Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).

Glycosciences.DB, the glycan structure database of the Glycosciences.de portal, collects various kinds of data on glycan structures, including carbohydrate moieties from worldwide Protein Data Bank (wwPDB) structures. This way it forms a bridge between glycomics and proteomics resources. A major update of this database combines a redesigned web interface with a series of new functions. These include separate entry pages not only for glycan structures but also for literature references and wwPDB entries, improved substructure search options, a newly available keyword search covering all types of entries in one query, and new types of information that is added to glycan structures. These new features are described in detail in this article, and options how users can provide information to the database are discussed as well. Glycosciences.DB is available at http://www.glycosciences.de/database/ and can be freely accessed.

Glycomics@ExPASy: Bridging the Gap.

Glycomics@ExPASy (https://www.expasy.org/glycomics) is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralize web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. The scarcity of data bridging these two disciplines led us to design tools as interactive as possible based on database connectivity to facilitate data exploration and support hypothesis building. Glycomics@ExPASy was designed, and is developed, with a long-term vision in close collaboration with glycoscientists to meet as closely as possible the growing needs of the community for glycoinformatics.

Lysozyme's lectin-like characteristics facilitates its immune defense function.

Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.

Low-Power and Low-Cost Environmental IoT Electronic Nose Using Initial Action Period Measurements.

In this work, we present a complete hardware development and current consumption study of a portable electronic nose designed for the Internet-of-Things (IoT). Thanks to the technique of measuring in the initial action period, it can be reliably powered with a moderate-sized battery. The system is built around the well-known SoC (System on Chip) ESP8266EX, using low-cost electronics and standard sensors from Figaro's TGS26xx series. This SoC, in addition to a powerful microcontroller, provides Wi-Fi connectivity, making it very suitable for IoT applications. The system also includes a precision analog-to-digital converter for the measurements and a charging module for the lithium battery. During its operation, the designed software takes measurements periodically, and keeps the microcontroller in deep-sleep state most of the time, storing several measurements before uploading them to the cloud. In the experiments and tests carried out, we have focused our work on the measurement and optimization of current consumption, with the aim of extending the battery life. The results show that taking measurements every 4 min and uploading data every five measurements, the battery of 750 mAh needs to be charged approximately once a month. Despite the fact that we have used a specific model of gas sensor, this methodology is quite generic and could be extended to other sensors with lower consumption, increasing very significantly the duration of the battery.

Precise Pollen Grain Detection in Bright Field Microscopy Using Deep Learning Techniques.

The determination of daily concentrations of atmospheric pollen is important in the medical and biological fields. Obtaining pollen concentrations is a complex and time-consuming task for specialized personnel. The automatic location of pollen grains is a handicap due to the high complexity of the images to be processed, with polymorphic and clumped pollen grains, dust, or debris. The purpose of this study is to analyze the feasibility of implementing a reliable pollen grain detection system based on a convolutional neural network architecture, which will be used later as a critical part of an automated pollen concentration estimation system. We used a training set of 251 videos to train our system. As the videos record the process of focusing the samples, this system makes use of the 3D information presented by several focal planes. Besides, a separate set of 135 videos (containing 1234 pollen grains of 11 pollen types) was used to evaluate detection performance. The results are promising in detection (98.54% of recall and 99.75% of precision) and location accuracy (0.89 IoU as the average value). These results suggest that this technique can provide a reliable basis for the development of an automated pollen counting system.

Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides.

Escherichia coli O-antigen database (ECODAB) is a web-based application to support the collection of E. coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as information on glycosyltransferases (GTs) involved in the assembly of O-antigen polysaccharides. The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository to one that can be used for generating novel data on its own. GT specificity is suggested through sequence comparison with GTs whose function is known. The migration of ECODAB to a relational database has allowed the automation of all processes to update, retrieve and present information, thereby, endowing the system with greater flexibility and improved overall performance. ECODAB is freely available at http://www.casper.organ.su.se/ECODAB/. Currently, data on 169 E. coli unique O-antigen entries and 338 GTs is covered. Moreover, the scope of the database has been extended so that polysaccharide structure and related information from other bacteria subsequently can be added, for example, from Streptococcus pneumoniae.

[Reprodcutive results of radical trachelectomy]. / Resultados reproductivos de la traquelectomía radical.

BACKGROUND: Historically, cervical cancer in early stages has been treated with radical hysterectomy and radiotherapy with no option in keeping the uterine-ovarian function. Since two decades ago, evidence shows these cases are candidates for radical trachelectomy, a procedure capable of preserving the fertility without affecting the oncological outcome. OBJECTIVE: To analyze reproductive results among patients treated with radical trachelectomy, in a reference center from the northeast of Mexico. MATERIAL AND METHOD: Between March 1999 and December 2013, 27 cases with cervical cancer in early stages were treated with vaginal or abdominal radical trachelectomy in the ISSSTE Regional Hospital in Monterrey, NL (Mexico). We obtained the gynecological, medical and surgical clinical history. Plan of analysis consisted of descriptive statistics. RESULTS: Age range was 27-39 years. Main complications were cervical stenosis (n=1) and erosion of cerclaje (n=2). Eighteen patients tried to get pregnant, 8 of them got a spontaneous pregnancy; 1 more patient required assisted reproduction technics and did not succeed. All pregnancies were delivered by cesarean section and were preterm births; 3 underwent premature rupture of membranes. Two pregnancies ended in abortion, one at 10 weeks with severe hemorrhage that needed hysterectomy; the second one, at 1 7 weeks, received a fine uterine curettage. Only 6 cases (33%) got a live birth. CONCLUSIONS: Only one third of the attempted pregnancies got a live birth. Assisted reproduction technics play an important role and should be offer to all cases. Cerclaje is an important factor to carry a pregnancy up to the third trimester.

An internet of things example: classrooms access control over near field communication.

The Internet of Things is one of the ideas that has become increasingly relevant in recent years. It involves connecting things to the Internet in order to retrieve information from them at any time and from anywhere. In the Internet of Things, sensor networks that exchange information wirelessly via Wi-Fi, Bluetooth, Zigbee or RF are common. In this sense, our paper presents a way in which each classroom control is accessed through Near Field Communication (NFC) and the information is shared via radio frequency. These data are published on the Web and could easily be used for building applications from the data collected. As a result, our application collects information from the classroom to create a control classroom tool that displays access to and the status of all the classrooms graphically and also connects this data with social networks.

Improving short term instability for quantitative analyses with portable electronic noses.

One of the main problems when working with electronic noses is the lack of reproducibility or repeatability of the sensor response, so that, if this problem is not properly considered, electronic noses can be useless, especially for quantitative analyses. On the other hand, irreproducibility is increased with portable and low cost electronic noses where laboratory equipment like gas zero generators cannot be used. In this work, we study the reproducibility of two portable electronic noses, the PEN3 (commercial) and CAPINose (a proprietary design) by using synthetic wine samples. We show that in both cases short term instability associated to the sensors' response to the same sample and under the same conditions represents a major problem and we propose an internal normalization technique that, in both cases, reduces the variability of the sensors' response. Finally, we show that the normalization proposed seems to be more effective in the CAPINose case, reducing, for example, the variability associated to the TGS2602 sensor from 12.19% to 2.2%.

Consistent performance measurement of a system to detect masses in mammograms based on blind feature extraction.

BACKGROUND: Breast cancer continues to be a leading cause of cancer deaths among women, especially in Western countries. In the last two decades, many methods have been proposed to achieve a robust mammography-based computer aided detection (CAD) system. A CAD system should provide high performance over time and in different clinical situations. I.e., the system should be adaptable to different clinical situations and should provide consistent performance. METHODS: We tested our system seeking a measure of the guarantee of its consistent performance. The method is based on blind feature extraction by independent component analysis (ICA) and classification by neural networks (NN) or SVM classifiers. The test mammograms were from the Digital Database for Screening Mammography (DDSM). This database was constructed collaboratively by four institutions over more than 10 years. We took advantage of this to train our system using the mammograms from each institution separately, and then testing it on the remaining mammograms. We performed another experiment to compare the results and thus obtain the measure sought. This experiment consists in to form the learning sets with all available prototypes regardless of the institution in which them were generated, obtaining in that way the overall results. RESULTS: The smallest variation from comparing the results of the testing set in each experiment (performed by training the system using the mammograms from one institution and testing with the remaining) with those of the overall result, considering the success rate for an intermediate decision maker threshold, was roughly 5%, and the largest variation was roughly 17%. But, if we considere the area under ROC curve, the smallest variation was close to 4%, and the largest variation was about a 6%. CONCLUSIONS: Considering the heterogeneity in the datasets used to train and test our system in each case, we think that the variation of performance obtained when the results are compared with the overall results is acceptable in both cases, for NN and SVM classifiers. The present method is therefore very general in that it is able to adapt to different clinical situations and provide consistent performance.

A compact and low cost electronic nose for aroma detection.

This article explains the development of a prototype of a portable and a very low-cost electronic nose based on an mbed microcontroller. Mbeds are a series of ARM microcontroller development boards designed for fast, flexible and rapid prototyping. The electronic nose is comprised of an mbed, an LCD display, two small pumps, two electro-valves and a sensor chamber with four TGS Figaro gas sensors. The performance of the electronic nose has been tested by measuring the ethanol content of wine synthetic matrices and special attention has been paid to the reproducibility and repeatability of the measurements taken on different days. Results show that the electronic nose with a neural network classifier is able to discriminate wine samples with 10, 12 and 14% V/V alcohol content with a classification error of less than 1%.

Ecogeography of Dioscorea remotiflora Kunth: An Endemic Species from Mexico.

Dioscorea remotiflora, a perennial climbing herbaceous plant native to Mexico, produces tubers with great nutritional and ethnobotanical value. However, most ecological aspects of this plant remain unknown, which limits its cultivation and use. This is why the objective of this research was to characterize the ecogeography of D. remotiflora as a source to determine its edaphoclimatic adaptability and current and potential distribution. A comprehensive database encompassing 480 geo-referenced accessions was assembled from different data sources. Using the Agroclimatic Information System for México and Central America (SIAMEXCA), 42 environmental variables were formulated. The MaxEnt model within the Kuenm R package was employed to predict the species distribution. The findings reveal a greater presence of D. remotiflora in harsh environments, characterized by arid to semiarid conditions, poor soils, and hot climates with long dry periods. Niche modeling revealed that seven key variables determine the geographical distribution of D. remotiflora: precipitation of the warmest quarter, precipitation of the driest month, minimum temperature of the coldest month, November-April solar radiation, annual mean relative humidity, annual moisture availability index, and May-October mean temperature. The current potential distribution of D. remotiflora is 428,747.68 km2. Favorable regions for D. remotiflora coincide with its current presence sites, while other suitable areas, such as the Yucatán Peninsula, northeast region, and Gulf of Mexico, offer potential expansion opportunities for the species distribution. The comprehensive characterization of Dioscorea remotiflora, encompassing aspects such as its soil habitats and climate adaptation, becomes essential not only for understanding its ecology but also for maximizing its economic potential. This will enable not only its sustainable use but also the exploration of commercial applications in sectors such as the pharmaceutical and food industries, thus providing a broader approach for its conservation and optimal utilization in the near future.

Latin American consensus recommendations on the risk of infections in people with multiple sclerosis treated with disease modifying drugs.

INTRODUCTION: The emergence of several therapeutic options in multiple sclerosis (MS), which significantly modify the immune system functioning, has led to the need for the consideration of additional factors, such as risk of infections, in the decision-making process. The aim of these consensus recommendations was to discuss and perform a practical guide to Latin American neurologists on the risk of infections at diagnosis, follow-up and prior to initiation of DMDs. METHODS: A panel of Latin American neurologists, experts in demyelinating diseases and dedicated to management and care of MS patients, gathered during 2021 and 2022 to make consensus recommendations on the risk of infections in PwMS treated with DMDs in Latin America. The RAND/UCLA methodology was developed to synthesize the scientific evidence and expert opinions on health care topics and was used for reaching a formal agreement. RESULTS: Recommendations were established based on relevant published evidence and expert opinion, focusing on: 1- baseline infection disease and vaccination status; 2- opportunistic infections; 3- progressive multifocal leukoencephalopathy; 4- genitourinary system infections; 5- respiratory tract infections; 6- digestive system infections, 7-others local infections and 8- COVID-19. CONCLUSION: The recommendations of this consensus seek to optimize the care, management and treatment of PwMS in Latin America. The standardized evidence-based care of pwMS infections will allow better outcomes.

Acetic acid detection threshold in synthetic wine samples of a portable electronic nose.

Wine quality is related to its intrinsic visual, taste, or aroma characteristics and is reflected in the price paid for that wine. One of the most important wine faults is the excessive concentration of acetic acid which can cause a wine to take on vinegar aromas and reduce its varietal character. Thereby it is very important for the wine industry to have methods, like electronic noses, for real-time monitoring the excessive concentration of acetic acid in wines. However, aroma characterization of alcoholic beverages with sensor array electronic noses is a difficult challenge due to the masking effect of ethanol. In this work, in order to detect the presence of acetic acid in synthetic wine samples (aqueous ethanol solution at 10% v/v) we use a detection unit which consists of a commercial electronic nose and a HSS32 auto sampler, in combination with a neural network classifier (MLP). To find the characteristic vector representative of the sample that we want to classify, first we select the sensors, and the section of the sensors response curves, where the probability of detecting the presence of acetic acid will be higher, and then we apply Principal Component Analysis (PCA) such that each sensor response curve is represented by the coefficients of its first principal components. Results show that the PEN3 electronic nose is able to detect and discriminate wine samples doped with acetic acid in concentrations equal or greater than 2 g/L.

Practical issues concerning the use of Magnetic Resonance Imaging in Multiple Sclerosis in Latin America: Discussion from 16 centres on behalf of the Foro Latam EM Study Group.

MAGNIMS-CMSC-NAIMS consensus recommendations on the use of MRI in patients with multiple sclerosis have been recently published, and they have been fundamental for improving patient care. Implementation of these and previous MAGNIMS recommendations have not been established in many countries. Addressing the local limitations behind these difficulties is needed. A panel of 14 MS neurologists from 16 different reference centres from Chile, Argentina, Mexico, Colombia, Ecuador, Panamá, Perú and Brazil met to discuss the current situation regarding the use of MRI in MS including a) Access and availability, b) Standardized acquisition protocols and reports, and c) Multicentric research potential.

CFTR allelic heterogeneity in Mexican patients with cystic fibrosis: implications for molecular screening.

INTRODUCTION: Cystic fibrosis, the most common autosomal recessive disorder, is caused by defects in the CF transmembrane conductance regulator gene (CFTR) that encodes a chloride channel. To date, over 1,800 mutations have been described related to the causative gene of CF, showing a variable frequency among populations. In a previous extensive analysis of the CFTR locus in 97 Mexican patients, 34 different mutations (75% of CF alleles) were found using several strategies for mutation screening; however, 63% had at least an uncharacterized allele. Despite the combined technologies used, there are still a great number of unknown mutations in the Mexican population. OBJECTIVE: Screening of the CFTR gene to provide additional evidence of the mutational wide spectrum responsible for CF in Mexican patients. MATERIAL AND METHODS: In this study, the number of unrelated CF patients was increased to 230, 133 new cases and the 97 previously reported to include 63% with at least an uncharacterized allele. Additional tools were used to improve the detection rate of CF mutations, such as a commercial kit for 36 mutations plus a single chain conformational polymorphism method and DNA sequencing. RESULTS: By using a combination of these strategies we characterized 77.7% of all the CF alleles, resulting in a total of 46 different mutations detected, including the identification of 12 additional mutations (p.R334W, p.A455E, c.3120+1G > A, c.3272-26A > G, c.711+1G > T, p.Q552X, p.W1282X, c.IVS8-5T, p.R1162X and p.R347P, p.D1152H and p.T1036N). Although these 12 mutations have been reported in other populations, they have not yet been reported in Mexican patients. This report shows that Mexico has one of the widest spectra of CFTR mutations worldwide. The knowledge of the ethnic and geographic distribution of CFTR mutations in this population will allow the development of more effective methods for diagnosis and treatment.

Cannabis and multiple sclerosis.

INTRODUCTION: Patients with multiple sclerosis (MS) may suffer from spasticity and pain during their disease course. Baclofen, dantrolene, diazepam and gabapentin have been used as first-line options to treat these conditions, with modest results. Medical use of marijuana smoking has bypassed traditional clinical trials and has been legalized as a therapeutic option for MS-related spasticity and pain in some countries. Cannabis-derived drugs have been tested and approved for medical use. AREAS COVERED: With the development of nabiximols by the pharmaceutical industry, more countries have made it possible for patients with MS to have legal access to cannabis-related therapies. The evidence-based data on nabiximols and MS-related spasticity, pain, and urinary symptoms is consistent. There are over 7,500 patients reported in 33 studies (12 from the United Kingdom and 11 from Italy). EXPERT OPINION: Nabiximols is safe and effective for patients with MS whose spasticity could not be treated with the first-line oral drugs. At present, legislation, bureaucracy and costs involved in prescribing this drug limit the experience of neurologists from many countries. There is no scientific evidence that smoking marijuana can be beneficial to patients with MS.

Symbol Digit Modalities Test-Oral Version: An Analysis of Culture Influence on a Processing Speed Test in Argentina, Mexico, and the USA.

The Symbol Digit Modalities Test (SDMT) is an information processing speed test. The aim of this study was to compare the SDMT across three samples: the USA, Mexico, and Argentina. The hypothesis is that performance will vary based on native language and cultural differences between these countries. The SDMT was administered to 129 healthy volunteers. Participants from the USA performed better than participants from Argentina and Mexico (p < .01), and no differences were observed between the latter groups (p = .15). Processing speed differs between the studied populations of Latin America and Anglo-America. Possible interpretations of this result are presented.

Uncovered Contribution of Kv7 Channels to Pulmonary Vascular Tone in Pulmonary Arterial Hypertension.

K+ channels play a fundamental role regulating membrane potential of pulmonary artery (PA) smooth muscle cells and their impairment is a common feature in pulmonary arterial hypertension (PAH). K+ voltage-gated channel subfamily Q (KCNQ1-5) or Kv7 channels and their regulatory subunits subfamily E (KCNE) regulatory subunits are known to regulate vascular tone, but whether Kv7 channel function is impaired in PAH and how this can affect the rationale for targeting Kv7 channels in PAH remains unknown. Here, we have studied the role of Kv7/KCNE subunits in rat PA and their possible alteration in PAH. Using the patch-clamp technique, we found that the total K+ current is reduced in PA smooth muscle cells from pulmonary hypertension animals (SU5416 plus hypoxia) and Kv7 currents made a higher contribution to the net K+ current. Likewise, enhanced vascular responses to Kv7 channel modulators were found in pulmonary hypertension rats. Accordingly, KCNE4 subunit was highly upregulated in lungs from pulmonary hypertension animals and patients. Additionally, Kv7 channel activity was enhanced in the presence of Kv1.5 and TASK-1 channel inhibitors and this was associated with an increased KCNE4 membrane abundance. Compared with systemic arteries, PA showed a poor response to Kv7 channel modulators which was associated with reduced expression and membrane abundance of Kv7.4 and KCNE4. Our data indicate that Kv7 channel function is preserved and KCNE4 is upregulated in PAH. Therefore, compared with other downregulated channels, the contribution of Kv7 channels is increased in PAH resulting in an enhanced sensitivity to Kv7 channel modulators. This study provides insight into the potential usefulness of targeting Kv7 channels in PAH.

[Analysis of asthma control and quality of life in severe allergic asthmatics under treatment with anti-IgE, omalizumab]. / Control del asma y de la calidad de vida en pacientes asmáticos alérgicos graves con tratamiento anti-IgE (omalizumab).

BACKGROUND AND OBJECTIVES: To evaluate anti-IgE (ie, omalizumab) efficacy on severe allergic asthma in order to achieve the efficacy of this treatment on severe allergic asthma progress by means of asthma control questionnaire (ACQ), asthma quality of life questionnaire (AQLQ) as well as pulmonary function (FEV1) and physician overall assessment. PATIENTS AND METHODS: Fourteen patients were studied who suffered from severe allergic asthma for several years; average 20.7yr. A positive skin prick test or specific IgE antibodies to a common aeroallergen were observed in all patients who were under treatment with high doses of inhaled corticosteroids (eight of them also with oral corticosteroids). Omalizumab 150-600 mg were administrated once or twice monthly and each patient was monthly evaluated until sixteen weeks, deciding at this time which patient was or not responder in order to follow up or not omalizumab treatment. RESULTS: Physician overall assessment improved in 11 out of every 14 patients. A marked improvement was observed at two months in ACQ and AQLQ (p<0.05) and at 3 and 4 moths only in AQLQ and AQLQ-symptoms respectively (p<0.05). The FEV1 improved by 9.4% average (p=0.24). Oral corticosteroids were reduced in 4 of 8 patients and in another one there was a definitive suspension. Two patients suffered adverse reactions which suspension of treatment despite the fact that they presented improvement in questionnaires of quality of life and control of asthma. CONCLUSIONS: Omalizumab showed a marked global efficacy in more than 3 out of 4 patients suffering severe allergic asthma as revealed by physician overall assessment. Moreover significant improvements were observed in ACQ; AQLQ; AQLQ-symptoms at 2, 3 and 4 months of treatment, without significant changes in FEV1 probably due to chronic irreversible changes in airways.