Miracle-dz/UniFAR-FTUs huggingface dataset:
Nocturnal plasma melatonin levels in patients suffering from chronic primary insomnia

Abstract: Polysomnographic sleep patterns and melatonin secretion were investigated in 10 patients (age: 41.3 ± 9.5 years) who suffered from chronic primary insomnia and complained predominantly about difficulties in maintaining sleep and in five healthy controls (age 27.2 ± 0.7 years). Nocturnal plasma melatonin concentrations were obtained hourly, measured by direct radioimmunoassay and statistically compared between insomniacs and controls with age as a covariate. Plasma melatonin levels in the patient group tended to begin increasing earlier in the evening and were significantly (P ± 0.01) lower during the middle of the night (peak value 82.5 ± 26.5 pg/ml) than in the healthy controls (peak value 116.8 ± 13.5 pg/ml). Among the patients, the most severely reduced nocturnal plasma melatonin levels were found in those patients with a history of sleep disturbance lasting for longer than five years (N = 6; age 41.8 ± 11.7 years; duration 15.3 ± 5.9 years; peak value 72.1 ± 25.0 pg/ml); whereas those chronic insomniacs affected for fewer than five years had relatively higher nocturnal levels (N = 4; age 40.6 ± 6.5 years; duration 3.8 ± 1.5 years; peak value 98.2 ± 23.9 pg/ml). These results show that the circadian rhythm of melatonin secretion is disturbed in patients with chronic primary insomnia, and that the nocturnal plasma melatonin secretion is increasingly more affected the longer the patients are unable to maintain a regular sleep pattern.
Worker Size in the Formosan Subterranean Termite in Relation to Colony Breeding Structure as Inferred from Molecular Markers

Abstract The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species that originated in China and has been introduced to Hawaii and the U.S. mainland. Colonies are headed either by a pair of reproductives (simple families) or by varying numbers of inbreeding reproductives (extended families), and therefore have variable degrees of inbreeding. Worker size also varies among colonies of Formosan termites. We tested whether variation in worker size can be explained by the breeding system. Workers were collected from colonies from three geographically separated populations (China, Hawaii, and Louisiana), and body weight and head size were measured. Microsatellite genotyping was used to establish whether colonies were simple or extended families and to determine the heterozygosity of workers and their degree of inbreeding relative to their colony (FIC, sensitive to the number of reproductives). All Chinese colonies contained multiple inbreeding neotenics. In Hawaii, 37% of the colonies were simple families and 63% were extended families, both having considerable degrees of inbreeding. In Louisiana, 57% of the colonies were simple families, which were mostly headed by unrelated pairs, and 43% were extended families. In simple families, size and body weight of workers were not associated with FIC or heterozygosity. In extended families of two populations, both size parameters were negatively correlated with FIC; however, heterozygosity was not associated with worker size in any of the populations. This suggests that the number of reproductives within colonies has a stronger influence on worker size than the individuals’ genetic diversity in Formosan subterranean termite colonies.
Methylphenidate decreases fat and carbohydrate intake in obese teenagers

Dopamine is a neurotransmitter that mediates the reward value of food. Methylphenidate (MPH) selectively binds and inhibits the dopamine transporter, thus increasing brain dopamine levels shortly after oral administration. This investigation studied whether a single dose of MPH decreases energy intake (EI) in obese teenagers compared to placebo (P).
MECHANISMS OF NEPHROTOXICITY FROM METAL COMBINATIONS: A REVIEW

The common environmental pollutants arsenic, lead, and cadmium are each known to induce chronic renal disease and the molecular mechanisms of such toxic events are being clarified. Nephrotoxicity of these metals is due to the fact that urinary elimination is a main route of excretion, and the proximal tubules are especially sensitive due to their high reabsorptive activity. Renal pathological effects of these metals vary with the chemical form of the metal, the dose, and whether the exposure is acute or chronic in nature. The few isolated studies of combined metal exposures indicate that these pathological effects may be altered due to unknown interactions of these metals within the kidney. Biological factors within the cell such as metal binding proteins and inclusion bodies may also influence metal-metal interactions. Further research is needed to specify the parameters or criteria by which metal interactions is to be assessed for unique biological response patterns to aid in the risk assessment analysis of environmental and occupational metal exposures.
Murine autosomal recessive polycystic kidney disease with multiorgan involvement induced by the cpk gene

Autosomal recessive (AR) polycystic kidney disease (PKD) is characterized in humans and mice as a rapidly progressive, collecting duct cystic disease usually leading to uremia in the neonatal or infantile period. In humans, ARPKD renal pathology can be variable in severity and is associated with the development of prominent bile duct and liver pathology. The C57BL/6J‐cpk/cpk mouse model of ARPKD is the most extensively studied murine model of inherited infantile PKD; however, these mice lack extrarenal pathology.
A Calorie is Still a Calorie, According to Rigorous New Evidence

Chronic degenerative “diseases of civilization” are the top challenges of all health systems globally[1]. Among them, obesity is the most pernicious because it a) has survived several meritorious lifestyle initiatives undeterred, b) is associated with intractable environmental promotion, c) there is no longterm medical treatment available, but also d) negatively affects several other cardiovascular risk factors, and e) is the leading cause of preventable life-years lost in the United States[2]. The misbelief that an unrestrained, permissive “diet,” effortless exercise “program”, or magic “diet pill” may exist continues to permeate popular thinking and media pieces. The combination of such fantasies, denial, and rejection of scientifically proven nutrition principles has enabled the triple epidemics of obesity, diabetes, and cardiovascular risk to continue. One of the controversies that recur is the question of whether a low-fat or low-carbohydrate is “healthier”[3]. Some authors argue a special case which, in their view, will help clarify the issue: do dietary calories count and are they equal? Classical experiments, particularly ones that used meticulously-controlled environments and metabolic ward measurements, indicate that calories do count[4]. Usually considered basic physiology, obesity ultimately results from a calorie intake in excess of calorie utilization, and the initial clinical approach is to correct this imbalance[5,6]. When done, it succeeds. Calorie utilization is comprised of the energy cost of resting metabolic processes (REE), physical work performed, and the thermal effect of food (TEF), with the most practical, safe and clinically meaningful target being physical activity. In contrast with the classical, accepted paradigm of excessive dietary calories as the most important cause of weight A Calorie is Still a Calorie, According to Rigorous New Evidence
An anatomical reinvestigation of the termination of the spinothalamic tract in the monkey

The projections of the spinothalamic tract in the macaque monkey have been reinvestigated using the Wiitanen modification of the Fink‐Heimer technique. In agreement with previous studies in the monkey (Mehler, Bowsher, Kerr) it was found that the spinothalamic tract ascends outside the medial lemniscus, enters the thalamus just dorsal to this structure, and terminates in the posterior, intralaminar and ventral regions, as well as in the zona incerta.
Optimized SIFTFlow for registration of whole-mount histology to reference optical images

Abstract. The registration of two-dimensional histology images to reference images from other modalities is an important preprocessing step in the reconstruction of three-dimensional histology volumes. This is a challenging problem because of the differences in the appearances of histology images and other modalities, and the presence of large nonrigid deformations which occur during slide preparation. This paper shows the feasibility of using densely sampled scale-invariant feature transform (SIFT) features and a SIFTFlow deformable registration algorithm for coregistering whole-mount histology images with blockface optical images. We present a method for jointly optimizing the regularization parameters used by the SIFTFlow objective function and use it to determine the most appropriate values for the registration of breast lumpectomy specimens. We demonstrate that tuning the regularization parameters results in significant improvements in accuracy and we also show that SIFTFlow outperforms a previously described edge-based registration method. The accuracy of the histology images to blockface images registration using the optimized SIFTFlow method was assessed using an independent test set of images from five different lumpectomy specimens and the mean registration error was 0.32±0.22 mm.
The number of deformed joints as a surrogate measure of damage in rheumatoid arthritis.

OBJECTIVE To evaluate the reliability and validity of the number of deformed joints (NDJ) as a surrogate measure of joint damage in rheumatoid arthritis (RA). METHODS We tested interrater reliability and validity in determining the NDJ as a surrogate for joint damage in consecutive patients with RA. We rated each of 48 joints as normal or abnormal in terms of alignment and range of motion, and expressed the results as the total number of deformed joints. We compared the NDJ with the severity of damage on a plain radiograph of the hands, scored using Sharp's technique, as the gold standard measure of joint damage. We also compared the correlation between the NDJ and radiographic joint damage, on the one hand, and disease duration, performance-based measures of physical function, and the self-reported level of disability. RESULTS The interrater reliability of the NDJ was excellent, with an intraclass correlation among four examiners of 0.94. To assess validity of the NDJ, we studied 273 RA patients from 5 clinical settings. Their average NDJ was 14 (range 0-43), and their average Sharp's score for joint space narrowing and erosions combined was 106 (range 4-309). The NDJ and the total Sharp's score were highly correlated (r = 0.83). Both measures were correlated to a similar degree with disease duration (r = 0.51 for each measure), grip strength (r = -0.49 for NDJ, and r = -0.51 for Sharp's score), walking velocity (r = -0.44 for NDJ, and r = -0.45 for Sharp's score), the timed button test (r = -0.62 for NDJ, and r = -0.57 for Sharp's score), and the Modified Health Assessment Questionnaire (r = 0.38 for NDJ, and r = 0.38 for Sharp's score). Both the Sharp's score and the NDJ worsened significantly in 38 patients for whom 1-2 year followup data were available. CONCLUSION The NDJ is reliable and is strongly associated with the standard measure of joint damage in RA. Because it is easily performed in a clinical setting, it could be used as an economical surrogate of joint damage in studies of the long-term outcome of RA.
Lung transplantation from donors after circulatory death using portable ex vivo lung perfusion.

BACKGROUND Donation after circulatory death is a novel method of increasing the number of donor lungs available for transplantation. Using organs from donors after circulatory death has the potential to increase the number of transplants performed. METHODS Three bilateral lung transplants from donors after circulatory death were performed over a six-month period. Following organ retrieval, all sets of lungs were placed on a portable ex vivo lung perfusion device for evaluation and preservation. RESULTS Lung function remained stable during portable ex vivo perfusion, with improvement in partial pressure of oxygen/fraction of inspired oxygen ratios. Mechanical ventilation was discontinued within 48 h for each recipient and no patient stayed in the intensive care unit longer than eight days. There was no postgraft dysfunction at 72 h in two of the three recipients. Ninety-day mortality for all recipients was 0% and all maintain excellent forced expiratory volume in 1 s and forced vital capacity values post-transplantation. CONCLUSION The authors report excellent results with their initial experience using donors after circulatory death after portable ex vivo lung perfusion. It is hoped this will allow for the most efficient use of available donor lungs, leading to more transplants and fewer deaths for potential recipients on wait lists.
Morphology-based Entity and Relational Entity Extraction Framework for Arabic

Rule-based techniques and tools to extract entities and relational entities from documents allow users to specify desired entities using natural language questions, finite state automata, regular expressions, structured query language statements, or proprietary scripts. These techniques and tools require expertise in linguistics and programming and lack support of Arabic morphological analysis which is key to process Arabic text. In this work, we present MERF; a morphology-based entity and relational entity extraction framework for Arabic text. MERF provides a user-friendly interface where the user, with basic knowledge of linguistic features and regular expressions, defines tag types and interactively associates them with regular expressions defined over Boolean formulae. Boolean formulae range over matches of Arabic morphological features, and synonymity features. Users define user defined relations with tuples of subexpression matches and can associate code actions with subexpressions. MERF computes feature matches, regular expression matches, and constructs entities and relational entities from user defined relations. We evaluated our work with several case studies and compared with existing application-specific techniques. The results show that MERF requires shorter development time and effort compared to existing techniques and produces reasonably accurate results within a reasonable overhead in run time.
Synthesis of Unmethylated Deoxyribonucleic Acid in a dnaB Temperature-Sensitive Mutant of Escherichia coli Starved for Methionine

Strain CRT 266, a polyauxotrophic dnaB temperature-sensitive mutant of Escherichia coli K, was investigated for residual deoxyribonucleic acid (DNA) synthesis when returned to the permissive temperature in the absence of protein synthesis. In the presence of methionine, a delayed extra-initiation occurs as well as an erratic long-lasting synthesis. In the absence of methionine, there is no evidence for extra-initiation, whereas the long-lasting synthesis is only slightly depressed. A direct role of methionine independent of protein synthesis in the extra-initiation process is postulated. The largest residual syntheses, with or without methionine, are obtained when (i) bacteria are first grown in a rich medium, (ii) bacteria are shifted to the nonpermissive temperature for 2 h in the same medium, and (iii) bacteria are then starved for aminoacid for 20 h at the permissive temperature. Under these conditions, DNA extracted from methionine-starved cells appears to be a mixture of half-methylated and unmethylated products. The possibility of the occurence of a few methyl groups on the so-called unmethylated DNA is discussed.
Endothelial CSN5 impairs NF-κB activation and monocyte adhesion to endothelial cells and is highly expressed in human atherosclerotic lesions

Summary The COP9 signalosome (CSN), a multifunctional protein complex involved in the regulation of cullin-RING-E3 ubiquitin ligases (CRLs), has emerged as a regulator of NF-κB signalling. As NF-κB drives the expression of pro-inflammatory and pro-atherosclerotic genes, we probed the yet unknown role of the CSN, in particular CSN5, on NF-KB-mediated atherogenic responses in endothelial cells. Co-immunoprecipitation in human umbilical vein endothelial cells (HUVECs) revealed the presence of a super-complex between IKK and CSN, which dissociates upon TNF-α stimulation. Furthermore, CSN5 silencing enhanced TNF-α-induced IKB-α degradation and NF-κB activity in luci-ferase reporter assays. This was paralleled by an increased NF-KB-driven upregulation of atherogenic chemokines and adhesion molecules, as measured by qPCR and flow cytometry, and translated into an enhanced arrest of THP-1 monocytes on TNF-α-stimulated, CSN5-depleted HUVECs. Reverse effects on NF-κB activity and THP-1 arrest were seen upon CSN5 overexpression. Finally, double-immunostaining confirmed the expression of CSN subunits in the endothelium of human atherosclerotic lesions, and revealed an increased expression of CSN5 which correlated with atheroprogression. In conclusion, endothelial CSN5 attenuates NF-KB-dependent pro-inflammatory gene expression and monocyte arrest on stimulated endothelial cells in vitro, suggesting that CSN5 might serve as a negative regulator of atherogenesis. Note: The review process for this manuscript was fully handled by G. Y. H. Lip, Editor in Chief.
Consumption Smoothing During the Financial Crisis: The Effect of Unemployment on Household Spending

Because of data limitations, the quantification of consumption smoothing in response to economic shocks has been challenging to investigate empirically. We used monthly data on total household spending, income, and labor force participation to estimate the effects of unemployment on household spending. The data come from the RAND American Life Panel, a standing survey sample that is representative of the United States adult population. We compare monthly spending and income of households prior to unemployment with spending and income following unemployment for up to 40 months. We compare spending and income following re-employment with spending and income while unemployed. We find that by month two of unemployment total household spending per month declined to about 83 percent of pre-unemployment spending. At about 14 months of unemployment, spending began to decline further, reaching 70 percent of pre-unemployment spending by month 30. Income declined much more sharply to 37 percent of its pre-unemployment level by month two of unemployment, with little change after that as the duration of unemployment increased. Thus, consumption does not decline as much as income, so that it is somewhat smoothed relative to income; yet, particularly over long-duration unemployment the decline is substantial. On re-employment, income increased rapidly, spending much less rapidly. As of the third month, high-frequency spending was about 9 percent above its value in the last month of unemployment. It continued to increase until it was about 20 percent higher. Just as with an income drop, spending is somewhat smoothed when income increases.
Two Transcription Factors Related with the Eucaryal Transcription Factors TATA-binding Protein and Transcription Factor IIB Direct Promoter Recognition by an Archaeal RNA Polymerase*

We reported previously that cell-free transcription in the Archaea Methanococcus and Pyrococcus depends upon two archaeal transcription factors, archaeal transcription factor A (aTFA) and archaeal transcription factor B (aTFB). In the genome of Pyrococcus genes encoding putative homologues of eucaryal transcription factors TATA-binding protein (TBP) and TFIIB have been detected. Here, we report that Escherichia coli synthesized Pyrococcus homologues of TBP and TFIIB are able to replace endogenous aTFB and aTFA in cell-free transcription reactions. Antibodies raised against archaeal TBP and TFIIB bind to polypeptides of identical molecular mass in the aTFB and aTFA fraction. These data identify aTFB as archaeal TBP and aTFA as the archaeal homologue of TFIIB. At the Pyrococcus glutamate dehydrogenase (gdh) promoter these two bacterially produced transcription factors and endogenous RNA polymerase are sufficient to direct accurate and active initiation of transcription. DNase I protection experiments revealed Pyrococcus-TBP producing a characteristic footprint between position −20 and −34 centered around the TATA box of gdh promoter. Pyrococcus-TFIIB did not bind to the TATA box but bound cooperatively with Pyrococcus-TBP generating an extended DNase I footprinting pattern ranging from position −19 to −42. These data suggest that the Pyrococcus homologue of TFIIB associates with the TBP-promoter binary complex as its eucaryal counterpart, but in contrast to eucaryal TFIIB, it causes an extension of the protection to the region upstream of the TATA box.
Melatonin attenuates inflammatory response‐induced brain edema in early brain injury following a subarachnoid hemorrhage: a possible role for the regulation of pro‐inflammatory cytokines

Melatonin is a strong anti‐oxidant that has beneficial effects against early brain injury (EBI) following a subarachnoid hemorrhage (SAH) in rats; protection includes the reduction of both mortality and neurological deficits. The molecular mechanisms underlying these clinical effects in the SAH model have not been clearly identified. This study examined the influence of melatonin on brain edema secondary to disruption of the blood–brain barrier (BBB) and the relationship between these effects and pro‐inflammatory cytokines in EBI following SAH using the filament perforation model of SAH in male Sprague–Dawley rats. Melatonin (150 mg/kg) or vehicle was given via an intraperitoneal injection 2 hr after SAH induction. Brain samples were extracted 24 hr after SAH. Melatonin treatment markedly attenuated brain edema secondary to BBB dysfunctions by preventing the disruption of tight junction protein expression (ZO‐1, occludin, and claudin‐5). Melatonin treatment also repressed cortical levels of pro‐inflammatory cytokines (IL‐1β, IL‐6, and TNF‐α), which were increased in EBI 24 hr after SAH. To further identify the mechanism of this protection, we demonstrated that administration of melatonin attenuated matrix metallopeptidase 9 expression/activity and vascular endothelial growth factor expression, which are related to the inflammatory response and BBB disruption in EBI after SAH. Taken together, this report shows that melatonin prevents disruption of tight junction proteins which might play a role in attenuating brain edema secondary to BBB dysfunctions by repressing the inflammatory response in EBI after SAH, possibly associated with regulation of pro‐inflammatory cytokines.
Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction

Polymerase chain reaction was used to amplify the low copy number of two 16S ribosomal gene fragments from soil and sediment extracts. Total DNA for polymerase chain reaction was extracted from 1 g of seeded or unseeded samples by a rapid freeze-and-thaw method. Amplified DNA fragments can be detected in DNA fractions isolated from seeded soil containing less than 3 Escherichia coli cells and from seeded sediments containing less than 10 cells. This research demonstrated that coupling polymerase chain reaction to direct DNA extraction improves sensitivity by 1 and 2 orders of magnitude for sediments and soils, respectively. This technique could become a powerful tool for genetic ecology studies.