lopinavir exposure with an increased dose of the new tablet formulation during the third trimester.


DESIGN
International Maternal Pediatric Adolescent AIDS Clinical Trials 1026s is a prospective nonblinded pharmacokinetic study in HIV-infected pregnant women, including a cohort receiving 2 lopinavir/ritonavir tablets (400 mg/100 mg) twice daily during the second trimester, 3 tablets (600 mg/150 mg) twice daily during the third trimester, and 2 tablets (400 mg/100 mg) twice daily post delivery through 2 weeks postpartum.


METHODS
Steady-state 12-hour pharmacokinetic profiles were performed during pregnancy and at 2 weeks postpartum. Lopinavir and ritonavir were measured by reverse-phase high-performance liquid chromatography (detection limit, 0.09 mcg/mL).


RESULTS
Thirty-three women were studied. Median lopinavir AUC for the second trimester (n = 11), third trimester (n = 33), and postpartum (n = 27) were 72, 96, and 133 mcg x hr/mL, respectively. Median minimum lopinavir concentrations were 3.4, 4.9, and 6.9 mcg/mL.


CONCLUSIONS
The higher lopinavir/ritonavir tablet dose (600 mg/150 mg) provided exposure during the third trimester similar to the average AUC (98 mcg x hr x mL(-1) in nonpregnant adults taking 400 mg/100 mg twice daily. The higher dose should be used during the second and third trimesters of pregnancy. Postpartum dosing can be reduced to standard dosing before 2 weeks postpartum.
On the Choice-Based Linear Programming Model for Network Revenue Management

G et al. [Gallego, G., G. Iyengar, R. Phillips, A. Dubey. 2004. Managing flexible products on a network. CORC Technical Report TR-2004-01, Department of Industrial Engineering and Operations Research, Columbia University, New York.] recently proposed a choice-based deterministic linear programming model (CDLP) for network revenue management (RM) that parallels the widely used deterministic linear programming (DLP) model. While they focused on analyzing “flexible products”—a situation in which the provider has the flexibility of using a collection of products (e.g., different flight times and/or itineraries) to serve the same market demand (e.g., an origin-destination connection)—their approach has broader implications for understanding choice-based RM on a network. In this paper, we explore the implications in detail. Specifically, we characterize optimal offer sets (sets of available network products) by extending to the network case a notion of “efficiency” developed by Talluri and van Ryzin [Talluri, K. T., G. J. van Ryzin. 2004. Revenue management under a general discrete choice model of consumer behavior. Management Sci. 50 15–33.] for the single-leg, choice-based RM problem. We show that, asymptotically, as demand and capacity are scaled up, only these efficient sets are used in an optimal policy. This analysis suggests that efficiency is a potentially useful approach for identifying “good” offer sets on networks, as it is in the case of single-leg problems. Second, we propose a practical decomposition heuristic for converting the static CDLP solution into a dynamic control policy. The heuristic is quite similar to the familiar displacement-adjusted virtual nesting (DAVN) approximation used in traditional network RM, and it significantly improves on the performance of the static LP solution. We illustrate the heuristic on several numerical examples.
Cost effective IP camera for video surveillance

IP cameras are key devices for a video surveillance system. This paper introduces a cost effective, power efficient and low profile IP Camera. The camera consists of a video preprocessing unit, an H.264 encoder, and an embedded streaming server. The video preprocessing unit is used for video data acquisition and format conversion; the H.264 encoder compresses the preprocessed data with H.264 baseline encoding tools; and the streaming server produces a continuous flow of data for the Internet video communication and surveillance applications. Both the encoder and the streaming server are implemented with the cost effective and power efficient Blackfin DSP and ARM9 processors. Key approaches for efficient usage of the DSP resources and main optimization methods for the encoding speed are presented in this paper. Performance tests and practical uses of the IP camera indicate that it is easy to use and able to deliver CIF or VGA size of real-time video clips directly to the Internet with high PSNR quality and low bitrates. Application of these IP cameras to the video surveillance systems may greatly lower the requirements for the network bandwidth, significantly improve the video quality, and efficiently enhance the system reliability accordingly.
Resolution and pebbling games

We define a collection of Prover-Delayer games to characterise some subsystems of propositional resolution. We give some natural criteria for the games which guarantee lower bounds on the resolution width. By an adaptation of the size-width tradeoff for resolution of [10] this result also gives lower bounds on proof size. 
 
We also use games to give upper bounds on proof size, and in particular describe a good strategy for the Prover in a certain game which yields a short refutation of the Linear Ordering principle. 
 
Using previous ideas we devise a new algorithm to automatically generate resolution refutations. On bounded width formulas, our algorithm is as least as good as the width based algorithm of [10]. Moreover, it finds short proofs of the Linear Ordering principle when the variables respect a given order. 
 
Finally we approach the question of proving that a formula F is hard to refute if and only if is “almost” satisfiable. We prove results in both directions when “almost satisfiable” means that it is hard to distuinguish F from a satisfiable formula using limited pebbling games.
Surgical management and long-term outcome of complicated liver hydatid cysts caused by Echinococcus granulosus.

BACKGROUND
The aim of this retrospective study was to evaluate clinical presentation and long-term outcome of patients treated surgically for complicated liver hydatid cysts.


PATIENTS AND METHODS
Eighty-four patients with liver hydatid cysts underwent an operation at the Geneva University Hospital between 1980 and 1999. Clinical presentation, postoperative morbidity, mortality, and long-term recurrence rate were evaluated.


RESULTS
Among the 84 patients with liver hydatid disease, 35 patients (41%) presented complicated cysts (ie, cysts that had developed a fistula into adjacent structures or organs). In most patients, the fistula communicated with the biliary tree (n = 25), but we also observed communication with the right lung (n = 3), the right diaphragm (n = 2), liver parenchyma (n = 1), and peritoneal cavity (n = 1). Complete removal of the cystic disease was possible in 24 of 35 patients (70%). In 11 patients, fragments of cysts were not removed because of their location adjacent to main vessels. Postoperatively, 8 patients (23%) developed a severe complication (grade II and III). There were no postoperative deaths, and no recurrences of hydatid disease were observed with a median follow-up of 8.6 years (complete follow-up was obtained in 69% of patients).


CONCLUSIONS
Complicated liver hydatid disease is frequent and was observed in almost half of patients operated for liver hydatid cysts at our center. Using a surgical strategy aimed at complete removal of cystic and pericystic tissue with simultaneous treatment of the fistulous tract, we observed 23% postoperative morbidity, no mortality, and no recurrence of disease with a median follow-up of >8 years.
A REVIEW OF CERAMIC THIN FILM TECHNOLOGY.

Abstract : The report comprises a detailed description of the materials, techniques and problems in each of the three major areas of thin film applications--dielectrics, magnetics and semiconductors. Included in the report are also basic theories necessary for a complete understanding of the physical and chemical processes related to the areas of interest. Theoretical analysis leads to a description of the critical physical, chemical and structural requirements of films for device applications. The state of the art of all aspects of ceramic thin film technology is critically reviewed, and recommendations are suggested to overcome existing limitations. (Author)
Body composition in older acute stroke patients after treatment with individualized, nutritional supplementation while in hospital

BACKGROUND
Individualized, nutritional support reduced undernutrition among older stroke patients and improved quality of life in our recent randomized, controlled trial. Weight control thus seems to be important after stroke, and methods for monitoring nutritional status need to be simple and non-invasive. Here we aimed to assess if the nutritional intervention altered body composition in men and women in this study cohort, and also to examine the correlation between the methods for assessing body-, fat- and fat-free mass.


METHODS
Acute stroke patients > 65 years at nutritional risk were randomized to either individualized, nutritional treatment with energy- and protein rich supplementation (intervention, n = 58) or routine, nutritional care (control, n = 66) while in hospital. Body composition was assessed with anthropometry and bioelectrical impedance. The follow-up period was three months.


RESULTS
During the first week while in hospital, weight loss was smaller in the intervention group compared with the controls (P = 0.013). After three months weight- and fat loss were significant in both men and women. Whereas no significant differences were found in changes in body composition between the male study groups, in the women both weight loss (P = 0.022) and fat loss (P = 0.005) was smaller in the intervention group compared with the controls. A high correlation (r = 0.87) between mid upper arm circumference (MUAC) and body mass index (BMI) was found.


CONCLUSIONS
Individualized nutritional support to older stroke patients in hospital was beneficial for maintaining an adequate body mass and body composition the first week and seemed to have a preventive effect on fat loss among women, but not among men after three months. Measurement of MUAC may be used in the assessment of nutritional status when BMI cannot be obtained.


TRIAL REGISTRATION
This trial is registered with ClinicalTrials.gov, number NCT00163007.
Vision Therapy for Post-Concussion Vision Disorders.

PURPOSE
To determine the frequency and types of vision disorders associated with concussion, and to determine the success rate of vision therapy for these conditions in two private practice settings.


METHODS
All records over an 18-month period of patients referred for post-concussion vision problems were reviewed from two private practices. Diagnoses of vergence, accommodative, or eye movement disorders were based on pre-established, clinical criteria. Vision therapy was recommended based on clinical findings and symptoms.


RESULTS
Two hundred eighteen patient records were found with a diagnosis of concussion. Fifty-six percent of the concussions were related to sports, 20% to automobile accidents, and 24% to school, work, or home-related incidents. The mean age was 20.5 years and 58% were female. Eighty-two percent of the patients had a diagnosis of an oculomotor problem [binocular problems (62%), accommodative problems (54%), eye movement problems (21%)]. The most prevalent diagnoses were convergence insufficiency (CI, 47%) and accommodative insufficiency (AI, 42%). Vision therapy was recommended for 80% of the patients. Forty-six per cent (80/175) either did not pursue treatment or did not complete treatment. Of the 54% (95/175) who completed therapy, 85% of patients with CI were successful and 15% were improved, and with AI, 33% were successful and 67% improved. Clinically and statistically significant changes were measured in symptoms, near point of convergence, positive fusional vergence, and accommodative amplitude.


CONCLUSIONS
In this case series, post-concussion vision problems were prevalent and CI and AI were the most common diagnoses. Vision therapy had a successful or improved outcome in the vast majority of cases that completed treatment. Evaluation of patients with a history of concussion should include testing of vergence, accommodative, and eye movement function. Prospective clinical trials are necessary to assess the natural history of concussion-related vision disorders and treatment effectiveness.
A model-driven approach for representing clinical archetypes for Semantic Web environments

The life-long clinical information of any person supported by electronic means configures his Electronic Health Record (EHR). This information is usually distributed among several independent and heterogeneous systems that may be syntactically or semantically incompatible. There are currently different standards for representing and exchanging EHR information among different systems. In advanced EHR approaches, clinical information is represented by means of archetypes. Most of these approaches use the Archetype Definition Language (ADL) to specify archetypes. However, ADL has some drawbacks when attempting to perform semantic activities in Semantic Web environments. In this work, Semantic Web technologies are used to specify clinical archetypes for advanced EHR architectures. The advantages of using the Ontology Web Language (OWL) instead of ADL are described and discussed in this work. Moreover, a solution combining Semantic Web and Model-driven Engineering technologies is proposed to transform ADL into OWL for the CEN EN13606 EHR architecture.
Steerable Dielectric Resonator Phased-Array Antenna Based on Inkjet-Printed Tunable Phase Shifter With BST Metal-Insulator-Metal Varactors

This letter presents a steerable phased-array antenna at C/X-band. The phase shifters used in the design, are implementing inkjet-printed barium strontium titanate (BST) thick-films. This method enables low-voltage tuning and low fabrication cost. The phase shifter is tuned by integrated metal-insulator-metal varactors, whose electrodes are fabricated by photolithography and inkjet-printed dielectric layer. A tunability of 46% at 8 GHz is achieved by applying 50 V across a 1.2- μm-thick BST film. The 11-unit-cells loaded-line tunable phase shifter achieves a figure of merit above 40°/dB from 7 to 8.5 GHz. Dielectric resonator antenna, fabricated from bulk-glass ceramic, has been implemented as radiating element with a stacked architecture for wide bandwidth and high gain. A beam steering of ±30° has been measured with a 1 ×4-element phased array in the anechoic chamber.
Plasma Free Hemoglobin Is an Independent Predictor of Mortality among Patients on Extracorporeal Membrane Oxygenation Support

BACKGROUND
Hemolysis is common in all extracorporeal circuits as evident by the elevated plasma free hemoglobin (PFHb) level. We investigated whether increased hemolysis during extracorporeal membrane oxygenation (ECMO) is an independent mortality predictor.


METHODS
We performed a retrospective observational study of consecutive subjects who received ECMO at a tertiary care facility from 2007-2013 to investigate independent predictors of in-hospital mortality. We examined variables related to patient demographics, comorbidities, markers of hemolysis, ECMO characteristics, transfusion requirements, and complications. 24-hour PFHb > 50 mg/dL was used as a marker of severe hemolysis.


RESULTS
154 patients received ECMO for cardiac (n = 115) or pulmonary (n = 39) indications. Patients' mean age was 51 years and 75.3% were males. Compared to nonsurvivors, survivors had lower pre-ECMO lactic acid (p = 0.026), lower 24-hour lactic acid (p = 0.023), shorter ECMO duration (P = 0.01), fewer RBC transfusions on ECMO (p = 0.008) and lower level of PFHb 24-hours post ECMO implantation (p = 0.029). 24-hour PFHb > 50 mg/dL occurred in 3.9 % versus 15.5% of survivors and nonsurvivors, respectively, p = 0.002. A Cox proportional hazard analysis identified PFHb > 50 mg/dL 24-hours post ECMO as an independent predictor of mortality (OR= 3.4, 95% confidence interval: 1.3 - 8.8, p = 0.011).


CONCLUSION
PFHb > 50 mg/dL checked 24-hour post ECMO implantation is a useful tool to predict mortality. We propose the routine checking of PFHb 24-hours after ECMO initiation for early identification and treatment of the cause of hemolysis.
Video event classification using string kernels

Event recognition is a crucial task to provide high-level semantic description of the video content. The bag-of-words (BoW) approach has proven to be successful for the categorization of objects and scenes in images, but it is unable to model temporal information between consecutive frames. In this paper we present a method to introduce temporal information for video event recognition within the BoW approach. Events are modeled as a sequence composed of histograms of visual features, computed from each frame using the traditional BoW. The sequences are treated as strings (phrases) where each histogram is considered as a character. Event classification of these sequences of variable length, depending on the duration of the video clips, are performed using SVM classifiers with a string kernel that uses the Needlemann-Wunsch edit distance. Experimental results, performed on two domains, soccer videos and a subset of TRECVID 2005 news videos, demonstrate the validity of the proposed approach.
Mechanisms of ceramic coating deposition in solution-precursor plasma spray

The solution-precursor plasma spray (SPPS) method is a new process for depositing thick ceramic coatings, where solution feedstock (liquid) is injected into a plasma. This versatile method has several advantages over the conventional plasma spray method, and it can be used to deposit nanostructured, porous coatings of a wide variety of oxide and non-oxide ceramics for a myriad of possible applications. In an effort to understand the SPPS deposition process, key diagnostic and characterization experiments were performed on SPPS coatings in the Y2O3-stabilized ZrO2 (YSZ) system. The results from these experiments show that there are multiple pathways to SPPS coating formation. The atomized precursor droplets undergo rapid evaporation and breakup in the plasma. This is followed by precipitation, gelation, pyrolysis, and sintering. The different types of particles reach the substrate and are bonded to the substrate or the coating by sintering in the heat of the plasma. The precursor also reaches the substrate or the coating. This precursor pyrolyzes in situ on the substrate, either after it reaches a “cold” substrate or upon contact on a “hot” substrate and helps bond the particles. The coating microstructure evolves during SPPS deposition as the coating temperature reaches approximately 770 °C.
Treatment of ischemic pain in patients suffering from peripheral vasculopathy with transdermal buprenorphine plus epidural morphine with ropivacaine vs. epidural morphine with ropivacaine.

AIM
This study compared the efficacy and safety of buprenorphine transdermal delivery system with peridural infusion of morphine and ropivacaine to peridural infusion alone for the control of ischemic pain in patients suffering from peripheral vasculopathy.


METHODS
Eighty-six patients were randomized into two groups. In the first group, a buprenorphine patch 35 microg/hour TTDS (transtec transdermal device plus ropivacaine and morphine) was applied, and a peridural infusion of ropivacaine/morphine (200 mg + 2 mg) was established. In the second group, ropivacaine and morphine analgesia was obtained using a peridural infusion and a placebo patch. The primary efficacy parameter was the visual analog scale score for pain. Secondary parameters of efficacy were the short-form McGill Pain Questionnaire scores and a score for pain interference with sleep obtained from patient diaries evaluated every week for a period of 4 weeks.


RESULTS
Subjects in the TTDS group reported a reduction in pain, increased sleep, and a lower incidence of side effects compared with the control group.


CONCLUSION
Transdermal buprenorphine use resulted in significant pain relief with excellent patient satisfaction, which may translate into improvement in mood and quality of life.