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Background: The global outbreak of the 2019 novel Coronavirus Disease (COVID-19) caused by the infection with the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which appeared in China at the end of 2019, signifies a major public health issue at the current time. Objective: The objective of the present study is to characterize the physicochemical properties of the SARS-CoV-2 proteins at a residues level, and to generate a “bioinformatics fingerprint” in the form of a “PIM® profile” created for each sequence utilizing the Polarity Index Method® (PIM®), suitable for the identification of these proteins. Methods: Two different bioinformatics approaches were used to analyze sequence characteristics of these proteins at the residues level, an in-house bioinformatics system PIM®, and a set of the commonly used algorithms for the predic-tion of protein intrinsic disorder predisposition, such as PONDR® VLXT, PONDR® VL3, PONDR® VSL2, PONDR® FIT, IUPred_short and IUPred_long. The PIM® profile was generated for four SARS-CoV-2 structural proteins and compared with the corresponding profiles of the SARS-CoV-2 non-structural proteins, SARS-CoV-2 putative proteins, SARS-CoV proteins, MERS-CoV proteins, sets of bacterial, fungal, and viral proteins, cell-penetrating peptides, and a set of intrinsically disordered proteins. We also searched for the UniProt proteins with PIM® profiles similar to those of SARS-CoV-2 structural, non-structural, and putative proteins. Results: We show that SARS-CoV-2 structural, non-structural, and putative proteins are characterized by a unique PIM® profile. A total of 1736 proteins were identified from the 562,253 “reviewed” proteins from the UniProt database, whose PIM® profile was similar to that of the SARS-CoV-2 structural, non-structural, and putative proteins. Conclusion: The PIM® profile represents an important characteristic that might be useful for the identification of proteins similar to SARS-CoV-2 proteins.

Background: Selective Cationic Amphipathic Antibacterial Peptides (SCAAPs) occupy a prominent place in the production of new drugs on account of their high toxicity towards bacteria and low toxicity towards mammalian cells, low hemolytic activity, and contribution to the protection of the human immune system. Aim: their number in nature is very low, and experimental tests are very protracted and costly. Therefore, it would be useful to have bioinformatics tools that would identify them in the existing databases and also propose new synthetic SCAAPs. Methods: In order to reduce the costs of identification and/or chemical synthesis and to know the physicochemical characteristics of SCAAPs at a residues level and to obtain a “bioiformatics fingerprint” suitable for their selection, we have modified the Polarity Index Method® (PIM®) and the α-helical configuration of each sequence is included in determining their individual “PIM® profile”. We have also used a set of the computer program to determine their “Intrinsic Disorder Predisposition”. This information was then compared with other protein groups, such as bacteria, fungi, virus and Cell-Penetrating Peptides (CPP) from the UniProt database and a set of intrinsically disordered proteins. Once the “fingerprint” of SCAAPs was obtained, it was used for searching among the 559228 “reviewed” proteins from the UniProt database and a set of synthetic SCAAPs characterized by the predefined “PIM® profile” selected. Results: Our results showed that the metric named “PIM® profile” can identify, with a high level of accuracy, a group of bacterial SCAAPs. This bioinformatics study was supported at residues level, using the in-house bioinformatics system Polarity Index Method the commonly used algorithm for the prediction of intrinsic disorder predisposition, PONDR® FIT. Conclusions: The Polarity Index Method seems highly efficient identifying SCAAP candidates.

Introducción: la ventilación mecánica es una práctica común en las unidades de cuidados intensivos y anestesiología. Tiene implicaciones terapéuticas, pero también es potencialmente nociva para el sistema respiratorio y los órganos distantes, por lo cual es imprescindible monitorizar los parámetros ventilatorios de manera continua. Objetivo: describir la ecuación del movimiento del sistema respiratorio y sus aplicaciones clínicas en el paciente bajo ventilación mecánica. Desarrollo: la ecuación del movimiento del sistema respiratorio integra las fuerzas dinámicas generadas por el ventilador y las propiedades intrínsecas del pulmón y la caja torácica. Expresa la presión en el sistema respiratorio en relación con el volumen, la elastancia, la resistencia, el flujo de aire y las presiones generadas por el ventilador y el paciente. Las presiones elevadas en el sistema respiratorio se asocian a una mayor mortalidad en pacientes con ventilación mecánica, por lo que la identificación de los componentes que condicionan la elevación de las presiones mediante la ecuación del movimiento del sistema respiratorio permite realizar modificaciones a los parámetros programados del ventilador para mantener una ventilación protectora. Conclusión: la toma de decisiones basada en la ecuación del movimiento del sistema respiratorio permite realizar ajustes en los parámetros ventilatorios según las características y enfermedades del paciente bajo ventilación mecánica.

Background: The female Aedes aegypti mosquito is a vector of several arthropod-borne viruses, such as Mayaro, Dengue, Chikungunya, Yellow Fever, and Zika. These viruses cause the death of at least 600000 people a year and temporarily disable several million more around the world. Up to date, there are no effective prophylactic measures that would prevent the contact and bite of this arthropod and, therefore, its consequential contagion. Objective: The objective of the present study was to search for the regularities of the proteins expressed by these five viruses, at residues level, and obtain a “bioinformatic fingerprint” to select them. Methods: We used two bioinformatic systems, our in-house bioinformatic system named Polarity Index Method® (PIM®) supported at residues level, and the commonly used algorithm for the prediction of intrinsic disorder predisposition, PONDR® FIT. We applied both programs to the 29 proteins that express the five groups of arboviruses studied, and we calculated for each of them their Polarity Index Method® profile and their intrinsic disorder predisposition. This information was then compared with analogous information for other protein groups, such as proteins from bacteria, fungi, viruses, and cell-penetrating peptides from the UniProt database, and a set of intrinsically disordered proteins. Once the “fingerprint” of each group of arboviruses was obtained, these “fingerprints” were searched among the 559228 “reviewed” proteins from the UniProt database. Results: In total, 1736 proteins were identified from the 559228 “reviewed” proteins from the UniProt database, with similar “PIM® profile” to the 29 mutated proteins that express the five groups of arboviruses. Conclusion: We propose that the “PIM® profile” of characterization of proteins might be useful for the identification of proteins expressed by arthropod-borne viruses transmitted by Aedes aegypti mosquito.

Background The dynamic interactions of severe infectious diseases with epidemic potential and their hosts are complex. Therefore, it remains uncertain if a sporadic zoonosis restricted to a certain area will become a global pandemic or something in between. Objective The objective of the study was to present a surveillance system for acute severe infections with epidemic potential based on a deterministic-stochastic model, the StochCum Method. Design The StochCum Method is founded on clinical, administrative, and sociodemographic variables that provide a space/time map as a preventive warning of possible outbreaks of severe infections that can be complemented based on the sum of all the first accumulated cases. If the outbreak is happening in high-risk areas, an early warning can be elicited to activate the health response system and save time while waiting for the confirmation of symptomatic cases. Results The surveillance system was tested virtually for 1 month on admissions to the emergency room of a public hospital located in Mexico City, Mexico. It promptly identified simulated cases of acute respiratory infections with epidemic potential. Conclusions The StochCum Method proved to be a practical and useful system for conducting epidemic surveillance on a hospital network.

El Sindrome de Takotsubo es una disfuncion ventricular aguda reversible en ausencia de obstruccion coronaria. Una mujer de 85 anos de edad con antecedentes de reemplazo valvular aortico transcateter, ingreso por dos semanas de dolor severo por una cadera desplazada por osteosintesis fallida. Mientras se programaba para cirugia, se documento hiponatremia severa secundaria a secrecion inapropiada de hormona antidiuretica. Subitamente desarrollo edema agudo pulmonar. El ecocardiograma confirmo una valvula protesica funcional y aquinesia medial y apical de las paredes del ventriculo izquierdo. Recibio tratamiento con ventilacion mecanica no invasiva, restriccion de liquidos y diureticos. La hiponatremia y la cardiomiopatia resolvieron. Takotsubo syndrome is a form of acute reversible left ventricular dysfunction in the absence of coronary obstruction. An 85-year-old lady with a medical history of transcatheter aortic valve replacement was readmitted complaining of 2 weeks of severe pain by a displaced hip and failed osteosynthesis. While she was scheduled for hip surgery, severe hyponatremia secondary to inappropriate antidiuretic hormone secretion was documented, and sudden-onset pulmonary edema ensued. Echocardiography confirmed normally functioning aortic prosthetic valve and classical features of Takotsubo. She was treated with non-invasive mechanical ventilation, water restriction, and diuretics. Hyponatremia and the cardiomyopathy resolved and the patient recovered completely.

Purpose Evaluate the associations of obesity and diabetes with the risk of mortality in critically ill patients infected with SARS-CoV-2. Materials and methods This cohort study included 115 adult patients admitted to the ICU with SARS-CoV-2 pneumonia. Anthropometric variables and biochemical (C-reactive protein, ferritin, leukocyte, neutrophils, and fibrinogen) were measured. Multivariate logistic regression analyses were used to investigate the associations. Results Mean age was 50.6 ± 11.2 years, 68.7% were male. Median BMI was 30.9 kg/m2. All patients had invasive mechanical ventilation. Patients with diabetes had increased risk of mortality with OR of 2.86 (CI 95% 1.1-7.4, p = 0.026); among those patients who, in addition to diabetes had obesity, the risk was de 3.17 (CI 95% 1.9-10.2, p = 0.038). Patients with obesity had 1.25 times greater risk of developing a severe SARS-CoV-2 infection (95% CI 1.09-1.46, p = 0.025). Negative correlation was observed between BMI and the PaO2/FiO2 ratio (r = -0.023, p

A low-cost video laryngoscope (VDL) called Hybrid 1.0 was developed using smart devices for visualization. To test its performance, we compared it with a high-end VDL device, using both in vitro and in vivo studies. During the in vitro study, medical students without experience in airway intubation were randomly asked to intubate a mannequin with different degrees of difficulty (Cormack&ndash, Lehane scales) by using either the Hybrid 1.0 VDL (GI) or a conventional laryngoscope (GII). During the in vivo study, N = 60 endotracheal intubations were performed by resident and base physicians, divided into two groups, the first group intubated with the Hybrid 1.0 VDL (GI) while the second group used a VDL C-Mac shovel (GII). As performance indexes, both studies reported the number of successful intubations (correct capnography signal) and intubation time. For the in vitro testing, no statistically significant differences were found regarding the number of successful intubations, while statistically significant differences were found regarding the intubation times. During the in vivo tests, procedures were performed by residents and by base physicians, and no statistically significant differences were found. The provided results point out that the VDL proposed can be clinically useful and offers technical characteristics similar to other VDLs that currently exist on the market.

Simultaneous mechanical ventilation of several patients with a single ventilator might reduce the deficit of these devices for the care of patients with acute respiratory failure due to Covid-19.To communicate the results of a mechanical ventilation exercise with a ventilator in a lung simulator, and simultaneously in two and four.No statistically significant differences were observed between programmed, recorded and measured positive end-expiratory pressure, mean airway pressure and peak pressure, except when simultaneously ventilating four lung simulators.Simultaneous mechanical ventilation should be implemented by medical personnel with experience in the procedure, be restricted to two patients and carried out in the intensive care unit.La ventilación mecánica simultánea a varios pacientes con un solo ventilador podría disminuir el déficit de esos dispositivos para atender a los enfermos con insuficiencia respiratoria aguda por Covid-19.Comunicar los resultados de un ejercicio de ventilación mecánica con un ventilador en un simulador de pulmón, y simultáneamente en dos y cuatro.No se observaron diferencias estadísticamente significativas entre la presión positiva al final de la espiración, presión media de la vía aérea y presión pico programadas, registradas y medidas, excepto al ventilar simultáneamente cuatro simuladores de pulmón.La ventilación mecánica simultánea debe ser instaurada por personal médico con experiencia en el procedimiento, restringirse a dos pacientes y ser realizada en la unidad de cuidados intensivos.

espanolIntroduccion: La ventilacion mecanica simultanea a varios pacientes con un solo ventilador podria disminuir el deficit de esos dispositivos para atender a los enfermos con insuficiencia respiratoria aguda por Covid-19. Objetivo: Comunicar los resultados de un ejercicio de ventilacion mecanica con un ventilador en un simulador de pulmon, y simultaneamente en dos y cuatro simuladores. Resultados: No se observaron diferencias estadisticamente significativas entre la presion positiva al final de la espiracion, presion media de la via aerea y presion pico programadas, registradas y medidas, excepto al ventilar simultaneamente cuatro simuladores de pulmon. Conclusiones: La ventilacion mecanica simultanea debe ser instaurada por personal medico con experiencia en el procedimiento, restringirse a dos pacientes y ser realizada en la unidad de cuidados intensivos. EnglishIntroduction: Simultaneous mechanical ventilation of several patients with a single ventilator might reduce the deficit of these devices for the care of patients with acute respiratory failure due to Covid-19. Objective: To communicate the results of a mechanical ventilation exercise with a ventilator in a lung simulator, and simultaneously in two and four. Results: No statistically significant differences were observed between positive end-expiratory pressure, mean airway pressure, and programmed, recorded and measured peak pressure, except when simultaneously ventilating four lung simulators. Conclusions: Simultaneous mechanical ventilation should be implemented by medical personnel with experience in the procedure, be restricted to two patients and carried out in the intensive care unit.

Measurement of intra-abdominal pressure (IAP) is realized with the Kron's method. However, this technique has drawbacks like an infusion of water into the bladder of the patient.The prove a new novel disposable sensor in the way to measure the IAP (DSIAP) this one addresses some limitations of the Kron method.The DSIAP was tested in vitro and clinical settings. The proposed technique was compared with Kron's method through Pearson correlation and Bland-Altman analysis. For in vitro tests, 159 measurements were taken performed by simulating the IAP in the bladder. For the clinical test, 20 pairs of measurements were made in patients with routine IAP monitoring in the intensive care unit.In vitro measurements showed a strong correlation between the DSIAP and the reference (r = 0.99, p-value2.2 × 10The results suggest that the proposed DSIAP showed a profile similar to pressure transducers already in clinical use while overcoming some limitations of the former.La medición de la presión intraabdominal (PIA) generalmente se realiza con el método de Kron, a pesar de presentar inconvenientes como la infusión de agua en la vejiga del paciente.Introducir un nuevo sensor desechable para medir la PIA (SDPIA) que aborda algunas limitaciones del método de Kron.Se probó el SDPIA en pruebas in vitro y clínicas. La técnica se contrastó con el método de Kron empleando la correlación de Pearson y el análisis de Bland-Altman. Para las pruebas in vitro se realizaron 159 mediciones simulando la PIA en la vejiga. Para las pruebas clínicas se realizaron 20 mediciones en pacientes con monitorización rutinaria de la PIA en la unidad de cuidados intensivos.En las mediciones in vitro se encontró una alta correlación (r = 0.99; p2.2 × 10Los resultados sugieren que el SDPIA propuesto muestra un desempeño similar al de los transductores de presión actualmente en uso clínico, mientras sobrelleva algunas limitaciones de estos últimos.

Diseases of viral origin in humans are among the most serious threats to health and the global economy. As recent history has shown the virus has a high pandemic potential, among other reasons, due to its ability to spread by air, hence the identification, investigation, containment, and treatment of viral diseases should be considered of paramount importance. In this sense, the bioinformatics research has focused on finding fast and efficient algorithms that can identify highly toxic antiviral peptides and to serve as a first filter, so that trials in the laboratory are substantially reduced. The work presented here contributes to this effort through the use of an algorithm already published by this team, called polarity index method, which identifies with high efficiency antiviral peptides from the exhaustive analysis of the polar profile, using the linear sequence of the peptide. The test carried out included all peptides in APD2 Database and 60 antiviral peptides identified by Kumar and co-workers (Nucleic Acids Res 40:W199–204, 2012), to build its AVPpred algorithm. The validity of the method was focused on its discriminating capacity so we included the 15 sub-classifications of both Databases. Electronic supplementary material The online version of this article (doi:10.1007/s12013-014-0084-4) contains supplementary material, which is available to authorized users.

Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study which evaluated the commonness and potential functionality of intrinsic disorder of these proteins and also made an attempt to characterize their origin. The origin of the preeclampsia-related proteins was assessed with a supervised technique, a Polarity Index Method (PIM), which evaluates the electronegativity of proteins based solely on their sequence. The commonness of intrinsic disorder was evaluated using several disorder predictors from the PONDR family, the charge-hydropathy plot (CH-plot) and cumulative distribution function (CDF) analyses, and using the MobiDB web-based tool, whereas potential functionality of intrinsic disorder was studied with the D2P2 resource and ANCHOR predictor of disorder-based binding sites, and the STRING tool was used to build the interactivity networks of the preeclampsia-related proteins. Peculiarities of the PIM-derived polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disordered proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. We also showed that many preeclampsia-related proteins contain numerous functional disordered regions. Therefore, these bioinformatics results led us to assume that the preeclampsia proteins are highly associated with the lipoproteins group, and that some preeclampsia-related proteins contain significant amounts of functional disorders.

In this paper we share some reflections regarding the care process in the emergency medical services, as well as some of the challenges with which these fundamental services deal. We highlight the increasing amount of patients and the complexity of some of the clinical cases, which are some of the causes that lead to the overcrowding of these services.En el presente artículo se presentan algunas reflexiones sobre el proceso de atención en los servicios de urgencias médicas, así como algunos de los retos que enfrentan estos componentes fundamentales del sector salud de nuestro país. Se hace énfasis en el creciente volumen y la complejidad de los casos atendidos en estos servicios, lo cual contribuye a su saturación.

The lipoproteins are an important group of cargo proteins known for their unique capability to transport lipids. By applying the Polarity index algorithm, which has a metric that only considers the polar profile of the linear sequences of the lipoprotein group, we obtained an analytical and structural differentiation of all the lipoproteins found in UniProt Database. Also, the functional groups of lipoproteins, and particularly of the set of lipoproteins relevant to atherosclerosis, were analyzed with the same method to reveal their structural preference, and the results of Polarity index analysis were verified by an alternate test, the Cumulative Distribution Function algorithm, applied to the same groups of lipoproteins.

In most places all over the world–including our country–services in emergency rooms are oversaturated. This situation frequently forces the continuously arriving ambulances to be redirected to other medical units, delaying the admission of patients moved and thus adversely affecting their physical condition.To introduce an improvement to the Índicede Saturación Modificado computational system, which monitors the degree of saturation of a network of emergency medical services, to include a network of ambulances, enabling in the system: (i) the effective allocation of ambulances to the site of the accident, or severe clinical event, and (ii) the remote booking of beds in the nearest and least saturated emergency room available.The evaluation and connectivity of the computational improvement to the Índicede Saturación Modificado system was carried out with a computational test verifying these two aspects, using only differences in postal codes, for time measuring.The verification of its sustainability online showed the new Índice de Saturación Modificado y Ambulancias system (ISMA) has a robust structure capable of being adapted to mobile phones, laptops or tablets, and can efficiently administrate: (i) the quantification of excessive demand in the emergency room services of a hospital network, (ii) the allocation of ambulances attending the site of the event or contingency, and (iii) the allocation of ambulances and patients, in the best distance-time conditions, from the site of the accident or clinical event to the nearest and least saturated emergency room service.This administrative management tool is efficient and simple to use, and it optimally relates independent service networks.

Las infecciones nosocomiales presentan un gran reto para la medicina hospitalaria, en general, y para las Unidades de Cuidados Intensivos, en particular. Su elevada prevalencia, la gran morbilidad y mortalidad asociadas, el incremento de la estancia hospitalaria y, en consecuencia, los costos de la atención médica han hecho que los programas de vigilancia, control y prevención de infecciones nosocomiales sean una parte toral de los protocolos de seguridad para el paciente y un indicador de calidad de la atención médica.

This work attempts to rationalize the possible prebiotic profile of the first dipeptides of about 4 billion years ago based on a computational discrete dynamic system that uses the final yields of the dipeptides obtained in Rode's experiments of salt-induced peptide formation (Rode et al., 1999, Peptides 20: 773-786). The system built a prebiotic scenario that allowed us to observe that (i) the primordial peptide generation was strongly affected by the abundances of the amino acid monomers, (ii) small variations in the concentration of the monomers have almost no effect on the final distribution pattern of the dipeptides and (iii) the most plausible chemical reaction of prebiotic peptide bond formation can be linked to Rode's hypothesis of a salt-induced scenario. The results of our computational simulations were related to former simulations of the Miller, and Fox & Harada experiments on amino acid monomer and oligomer generation, respectively, offering additional information to our approach.

Typhoid fever remains a serious public health problem. We have developed a vaccine from Salmonella enterica serovar typhi (S. typhi) outer-membrane proteins (OMPs) known as porins. A single subcutaneous dose of 10 microg of porins induced a five-fold (P = 0.05) seroconversion index consisting of IgM and IgG at 7 and 15 days after vaccination as well as the production of IgG1 and IgG2 isotypes. The porins-based vaccine induced a two-fold increase (P = 0.05) in bactericidal titres in volunteers, whom also developed a T-cell response characterized by the production of interferon-gamma (INF-gamma). Side effects after vaccination were mild and transient. The data showed that our S. typhi porins-based candidate vaccine is safe and immunogenic in healthy humans.

Most epidemiological surveillance systems for severe infections with epidemic potential are based on accumulated symptomatic cases in defined geographical areas. Eventually, all cases have to be clinically verified to confirm an outbreak. These patients will present high fever at the early stages of the disease. Here, we introduce a non-invasive low-cost electronic device (bracelet) that measures and reports 24/7, year-round information on the temperature, geographical location, and identification of the subject using the device. The data receiver can be installed in a tower (ground) or a drone (air) in densely populated or remote areas. The prototype was made with low-cost electronic components, and it was tested indoors and outdoors. The prototype shows efficient ground and air connectivity. This electronic device will allow health professionals to monitor the prevalence of fever in a geographical area and to reduce the time span between the presentation of the first cases of a potential outbreak and their medical evaluation by giving an early warning. Field tests of the device, programs, and technical diagrams of the prototype are available as Supplementary Materials.

With almost one third of the world population infected, tuberculosis is one of the most devastating diseases worldwide and it is a major threat to any healthcare system. With the mathematical-computational method named "Polarity Index Method", already published by this group, we identified, with high accuracy (70%), proteins related to Mycobacterium tuberculosis bacteria virulence pathway from the Tuberculist Database. The test considered the totality of proteins cataloged in the main domains: fungi, bacteria, and viruses from three databases: Antimicrobial Peptide Database (APD2), Tuberculist Database, Uniprot Database, and four antigens of Mycobacterium tuberculosis: PstS-1, 38-kDa, 19-kDa, and H37Rv ORF. The method described was calibrated with each database to achieve the same performance, showing a high percentage of coincidence in the identification of proteins associated with Mycobacterium tuberculosis bacteria virulence pathway located in the Tuberculist Database, and identifying a polar pattern regardless of the group studied. This method has already been used in the identification of diverse groups of proteins and peptides, showing that it is an effective discriminant. Its metric considers only one physico-chemical property, i.e. polarity.

The increase in the number of pathogens due to fungi that are tolerant to therapies does not grow at the same speed than the advance on new antifungal drugs. In this sense, it is imperative to find anti-fungi peptides that are not detrimental to mammalian cells and have an effective toxicity to fungi. In this work, we use a method called polarity index, to identify anti-fungi peptides with an efficiency of 70 %. This method already published, initially identified selective antibacterial peptides from APD2 Database, and was characterized by developing a comprehensive analysis of the polar dynamics of a peptide from its linear sequence. Discriminating tests showed that in addition to being efficient in this identification, it was also good at rejecting other classifications of peptides found in that same database.

In accordance with the second law of thermodynamics, the Universe as a whole tends to higher entropy. However, the sequence of far-from-equilibrium events that led to the emergence of life on Earth could have imposed order and complexity during the course of chemical reactions in the so-called primordial soup of life. Hence, we may expect to find characteristic profiles or biases in the prebiotic product mixtures, as for instance among the first amino acids. Seeking to shed light on this hypothesis, we have designed a high performance computer program that simulates the spontaneous formation of the amino acid monomers in closed environments. The program was designed in reference to a prebiotic scenario proposed by Sydney W. Fox. The amino acid abundances and their polarities as the two principal biases were also taken into consideration. We regarded the computational model as exhaustive since 200,000 amino acid dimers were formed by simulation, subsequently expressed in a vector and compared with the corresponding amino acid dimers that were experimentally obtained by Fox. We found a very high similarity between the experimental results and our simulations.

There is a natural protein form, insoluble and resistant to proteolysis, adopted by many proteins independently of their amino acid sequences via specific misfolding-aggregation process. This dynamic process occurs in parallel with or as an alternative to physiologic folding, generating toxic protein aggregates that are deposited and accumulated in various organs and tissues. These proteinaceous deposits typically represent bundles of β-sheet-enriched fibrillar species known as the amyloid fibrils that are responsible for serious pathological conditions, including but not limited to neurodegenerative diseases, grouped under the term amyloidoses. The proteins that might adopt this fibrillar conformation are some globular proteins and natively unfolded (or intrinsically disordered) proteins. Our work shows that intrinsically disordered and intrinsically ordered proteins can be reliably identified, discriminated, and differentiated by analyzing their polarity profiles generated using a computational tool known as the polarity index method (Polanco & Samaniego, 2009; Polanco et al., 2012; 2013; 2013a; 2014; 2014a; 2014b; 2014c; 2014d). We also show that proteins expressed in neurons can be differentiated from proteins in these two groups based on their polarity profiles, and also that this computational tool can be used to identify proteins associated with amyloidoses. The efficiency of the proposed method is high (i.e. 70%) as evidenced by the analysis of peptides and proteins in the APD2 database (2012), AVPpred database (2013), and CPPsite database (2013), the set of selective antibacterial peptides from del Rio et al. (2001), the sets of natively unfolded and natively folded proteins from Oldfield et al. (2005), the set of human revised proteins expressed in neurons, and non-human revised proteins expressed in neurons, from the Uniprot database (2014), and also the set of amyloidogenic proteins from the AmyPDB database (2014).

Overcrowd of emergency rooms affects efficiency and quality of medical care.To describe the mathematical-computational system modified overcrowd index which measures in real time and in four levels of warnings (non crowded, crowded, overcrowded and extreme overcrowded) emergency room saturation in a network of hospitals, from only seven simple variables (number of available beds, physicians and nurses, number of patients in the waiting room, in medical consultation and admitted for further evaluation, as well as number of critically ill patients admitted).The modified overcrowd index was exhaustively tested with 245,280 virtual transactions from seven hospitals in an uninterrupted schedule basis simulating hourly surveillance for four years.From 224 episodes of overcrowd, 216 (97%) where correctly identified and verified by the network of hospitals warnings, its time series also provided useful information about available personnel and resource distribution within the hospital network.Modified overcrowd index is an efficient tool detecting emergency room overcrowd outbreaks in a network of hospitals.

Selective antibacterial peptides containing less than 30 amino acid residues, cationic, with amphipathic properties, have been the subject of several studies due to their active participation and beneficial effects in strengthening the immune system of all living organisms. This manuscript reports the results of a comparison between the group of selective antibacterial peptides and another group called "cell penetrating peptides". An important number of the selective antibacterial peptides are cell penetrating peptides, suggesting that their toxicity is related to their uptake mechanism. The verification of this observation also includes the adaptation of a method previously published, called Polarity index, which reproduces and confirms the action of this new set of peptides. The efficiency of this method was verified based on four different databases, yielding a high score. The verification was based exclusively on the peptides already reported in the databases which have been experimentally verified.

A severe respiratory disease epidemic outbreak correlates with a high demand of specific supplies and specialized personnel to hold it back in a wide region or set of regions; these supplies would be beds, storage areas, hemodynamic monitors, and mechanical ventilators, as well as physicians, respiratory technicians, and specialized nurses. We describe an online cumulative sum based model named Overcrowd-Severe-Respiratory-Disease-Index based on the Modified Overcrowd Index that simultaneously monitors and informs the demand of those supplies and personnel in a healthcare network generating early warnings of severe respiratory disease epidemic outbreaks through the interpretation of such variables. Apost hochistorical archive is generated, helping physicians in charge to improve the transit and future allocation of supplies in the entire hospital network during the outbreak. The model was thoroughly verified in a virtual scenario, generating multiple epidemic outbreaks in a 6-year span for a 13-hospital network. When it was superimposed over the H1N1 influenza outbreak census (2008–2010) taken by the National Institute of Medical Sciences and Nutrition Salvador Zubiran in Mexico City, it showed that it is an effective algorithm to notify early warnings of severe respiratory disease epidemic outbreaks with a minimal rate of false alerts.

Antimicrobial peptides occupy a prominent place in the production of pharmaceuticals, because of their effective contribution to the protection of the immune system against almost all types of pathogens. These peptides are thoroughly studied by computational methods designed to shed light on their main functions. In this paper, we propose a computational approach, named the Polarity Profile method that represents an improvement to the former Polarity Index method. The Polarity Profile method is very effective in detecting the subgroup of antibacterial peptides called selective cationic amphipathic antibacterial peptides (SCAAP) that show high toxicity towards bacterial membranes and exhibit almost zero toxicity towards mammalian cells. Our study was restricted to the peptides listed in the antimicrobial peptides database (APD2) of December 19, 2012. Performance of the Polarity Profile method is demonstrated through a comparison to the former Polarity Index method by using the same sets of peptides. The efficiency of the Polarity Profile method exceeds 85% taking into account the false positive and/or false negative peptides.

The design of drugs with bioinformatics methods to identify proteins and peptides with a specific toxic action is increasingly recurrent. Here, we identify toxic proteins towards the influenza A virus subtype H1N1 located at the UniProt database. Our quantitative structure-activity relationship (QSAR) approach is based on the analysis of the linear peptide sequence with the so-called Polarity Index Method that shows an efficiency of 90% for proteins from the Uniprot Database. This method was exhaustively verified with the APD2, CPPsite, Uniprot, and AmyPDB databases as well as with the set of antibacterial peptides studied by del Rio et al. and Oldfield et al.

When I was using the Polarity-Index method a few days ago, I noticed differences in Table 3, as published. However, it should be as in Table 3. Table 1 Number of matches in a typical SCAAP sequence in each peptide database with single or multiple action on fungi, viruses, mammalian cells, Gram+/Gram− bacteria, cancer cells, insects, parasites, and sperms (see also Section 2.6) [7]. These changes do not affect neither the efficiency of the method nor any section of the paper. I also noted the difficulty to compare information on the same APD2 database (November 2011), as it changes weekly. Therefore I am sending a file to support that test, in case the journal has backup for additional information. Otherwise I will to keep this information for three years.