Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient organ localization using multi-label convolutional neural networks in thorax-abdomen CT scans

Automatic localization of organs and other structures in medical images is an important preprocessing step that can improve and speed up other algorithms such as organ segmentation, lesion detection, and registration. This work presents an efficient method for simultaneous localization of multiple structures in 3D thorax-abdomen CT scans. Our approach predicts the location of multiple structures using a single multi-label convolutional neural network for each orthogonal view. Each network takes extra slices around the current slice as input to provide extra context. A sigmoid layer is used to perform multi-label classification. The output of the three networks is subsequently combined to compute a 3D bounding box for each structure. We used our approach to locate 11 structures of interest. The neural network was trained and evaluated on a large set of 1884 thorax-abdomen CT scans from patients undergoing oncological workup. Reference bounding boxes were annotated by human observers. The performance of our method was evaluated by computing the wall distance to the reference bounding boxes. The bounding boxes annotated by the first human observer were used as the reference standard for the test set. Using the best configuration, we obtained an average wall distance of 3.20 ± 7.33 mm in the test set. The second human observer achieved 1.23 ± 3.39 mm. For all structures, the results were better than those reported in previously published studies. In conclusion, we proposed an efficient method for the accurate localization of multiple organs. Our method uses multiple slices as input to provide more context around the slice under analysis, and we have shown that this improves performance. This method can easily be adapted to handle more organs.
Annotation: Care of children in hospital

Summary The Charter for Children in Hospitals, drawn up by professional and women's groups from a number of European countries at the First Conference for the Care of Children in Hospital (Netherlands 1988) presents many fine guidelines for. protecting the rights of children and their parents before, during and after hospitalization. The development of these guidelines, their current acceptance in Europe and the psychological principles underlying them, are outlined here.
Test-retest reliability of muscle fiber conduction velocity and fractal dimension of surface EMG during isometric contractions

Objective. The aim of this study was to determine the test-retest reliability of muscle fiber conduction velocity (CV) and fractal dimension (FD) obtained from multichannel surface electromyographic (sEMG) recordings. Approach. Forty healthy recreationally active subjects (20 men and 20 women) performed two elbow flexions on two trials with a 1 week interval. The first was a 20% maximal voluntary contraction (MVC) of 120 s, and the second at 60% MVC held until exhaustion. sEMG signals were detected from the biceps brachii, using bi-dimensional arrays. Main results. Initial values and slope of CV and FD were used for the reliability analysis. The intraclass correlation coefficient (ICC) values for the isometric contraction at 20% MVC were (−0.09) and 0.67 for CV and FD respectively; whereas the ICC values at 60% MVC were 0.78 and 0.82 for CV and FD respectively. The Bland Altman plots for the two isometric contractions showed a mean difference close to zero, with no evident outliers between the repeated measurements: at 20% MVC 0.001 53 for FD and −0.0277 for CV, and at 60% MVC 0.006 66 for FD and 0.009 07 for CV. Significance. Overall, our findings suggest that during isometric fatiguing contractions, CV and FD slopes are reliable variables, with potential application in clinical populations.
High-accuracy automatic classification of Parkinsonian tremor severity using machine learning method

Motivation: Although clinical aspirations for new technology to accurately measure and diagnose Parkinsonian tremors exist, automatic scoring of tremor severity using machine learning approaches has not yet been employed. Objective: This study aims to maximize the scientific validity of automatic tremor-severity classification using machine learning algorithms to score Parkinsonian tremor severity in the same manner as the unified Parkinson’s disease rating scale (UPDRS) used to rate scores in real clinical practice. Approach: Eighty-five PD patients perform four tasks for severity assessment of their resting, resting with mental stress, postural, and intention tremors. The tremor signals are measured using a wristwatch-type wearable device with an accelerometer and gyroscope. Displacement and angle signals are obtained by integrating the acceleration and angular-velocity signals. Nineteen features are extracted from each of the four tremor signals. The optimal feature configuration is decided using the wrapper feature selection algorithm or principal component analysis, and decision tree, support vector machine, discriminant analysis, and k-nearest neighbour algorithms are considered to develop an automatic scoring system for UPDRS prediction. The results are compared to UPDRS ratings assigned by two neurologists. Main results: The highest accuracies are 92.3%, 86.2%, 92.1%, and 89.2% for resting, resting with mental stress, postural, and intention tremors, respectively. The weighted Cohen’s kappa values are 0.745, 0.635 and 0.633 for resting, resting with mental stress, and postural tremors (almost perfect agreement), and 0.570 for intention tremors (moderate). Significance: These results indicate the feasibility of the proposed system as a clinical decision tool for Parkinsonian tremor-severity automatic scoring.
Posttraumatic and postoperative cardiac luxation: computed tomography findings in nine patients.

BACKGROUND Posttraumatic and postoperative cardiac luxation represents a serious complication of pericardial rupture, and early diagnosis is important. The purpose of this study is to determine signs of left cardiac luxation on computed tomography (CT). METHODS CT scans in nine patients with pericardial rupture and cardiac luxation after blunt chest trauma (n = 7) and postoperatively after extended left pneumectomy (n = 2) were reviewed for abnormalities. We analyzed the clinical history, clinical findings, and the imaging findings. RESULTS Dislocation of the heart to the left and pneumopericardium were seen in nine patients. Five of these nine patients revealed "entrapment" of the left heart between the proximal ascending aorta and the descending aorta. All patients underwent a pneumopericardium. All patients with a history of trauma showed a left-sided pneumothorax but no pericardial effusion. CONCLUSIONS CT plays a key role for early diagnosis of cardiac luxation. Dislodgment of the heart, entrapment of the left atrium and ventricle, and pneumopericardium associated with pneumothorax are the most important CT findings.
Is distal aortic perfusion in traumatic thoracic aortic injuries necessary to avoid paraplegic postoperative outcomes?

OBJECTIVES Traumatic thoracic aorta injuries account for nearly 8,000 deaths annually in the United States. Clamp-and-sew techniques can lead to high rates of paraplegia. Use of distal aortic perfusion can lead to heparin-related complications, particularly with associated head trauma. Our objective was to evaluate whether or not an individualized approach to operative management provides acceptable neurologic outcomes. METHODS A retrospective review (1991-2004) of patients with a traumatic thoracic aortic injury at a Level I trauma center was performed. RESULTS A total of 67 patients fit the study criteria. Ninety-one percent of patients had concomitant injuries. Median time from injury to evaluation was 38.0 minutes and from evaluation to operating room (OR) 111.0 minutes. Fifty-three percent of patients died before definitive repair could be undertaken; 29% were in the emergency department and 24% were in the OR. When definitive repair occurred, distal aortic perfusion was used in 81% of cases (75% left heart bypass, 6% cardiopulmonary bypass). The remaining 19% underwent clamp-and-sew technique without heparinization. There were no spinal cord deficits or adverse cerebral events related to repair. If definitive repair was completed, the mortality was 16%. Male sex and increasing time, both to evaluation and to OR, were the only risk factors associated with increased mortality. CONCLUSIONS Judicious use of clamp-and-sew techniques can achieve excellent neurologic outcomes, equivalent to distal aortic perfusion. Prompt evaluation leads to improved survival. Factors such as age, mechanism of injury, site of aortic injury, or operative technique did not affect mortality.
Host immune evasion strategies of malaria blood stage parasite.

Host immune evasion is a key strategy for the continual survival of many microbial pathogens including Apicomplexan protozoan: Plasmodium spp. , the causative agent of Malaria. The malaria parasite has evolved a variety of mechanisms to evade the host immune responses within its two hosts: the female Anopheles mosquito vector and vertebrate host. In this review, we will focus on the molecular mechanisms of the immune evasion strategies used by the Plasmodium parasite at the blood stage which is responsible for the clinical manifestations of human malaria. We also aim to provide some insights on the potential targets for malaria interventions through the recent advancement in understanding the molecular biology of the parasite.
Lipid droplet organelle distribution in populations of dividing cells studied by simulation

One of the key questions in cell biology is how organelles are passed from parent to daughter cells. To help address this question, I used Brownian dynamics to simulate lipid droplets as model organelles in populations of dividing cells. Lipid droplets are dynamic bodies that can form both de novo and by fission, they can also be depleted. The quantitative interplay among these three events is unknown but would seem crucial for controlling droplet distribution in populations of dividing cells. Surprisingly, of the three main events studied: biogenesis, fission, and depletion, the third played the key role in maintaining droplet organelle number-–and to a lesser extent volume-–in populations of dividing cells where formation events would have seemed paramount. In the case of lipid droplets, this provides computational evidence that they must be sustained, most likely through contacts with the endoplasmic reticulum. The findings also agree with video microscopy experiments over much shorter timescales where droplet depletion in fission yeast cells was not observed. In general, this work shows that organelle maintenance is invaluable and lack thereof cannot necessarily be compensated for by organelle formation. This study provides a time-accurate, physical-based template for long-term cell division studies.
Komplexe Differenzialdiagnostik - Erstdiagnostik und Therapie der Dyspnoe aus Sicht des Pneumologen

D ie Dyspnoe ist keine eigene Krankheitsentität, sondern ein physiologisches Phänomen: Sie kann bei maximaler, körperlicher Anstrengung beim Gesunden, aber auch im Rahmen einer unzureichenden Belastbarkeit beim Kranken als Ausdruck einer zu der aktuellen Belastung inadäquaten Funktion der Atmungskette auftreten. Die Atemnot dient dabei als biologisches Warnsignal, um eine Störung der Homöostase zu verhindern. Neben Husten und Auswurf ist sie eines der Kardinalsymptome verschiedener Krankheiten der Atmungsorgane. Die Atmungsorgane werden ihrerseits aber auch von zahlreichen anderen Organkrankheiten belastet, sodass die Differenzialdiagnose der Dyspnoe sehr breit ist. Die Bedeutung der Dyspnoe auch als Prognosefaktor kommt in dem BODE-Index (8, 16) zum Ausdruck, der besonders bei Patienten mit chronisch-obstruktiver Lungenerkrankung Anwendung findet und zusätzlich den Body-mass-Index (BMI), die Einsekundenkapazität (FEV1) und die Belastungskapazität als Sechs-Minuten-Gehtest („6-minute walk test“; 6MWT) berücksichtigt.
Construction and characterization of mutated LEA peptides in Escherichia coli to develop an efficient protein expression system

To develop an efficient protein expression system, we designed a late embryogenesis abundant (LEA) peptide by mutating the LEA peptide constructed in our previous study (LEA‐I). The peptide is based on the repeating units of an 11mer motif characteristic of LEA proteins from Polypedilum vanderplanki larvae. In the amino acid sequence of the 13mer LEA peptide, glycine at the 6th and 12th positions was replaced with other amino acids via point mutations. Glutamic acid, lysine, leucine, and asparagine in the LEA peptide at the 6th and 12th positions increased green fluorescence protein (GFP) expression. The GFP expression of the mutated LEA peptide was 1.5 to 2.0 times higher than that without LEA peptide. In contrast, the serine‐containing mutated LEA peptide has low GFP expression levels. We hypothesize that the position of amino acids and the nature of amino acid in LEA peptide are important for our coexpression system. These data suggest that the size, structure, and charge of amino acids in the LEA peptide improve the protection and expression of the target protein. The amino acid balance also plays an important role in the expression of the target protein.
Examining Self-Care Behaviors and Their Associated Factors Among Adolescent Girls With Dysmenorrhea: An Application of Orem's Self-Care Deficit Nursing Theory.

PURPOSE To test a hypothesized model that examines the relationship between selected basic conditioning factors, self-care agency, and self-care behaviors among adolescent girls with dysmenorrhea using Orem's self-care deficit nursing theory as a framework. DESIGN This was a predictive correlational study conducted with a total of 531 secondary school girls. METHODS Self-care agency, self-care behaviors, and 11 variables that have been theoretically or empirically justified in previous studies as relevant to basic conditioning factors were selected and collected by means of structured questionnaires. Path analyses were performed to test the hypothesized linkages among variables. FINDINGS Path analysis revealed that age and received menstrual education had both direct and indirect effects through self-care agency on self-care behaviors. Mother's and father's educational level, pain intensity, and self-medication used when experiencing dysmenorrhea only affected the self-care behaviors directly. CONCLUSIONS This is the first study that provided information about the relationship between basic conditioning factors, self-care agency, and self-care behaviors among adolescent girls with dysmenorrhea. Knowledge of the factors influencing self-care behaviors in these adolescent girls will assist healthcare professionals in developing effective interventions to promote self-care and ameliorate the adverse impact of this condition. CLINICAL RELEVANCE Interventional strategies that aim at promoting self-care behaviors among adolescent girls with dysmenorrhea should strengthen girls' self-care agency and should target those with a younger age, higher pain intensity, mother with a higher educational level, father with a lower educational level, and those who do not take self-medication for dysmenorrhea.
Brains studying brains: look before you think in vision

Using our own brains to study our brains is extraordinary. For example, in vision this makes us naturally blind to our own blindness, since our impression of seeing our world clearly is consistent with our ignorance of what we do not see. Our brain employs its ‘conscious’ part to reason and make logical deductions using familiar rules and past experience. However, human vision employs many ‘subconscious’ brain parts that follow rules alien to our intuition. Our blindness to our unknown unknowns and our presumptive intuitions easily lead us astray in asking and formulating theoretical questions, as witnessed in many unexpected and counter-intuitive difficulties and failures encountered by generations of scientists. We should therefore pay a more than usual amount of attention and respect to experimental data when studying our brain. I show that this can be productive by reviewing two vision theories that have provided testable predictions and surprising insights.
An investigation of the dynamic relationship between navicular drop and first metatarsophalangeal joint dorsal excursion

The modern human foot is a complex biomechanical structure that must act both as a shock absorber and as a propulsive strut during the stance phase of gait. Understanding the ways in which foot segments interact can illuminate the mechanics of foot function in healthy and pathological humans. It has been proposed that increased values of medial longitudinal arch deformation can limit metatarsophalangeal joint excursion via tension in the plantar aponeurosis. However, this model has not been tested directly in a dynamic setting. In this study, we tested the hypothesis that during the stance phase, subtalar pronation (stretching of the plantar aponeurosis and subsequent lowering of the medial longitudinal arch) will negatively affect the amount of first metatarsophalangeal joint excursion occurring at push‐off. Vertical descent of the navicular (a proxy for subtalar pronation) and first metatarsophalangeal joint dorsal excursion were measured during steady locomotion over a flat substrate on a novel sample consisting of asymptomatic adult males and females, many of whom are habitually unshod. Least‐squares regression analyses indicated that, contrary to the hypothesis, navicular drop did not explain a significant amount of variation in first metatarsophalangeal joint dorsal excursion. These results suggest that, in an asymptomatic subject, the plantar aponeurosis and the associated foot bones can function effectively within the normal range of subtalar pronation that takes place during walking gait. From a clinical standpoint, this study highlights the need for investigating the in vivo kinematic relationship between subtalar pronation and metatarsophalangeal joint dorsiflexion in symptomatic populations, and also the need to explore other factors that may affect the kinematics of asymptomatic feet.
Inhibitory Effects of Thiopental, Ketamine, and Propofol on Voltage‐dependent Calcium sup 2+ Channels in Porcine Tracheal Smooth Muscle Cells

Background Intravenously administered anesthetics directly inhibit airway smooth muscle contraction. Because many anesthetic agents affect membrane ion channel function and sustained contraction of airway smooth muscle requires the influx of Calcium2+ through voltage‐dependent Calcium2+ channels, it was hypothesized that intravenous anesthetics inhibit airway smooth muscle voltage‐dependent Calcium2+ channels.
Hydrophobicity of methylated DNA as a possible mechanism for gene silencing

AFM images show that chromatin reconstituted on methylated DNA (meDNA) is compacted when imaged under water. Chromatin reconstituted on unmethylated DNA is less compacted and less sensitive to hydration. These differences must reflect changes in the physical properties of DNA on methylation, but prior studies have not revealed large differences between methylated and unmethylated DNA. Quasi-elastic light scattering studies of solutions of methylated and unmethylated DNA support this view. In contrast, AFM images of molecules at a water/solid interface yield a persistence length that nearly doubles (to 92.5 ± 4 nm) when 9% of the total DNA is methylated. This increase in persistence length is accompanied by a decrease in contour length, suggesting that a significant fraction of the meDNA changes into the stiffer A form as the more hydrophobic meDNA is dehydrated at the interface. This suggests a simple mechanism for gene silencing as the stiffer meDNA is more difficult to remove from nucleosomes.
Intra-abdominal pressure development after different temporary abdominal closure techniques in a porcine model.

BACKGROUND Decompressive laparotomy followed by temporary abdominal closure (TAC) is an established prophylaxis and treatment for abdominal compartment syndrome. The herein presented study aimed at the comparison of volume reserve capacity and development of intra-abdominal hypertension after forced primary abdominal closure and different TAC techniques in a porcine model. METHODS Eight anesthesized and mechanically ventilated domestic pigs underwent a standardized midline laparotomy. A bag was placed into the abdominal cavity. Before abdominal closure, the bag was prefilled with 3,000 mL water to simulate increased intra-abdominal volume. The intra-abdominal pressure (IAP) was then increased in 2 mm Hg steps up to 30 mm Hg by adding volume (volume reserve capacity) to the intra-abdominal bag. Volume reserve capacity with the corresponding IAP were analyzed and compared for primary abdominal closure, bag silo closure, a zipper system, and vacuum-assisted closure (VAC) with different negative pressures (-50, -100, and -150 mm Hg). Hemodynamic and pulmonary parameters were monitored throughout the experiment. RESULTS Volume reserve capacity was the highest for bag silo closure followed by the zipper system and VAC with primary abdominal closure providing the least volume reserve capacity in the whole IAP range. Of interest, VAC -50 mm Hg resulted in a lower volume reserve capacity when compared with VAC -100 and -150 mm Hg. Pulmonary and hemodynamic parameters demonstrated no significant differences between primary abdominal closure and the evaluated TAC techniques at all IAP levels. CONCLUSIONS The present experimental in vivo study indicates that bag silo closure and zipper systems may be favorable TAC techniques after decompressive laparotomy. In contrast, the VAC techniques resulted in lower volume reserve capacity and therefore may bear an increased risk for recurrent intra-abdominal hypertension in the initial phase after decompressive laparotomy.
Anatomy of hepatic arteriolo‐portal venular shunts evaluated by 3D micro‐CT imaging

The liver differs from other organs in that two vascular systems deliver its blood – the hepatic artery and the portal vein. However, how the two systems interact is not fully understood. We therefore studied the microvascular geometry of rat liver hepatic artery and portal vein injected with the contrast polymer Microfil®. Intact isolated rat livers were imaged by micro‐CT and anatomic evidence for hepatic arteriolo‐portal venular shunts occurring between hepatic artery and portal vein branches was found. Simulations were performed to rule out the possibility of the observed shunts being artifacts resulting from image blurring. In addition, in the case of specimens where only the portal vein was injected, only the portal vein was opacified, whereas in hepatic artery injections, both the hepatic artery and portal vein were opacified. We conclude that mixing of the hepatic artery and portal vein blood can occur proximal to the sinusoidal level, and that the hepatic arteriolo‐portal venular shunts may function as a one‐way valve‐like mechanism, allowing flow only from the hepatic artery to the portal vein (and not the other way around).