Miracle-dz/UniFAR-FTUs huggingface dataset:
Patients with unresponsive wakefulness syndrome respond to the pain cries of other people

Objective: Recent publications show that using imagery instructions, brain activation patterns indicating consciousness can be found in approximately 10% of patients with unresponsive wakefulness syndrome (UWS; previously called vegetative state). It is possible, however, that patients who cannot follow instructions (because of limited memory/attention capacities, for example) are nevertheless conscious and retain emotional abilities to feel pain and pleasure. The aim of this study was to assess residual affective consciousness in a specific network of brain structures, the so-called pain matrix (PM) of the brain. Methods: We examined 44 carefully diagnosed UWS patients at 2 imaging centers. fMRI was used to investigate the brain hemodynamic responses to (a) imagery instructions, and (b) pain cries as opposed to neutral human vocalizations. Results: In line with the data of other groups, consistent responses to imagery instructions were obtained in 5 patients. In contrast, the PM was activated by pain cries in 24 patients. The PM consists of a sensory subsystem, which underlies pain sensation, and an affective subsystem, which underlies the characteristic aversive emotional tone of pain. The former was activated in 34% of patients, the latter in 30% of patients. Conclusion: Although there is debate about whether patients with UWS can perceive their own pain, our data indicate that many of them respond to the signals of pain in others. One can speculate that “affective consciousness” can remain even in patients with very severe brain damage who have no capacity for cognition.
Sentinel node metastasis mitotic rate (SN‐MMR) as a prognostic indicator of rapidly progressing disease in patients with sentinel node‐positive melanomas

Risk stratification of sentinel lymph node biopsy (SNB)‐positive patients with malignant melanoma differs among current classification systems. To improve classification of patients with rapidly progressive disease who may profit from adjuvant therapy with novel immune or targeted treatment modalities, a single‐center retrospective analysis was performed including all melanoma patients diagnosed with a positive SN at a university‐based skin cancer center over a 10‐year period (2002–2012) (96 of 419 patients). Sentinel node metastasis mitotic rate (SN‐MMR) and further histologic parameters were determined by blinded histological re‐evaluation and correlated with clinical follow‐up (overall [OS], melanoma‐specific [MSS], and disease‐free survival [DFS]). Median follow‐up was 53 months. In univariate analyses, SN tumor penetrative depth (TPD), maximum tumor diameter (MTD), number of positive SN, SN‐MMR and the S‐, Rotterdam, RDC, Hannover I and II classification systems correlated with OS, MSS and DFS. Multivariate Cox regression analyses showed that a binary classification system based only on the SN‐MMR (<1 vs. ≥1 mitoses/mm2) was the strongest independent prognostic indicator for all endpoints analyzed. Kaplan‐Meier analyses confirmed binary SN‐MMR to be superior to stratify patients into high‐ and low‐risk groups (45.45% vs. 87.92% 5‐yr MSS). The general prognostic validity of the published SN classification systems was confirmed. The novel SN‐MMR classification system may improve discrimination of patients with slowly and rapidly progressive disease. We therefore propose its implementation into clinical practice as the SN‐MMR can be easily and reliably determined in routine pathology reports. Its prognostic value for the selection of patients amenable to adjuvant therapies should be studied in clinical trials.
Identification of Streptococcus pneumoniae Revisited

ABSTRACT The sensitivities and specificities of several different diagnostic assays for Streptococcus pneumoniae were assessed using 99 clinical isolates of S. pneumoniae and 101 viridans streptococci and were as follows: Pneumoslide, 99 and 87%, respectively; Directigen, 100 and 85%, respectively; Phadebact, 100 and 98%, respectively; deoxycholate drop test, 99 and 98%, respectively; deoxycholate tube test, 100 and 99%, respectively; optochin, 99 and 98%, respectively; and Gram Positive Identification Card, 90 and 96%, respectively. Identification of clinical isolates ofS. pneumoniae should be confirmed using one or more diagnostic assays with well-documented high (e.g., ≥95%) sensitivities and specificities.
Enhanced crude oil biodegradative potential of natural phytoplankton‐associated hydrocarbonoclastic bacteria

Phytoplankton have been shown to harbour a diversity of hydrocarbonoclastic bacteria (HCB), yet it is not understood how these phytoplankton-associated HCB would respond in the event of an oil spill at sea. Here, we assess the diversity and dynamics of the bacterial community associated with a natural population of marine phytoplankton under oil spill-simulated conditions, and compare it to that of the free-living (non phytoplankton-associated) bacterial community. While the crude oil severely impacted the phytoplankton population and was likely conducive to marine oil snow formation, analysis of the MiSeq-derived 16S rRNA data revealed dramatic and differential shifts in the oil-amended communities that included blooms of recognized HCB (e.g., Thalassospira, Cycloclasticus), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential (Olleya, Winogradskyella, and members of the inconspicuous BD7-3 phylum). Notably, the oil biodegradation potential of the phytoplankton-associated community exceeded that of the free-living community, and it showed a preference to degrade substituted and non-substituted polycyclic aromatic hydrocarbons. Our study provides evidence of compartmentalization of hydrocarbon-degrading capacity in the marine water column, wherein HCB associated with phytoplankton are better tuned to degrading crude oil hydrocarbons than that by the community of planktonic free-living bacteria.
Sepsis in Pediatric Cardiac Intensive Care

Objectives: In this review, we will discuss risk factors for developing sepsis; the role of biomarkers in establishing an early diagnosis, in monitoring therapeutic efficacy, in stratification, and for the identification of sepsis endotypes; and the pathophysiology and management of severe sepsis and septic shock, with an emphasis on the impact of sepsis on cardiovascular function. Data Source: MEDLINE and PubMed. Conclusions: There is a lot of excitement in the field of sepsis research today. Scientific advances in the diagnosis and clinical staging of sepsis, as well as a personalized approach to the treatment of sepsis, offer tremendous promise for the future. However, at the same time, it is also evident that sepsis mortality has not improved enough, even with progress in our understanding of the molecular pathophysiology of sepsis.
Fast Decoupled State Estimation and Bad Data Processing

This paper presents fast-decoupled state estimators, using also decoupled detection and identification of bad data. Bad data is eliminated by pseudo-measurement generation. This procedure avoids gain-matrix retriangulations or the use of modification techniques like Woodbury formula. In the identification process, the diagonal of the covariance matrix of the measurement residuals is calculated using the sparse inverse matrix method. Two main types of fast-decoupled estimators were tested : algorithm- decoupled and model-decoupled. The methods have been tested on IEEE 30-bus load-flow test system, and the FURNAS and CPFL systems that form part of the 835-bus interconnected 15 GW power system of the S.E. Brazil.
Comparison of the microhardness of primary and permanent teeth after immersion in two types of carbonated beverages

Objectives: The consumption of carbonated beverages is one of the etiological factors that cause dental erosion. The purpose of this research was to compare changes in the microhardness of permanent and primary teeth after immersion in two types of carbonated beverages. Materials and Methods: This investigation was done on 30 healthy permanent molars and 30 healthy primary canines. Each group of primary and permanent teeth was subdivided into three groups of 10 teeth. The teeth was immersed in 40 ml of each of the three beverages for 5 min. One subgroup was immersed in water (as a control). The next was immersed in Lemon Delster and the last subgroup was immersed in Coca-Cola. The microhardness of enamel was measured using the Vickers method before and after immersion. Finally, the data was analyzed by paired t-test, one-way analysis of variance, and t-test. Results: Microhardness reduction in the primary teeth was significant in both the Lemon Delster and Coca-Cola groups (P < 0.05). This reduction was also statistically significant in the permanent teeth (P < 0.05). A comparison of the enamel changes in the primary teeth with permanent teeth after immersion in both beverages showed a greater microhardness reduction in the primary teeth in both the experimental groups. Conclusions: Coca-Cola and Lemon Delster caused a significant reduction of microhardness in tooth enamel. This reduction was greater in primary teeth than in permanent teeth, and was also greater after immersion in Coca-Cola than after immersion in Lemon Delster.
Detection of Some Safe Plant-Derived Foods for LTP-Allergic Patients

Background: Lipid transfer protein (LTP) is a widely cross-reacting plant pan-allergen. Adverse reactions to Rosaceae, tree nuts, peanut, beer, maize, mustard, asparagus, grapes, mulberry, cabbage, dates, orange, fig, kiwi, lupine, fennel, celery, tomato, eggplant, lettuce, chestnut and pineapple have been recorded. Objective: To detect vegetable foods to be regarded as safe for LTP-allergic patients. Methods: Tolerance/intolerance to a large spectrum of vegetable foods other than Rosaceae, tree nuts and peanut was assessed by interview in 49 subjects monosensitized to LTP and in three distinct groups of controls monosensitized to Bet v 1 (n = 24) or Bet v 2 (n = 18), or sensitized to both LTP and birch pollen (n = 16), all with a history of vegetable food allergy. Patients and controls underwent skin prick test (SPT) with a large spectrum of vegetable foods. The absence of IgE reactivity to foods that were negative in both clinical history and SPT was confirmed by immunoblot analysis and their clinical tolerance was finally assessed by open oral challenge (50 g per food). Results: All patients reported tolerance and showed negative SPT to carrot, potato, banana and melon; these foods scored positive in SPT and elicited clinical symptoms in a significant proportion of patients from all three control groups. All patients tolerated these four foods on oral challenge. Immunoblot analysis confirmed the lack of IgE reactivity to these foods by LTP-allergic patients. Conclusion: Carrot, potato, banana and melon seem safe for LTP-allergic patients. This finding may be helpful for a better management of allergy to LTP.
Epigenetic silencing of the PRSS3 putative tumor suppressor gene in non‐small cell lung cancer

The serine protease family member PRSS3 (trypsinogen‐IV) has been implicated as a putative tumor suppressor gene due to its loss of expression, which is correlated with promoter hypermethylation, in esophageal squamous cell carcinoma and gastric adenocarcinoma. As epigenetic alteration is common in non‐small cell lung cancer (NSCLC), we sought to determine if promoter hypermethylation of PRSS3 occurred in this disease, and if it was associated with clinical features of NSCLC or tobacco‐related exposures in these patients. Using methylation‐specific PCR, we determined the promoter hypermethylation status of PRSS3 in a case series study of primary NSCLC, and found methylation of this gene to be common, occurring in 53% (86 of 166) of tumors examined. There was no association of this alteration with patient demographics, tumor features, or exposure histories of the patients. The lack of association is of interest, as it may suggest a lack of specific selection for inactivation of this gene. On the other hand, the high prevalence of this alteration makes PRSS3 methylation an attractive biomarker for use in diagnostic or screening applications in NSCLC. © 2005 Wiley‐Liss, Inc.
Location and architecture of the Caulobacter crescentus chemoreceptor array

A new method for recording both fluorescence and cryo‐EM images of small bacterial cells was developed and used to identify chemoreceptor arrays in cryotomograms of intact Caulobacter crescentus cells. We show that in wild‐type cells preserved in a near‐native state, the chemoreceptors are hexagonally packed with a lattice spacing of 12 nm, just a few tens of nanometers away from the flagellar motor that they control. The arrays were always found on the convex side of the cell, further demonstrating that Caulobacter cells maintain dorsal/ventral as well as anterior/posterior asymmetry. Placing the known crystal structure of a trimer of receptor dimers at each vertex of the lattice accounts well for the density and agrees with other constraints. Based on this model for the arrangement of receptors, there are between one and two thousand receptors per array.
Isolation of Mouse Neutrophils

Neutrophils represent the first line of defense against bacterial and fungal pathogens. Indeed, patients with inherited or acquired qualitative and quantitative neutrophil defects are at high risk for developing bacterial and fungal infections and suffering adverse outcomes from these infections. Therefore, research aiming at defining the molecular factors that modulate neutrophil effector function under homeostatic conditions and during infection is essential for devising strategies to augment neutrophil function and improve the outcomes of infected individuals. This article describes reproducible density‐gradient‐centrifugation‐based as well as positive and negative immunomagnetic selection protocols that can be applied in any laboratory to harvest large numbers of highly enriched and highly viable neutrophils from the bone marrow of mice. In another protocol, we also present a method that combines gentle enzymatic tissue digestion with a positive immunomagnetic selection technique or fluorescence‐activated cell sorting (FACS) to harvest highly pure and highly viable preparations of neutrophils directly from mouse tissues such as the kidney, the liver, or the spleen. Mouse neutrophils isolated by these protocols can be used to examine several aspects of cellular function ex vivo, including pathogen binding, phagocytosis, and killing, neutrophil chemotaxis, oxidative burst, degranulation, and cytokine production, and for performing neutrophil adoptive transfer experiments. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Structure Analysis of the Major Capsid Proteins of Human Polyomaviruses 6 and 7 Reveals an Obstructed Sialic Acid Binding Site

ABSTRACT Human polyomavirus 6 (HPyV6) and HPyV7 are commonly found on human skin. We have determined the X-ray structures of their major capsid protein, VP1, at resolutions of 1.8 and 1.7 Å, respectively. In polyomaviruses, VP1 commonly determines antigenicity as well as cell-surface receptor specificity, and the protein is therefore linked to attachment, tropism, and ultimately, viral pathogenicity. The structures of HPyV6 and HPyV7 VP1 reveal uniquely elongated loops that cover the bulk of the outer virion surfaces, obstructing a groove that binds sialylated glycan receptors in many other polyomaviruses. In support of this structural observation, interactions of VP1 with α2,3- and α2,6-linked sialic acids could not be detected in solution by nuclear magnetic resonance spectroscopy. Single-cell binding studies indicate that sialylated glycans are likely not required for initial attachment to cultured human cells. Our findings establish distinct antigenic properties of HPyV6 and HPyV7 capsids and indicate that these two viruses engage nonsialylated receptors. IMPORTANCE Eleven new human polyomaviruses, including the skin viruses HPyV6 and HPyV7, have been identified during the last decade. In contrast to better-studied polyomaviruses, the routes of infection, cell tropism, and entry pathways of many of these new viruses remain largely mysterious. Our high-resolution X-ray structures of major capsid proteins VP1 from HPyV6 and from HPyV7 reveal critical differences in surface morphology from those of all other known polyomavirus structures. A groove that engages specific sialic acid-containing glycan receptors in related polyomaviruses is obstructed, and VP1 of HPyV6 and HPyV7 does not interact with sialylated compounds in solution or on cultured human cells. A comprehensive comparison with other structurally characterized polyomavirus VP1 proteins enhances our understanding of molecular determinants that underlie receptor specificity, antigenicity, and, ultimately, pathogenicity within the polyomavirus family and highlight the need for structure-based analysis to better define phylogenetic relationships within the growing polyomavirus family and perhaps also for other viruses.
Reinforcing and Subject-Rated Effects of Methylphenidate and d-Amphetamine in Non–Drug-Abusing Humans

The reinforcing effects of methylphenidate (20– 40 mg), d-amphetamine (10–20 mg), and placebo were assessed in eight healthy, non–sleep-deprived, non–drug-abusing outpatient volunteers. A modified progressive-ratio schedule was used to assess drug reinforcement in which a sampling session always preceded a self-administration session. During sampling sessions, volunteers received a drug dose to acquaint them with the drug effects. Drug doses were administered in eight identical capsules (i.e., each capsule contained 12.5% of the total dose). During self-administration sessions, which generally were conducted the next day, volunteers were given eight opportunities to work on a computer and could earn all, or some, of the capsules that were administered the previous day. To earn the first capsule, volunteers had to click a computer mouse 50 times. The number of clicks required to earn each additional capsule doubled (i.e., 100, 200, 400, 800, 1,600, 3,200, and 6,400 clicks). The dependent measure on this task was the break point (i.e., the last ratio completed). To characterize more fully the behavioral effects of methylphenidate and d-amphetamine, a battery of subject-rated drug-effect questionnaires, performance tasks, and physiologic measures was also used. Both doses of d-amphetamine increased the break point significantly above placebo levels, whereas only the high dose of methylphenidate did so. Break-point values for the doses of methylphenidate and d-amphetamine that maintained the greatest responding did not differ significantly. Methylphenidate and d-amphetamine produced some stimulantlike subject-rated drug effects (e.g., increased ratings of “drug liking”). These data suggest that methylphenidate, like d-amphetamine, can function as a reinforcer under a modified progressive-ratio schedule and, by inference, has at least some abuse potential in healthy, non–sleep-deprived, non–drug-abusing volunteers.
The Impact of Family Engagement and Child Welfare Services on Maltreatment Re-reports and Substantiated Re-reports

Despite decades of debate about the most effective ways to intervene with families reported to child protective services (CPS), little evidence exists regarding the types of services or approach that reduce children’s risk of additional maltreatment. The current study used data collected during a statewide experimental evaluation of CPS to examine the impact of numerous service variables, family engagement, and family characteristics on the risk of maltreatment re-reports and substantiated re-reports among families initially reported for neglect and risk of harm. The sample included 4,868 families with screened-in reports that were randomly assigned to receive either an investigation or an assessment. The results of the Cox regression analyses found that service duration, intensity, and breadth were unrelated to maltreatment re-report or substantiated re-reports, but caseworker ratings of the service-need match were associated with both. The provision of domestic violence services was related to decreased risk of maltreatment re-reports. Increased levels of family engagement were associated with lowered risk of both maltreatment re-reports and substantiated re-reports. Once the effects of services, engagement, and family characteristics were taken into account, CPS response pathway (investigation or assessment) had no relationship to maltreatment re-reports or substantiated re-reports.
Addressing unknown word problem for neural machine translation using distributee representations of words as input features

In recent years, the machine translation system based on neural network, called Neural Machie Translation, have attracted much attention, in which the entire translation steps are implemented in a single large neural network. In this framework, dealing with a large vocabulary size on its input (source) and output (target) often make the training computationally intractable. Therefore, the most frequent words in training data are retained to form a small vocabulary (shortlist), and the other, not frequent, words are all mapped to a single shared token. That causes so-called the unknown word problem. In this work, we propose three, rather simple, methods to overcome the unknown word problem based on distributed representation of words. We compared the translation performances of baseline and the proposed methods through experimental evaluation. Though the proposed methods did not improved the baseline in terms of BLEU, we found several evidences that the proposed methods successfully select appropriate target words even if their source words are out-of-vocabulary.
PROTECTIVE EFFECTS OF MAGNESIUM AGAINST ISCHAEMIA–REPERFUSION INJURY THROUGH INHIBITION OF P‐SELECTIN IN RATS

1 The leucocyte‐mediated inflammatory response plays a pivotal role in ischaemia–reperfusion injury. P‐Selectin and CD11b are important mediators for the recruitment of leucocytes into the endothelium. However, the time‐course of changes in P‐selectin and CD11b expression during reperfusion is not defined. Magnesium has been shown to have a protective role in reperfusion injury, but the mechanism of its action is not yet clear. 2 In the present study, 90 male Sprague‐Dawley rats were randomized into three groups, namely a sham‐operated group, an IR group (subjected to 45 min of coronary occlusion followed by reperfusion for up to 6 h) and an MgSO4‐treated group, which received an infusion of MgSO4 starting 30 min before occlusion and continuing until the onset of reperfusion. The expression of P‐selectin on platelets and CD11b on leucocytes, endothelial P‐selectin on cardiac microvessels and P‐selectin mRNA in myocardial tissue were measured by flow cytometry, immunohistochemistry and reverse transcription–polymerase chain reaction, respectively, at different time points during reperfusion. The degree of myocardial necrosis and arrhythmia was assessed. 3 The present study shows that P‐selectin expression on platelets and cardiac microvessels, P‐selectin mRNA in myocardial tissue and CD11b expression on leucocytes in the IR group were significantly upregulated compared with the sham‐operated group in a time‐dependent manner during reperfusion. Treatment with MgSO4 attenuated the upregulation of P‐selectin expression, in addition to inhibiting myocardial necrosis and arrhythmia, but had no effect on CD11b expression on leucocytes. 4 These results suggest that the expression of P‐selectin and CD11b is upregulated after reperfusion and magnesium pretreatment plays a cardioprotective role in ischaemia–reperfusion injury, possibly by inhibiting the upregulation of P‐selectin expression.