Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human Tim/Tipin Complex Coordinates an Intra-S Checkpoint Response to UV That Slows Replication Fork Displacement

ABSTRACT UV-induced DNA damage stalls DNA replication forks and activates the intra-S checkpoint to inhibit replicon initiation. In response to stalled replication forks, ATR phosphorylates and activates the transducer kinase Chk1 through interactions with the mediator proteins TopBP1, Claspin, and Timeless (Tim). Murine Tim recently was shown to form a complex with Tim-interacting protein (Tipin), and a similar complex was shown to exist in human cells. Knockdown of Tipin using small interfering RNA reduced the expression of Tim and reversed the intra-S checkpoint response to UVC. Tipin interacted with replication protein A (RPA) and RPA-coated DNA, and RPA promoted the loading of Tipin onto RPA-free DNA. Immunofluorescence analysis of spread DNA fibers showed that treating HeLa cells with 2.5 J/m2 UVC not only inhibited the initiation of new replicons but also reduced the rate of chain elongation at active replication forks. The depletion of Tim and Tipin reversed the UV-induced inhibition of replicon initiation but affected the rate of DNA synthesis at replication forks in different ways. In undamaged cells depleted of Tim, the apparent rate of replication fork progression was 52% of the control. In contrast, Tipin depletion had little or no effect on fork progression in unirradiated cells but significantly attenuated the UV-induced inhibition of DNA chain elongation. Together, these findings indicate that the Tim-Tipin complex mediates the UV-induced intra-S checkpoint, Tim is needed to maintain DNA replication fork movement in the absence of damage, Tipin interacts with RPA on DNA and, in UV-damaged cells, Tipin slows DNA chain elongation in active replicons.
Mediodorsal Thalamic Lesions Impair Long‐Term Visual Associative Memory in Macaques

Six cynomolgus monkeys (Macaca fascicularis) were trained to associate visual stimuli with the delivery of various amounts of food reward. The animals had to choose correctly between pairs of stimuli drawn from a population of 16. Four of these stimuli were associated with 0 reward pellets, four with 1 pellet, four with 2 pellets and four with 4 pellets. Mediodorsal thalamic lesions including the medial part of the mediodorsal nucleus, similar to those which are frequently seen in Korsakoff amnesia, produced a severe impairment in this task. The impairment was seen both in memory for the quantity of reward, as expressed in choices between 1‐pellet and 2‐pellet stimuli or choices between 2‐pellet and 4‐pellet stimuli, and also in memory for the qualitative absence or presence of reward, as expressed in choices between 0‐pellet and 1‐pellet stimuli. The deficit in this task establishes that mediodorsal thalamic lesions in monkeys can impair long‐term memory tasks, in addition to their known effects on several short‐term memory tasks. The contrast between the present results and those of previous experiments on visual long‐term memory in the monkey following mediodorsal thalamic lesions can be related to similar contrasts in studies of lesions in the amygdala, suggesting that the functions of these two structures are related.
Predictors of vitamin D status in predialysis chronic kidney disease patients: a cross-sectional analysis in a high ultraviolet climate.

OBJECTIVE To determine vitamin D status in a subtropical climate among an unselected, referred predialysis chronic kidney disease (CKD) population; assess risks and correlates; and review whether higher 25-hydroxyvitamin D (25-OHD) concentration can mitigate the decrement in circulating 1,25-dihydroxyvitamin D (1,25-OHD) normally encountered with advancing CKD. DESIGN Prospective cross-sectional cohort study. SETTING Renal unit in Brisbane, Australia (27°28' S). SUBJECTS Five hundred ninety-three consecutive CKD patients (stage 1 to 5). MAIN OUTCOME MEASURE 25-OHD insufficiency (concentrations: 15 to 30 ng/mL) and deficiency (<15 ng/mL), bone-mineral parameters, including 1,25-OHD, calcium, and phosphate. RESULTS Despite potentially higher environmental ultraviolet (UV) exposure, only 48% of patients with CKD were 25-OHD sufficient. Traditional risks for hypovitaminosis D were maintained, and sufficiency was independently predicted by testing in the summer/autumn period (odds ratio [OR]: 2.77, 95% confidence interval [CI]: 1.88 to 4.08, P < .001), male gender (OR: 2.18, 95%CI: 1.46 to 3.24, P < .001), Caucasian race (OR: 2.28, 95%CI: 1.37 to 3.78, P = .001), hypoalbuminemia (OR: 0.47, 95%CI: 0.25 to 0.85, P = .01), macroalbuminuria (OR: 0.60, 95%CI: 0.39 to 0.92, P = .02), and normal body mass index (OR: 1.94, 95%CI: 1.22 to 3.07, P = .005). Vitamin D sufficiency was also associated with higher corrected calcium (0.4 mg/dL increments; OR: 1.29, 95%CI: 1.08 to 1.55, P = .005). Although circulating 25-OHD concentrations were relatively maintained across the range of renal function observed, 1,25-OHD concentrations decreased with advancing CKD. CONCLUSION 25-OHD insufficiency is mitigated but still highly prevalent in patients with CKD in a high ambient UV environment. Despite the maintenance of relatively higher 25-OHD concentrations with advancing CKD, substrate availability does not appear to be a major determinant of circulating 1,25-OHD.
An Adaptive Caching Technique Using Learning Automata in Disruption Tolerant Networks

In Disruption Tolerant Network(DTN), determining the exact location of data and amount of delay to query the data by a requester is a major concern. It is costly for a node to maintain information of opportunistic paths to every other node in a DTN. Identifying appropriate caching locations is a difficult task. In this paper, we propose a technique for selecting the nodes for caching data based on the past performance of the respective nodes so that data queries can be fulfilled with less delay. In the proposed scheme, initially a Connected Dominating Set(CDS) is selected which serves as virtual backbone for the network. The CDS serves as the initial probable set of caching nodes. Further, an accurate caching set has been determined using a learning method called Learning Automata(LA). A Least Recently Used cache replacement method is used for replacing the data from the buffer of caching nodes, once the buffer is filled. The caching nodes cache the data generated by source node and forwards the data to other caching nodes. A requester node broadcasts the data query to the neighbors and the query is replied by a caching node. Simulation results show the efficacy of the proposed approach in terms of data delivery ratio and packet delay.
Estimated and predicted changes in the cat population of Australian households from 1979 to 2005

Results Australia’s household cat population increased steadily from 2.23 million in 1979 to peak at 3.24 million in 1988. Since then it has steadily declined to 2.60 million in 1999. The population size predicted from the mathematical model was similar to that from surveys for the years 1996 to 1999. It is predicted that the population will continue to decline to approximately 2.19 million in 2005. The proportion of Australian households owning cats fell from 31.1% in 1994 to 25.8% in 1999, while the average number of cats per catowning household remained relatively constant at 1.47.
Assessment of response to induction therapy and its influence on 5-year failure-free survival in group III rhabdomyosarcoma: the Intergroup Rhabdomyosarcoma Study-IV experience--a report from the Soft Tissue Sarcoma Committee of the Children's Oncology Group.

PURPOSE Initial response to induction chemotherapy predicts failure-free survival (FFS) in osteosarcoma and Ewing's sarcoma. For Intergroup Rhabdomyosarcoma Study (IRS) IV patients with group III rhabdomyosarcoma, we assessed whether reported response assessed by anatomic imaging at week 8 predicted FFS. PATIENTS AND METHODS We studied 444 group III patients who received induction therapy, had response assessed at week 8 by anatomic imaging, and continued with protocol therapy. Induction chemotherapy was generally followed by radiation therapy (RT) starting after week 9. Response to induction therapy was determined at weeks 0 and 8. Local institutions coded response. RESULTS Response rate for the entire cohort at week 8 was 77% (95% CI, 73% to 81%; complete response [CR], 21%; partial response [PR], 56%) but response had no influence on FFS (P = .57). Two hundred seventy-two patients received standard-timing RT at week 9 and thus only chemotherapy during induction. Response rate was 81% (95% CI, 76% to 86%; CR, 22%; PR, 59%). In these patients, response did not influence FFS except for those with alveolar histology. One hundred thirty-two other patients received chemotherapy and RT during induction (up-front RT). Response rate was 65% (95% CI, 57% to 73%; CR, 12%; PR, 53%), but response had no influence on FFS (P = .69). Forty patients received no RT at all (protocol violation) and response to induction therapy had no effect on FFS. CONCLUSION In IRS-IV, response rate to induction therapy was 77% in group III patients, was independent of histology, and had no influence on FFS overall.
Adipose Tissue Hormones and the Regulation of Food Intake

Over the past decade, adipose tissue has been shown to produce numerous factors that act as hormones. Many of these act on the brain to regulate energy balance via dual effects on food intake and energy expenditure. These include well‐characterised hormones such as leptin, oestrogen and glucocorticoids and novel factors such as adiponectin and resistin. This review provides a perspective on the role of these factors as lipostats.
Manipulating crop row orientation and crop density to suppress Lolium rigidum

Summary Light is an important resource that crops and weeds compete for and so increased light interception by the crop can be used as a method of weed suppression in cereal crops. This research investigated the impact of altered availability of photosynthetically active radiation (PAR) (from crop row orientation or seeding rate) on the growth and fecundity of Lolium rigidum. Wheat and barley crops were sown in an east–west (EW) or north–south (NS) direction, at a high or low seeding rate, in three field trials in 2010 and 2011 (at Merredin, Wongan Hills and Katanning, Western Australia). The average PAR available to L. rigidum in the inter-row space of EW crops compared with NS crops was 78% to 91% at crop tillering, 39% to 56% at stem elongation, 28% to 53% at boot/anthesis and 41% to 59% at grain fill. Reduced PAR in the EW crop rows resulted in reduced L. rigidum fecundity in five of the six trials (average of 2968 and 5705 L. rigidum seeds m−2 in the EW and NS crops). Availability of PAR was not influenced by seeding rate, but the high seeding rate reduced fecundity in three of the six trials (average of 3354 and 5092 seeds m−2 in the crops with high and low seeding rate). Increased competitive ability of crops (through increased interception of PAR or increased crop density) was highly effective in reducing L. rigidum fecundity and is an environmentally friendly and low cost method of weed suppression.
THE OCCURRENCE OF POTENTIALLY HABITABLE PLANETS ORBITING M DWARFS ESTIMATED FROM THE FULL KEPLER DATASET AND AN EMPIRICAL MEASUREMENT OF THE DETECTION SENSITIVITY

We present an improved estimate of the occurrence rate of small planets orbiting small stars by searching the full four-year Kepler data set for transiting planets using our own planet detection pipeline and conducting transit injection and recovery simulations to empirically measure the search completeness of our pipeline. We identified 156 planet candidates, including one object that was not previously identified as a Kepler Object of Interest. We inspected all publicly available follow-up images, observing notes, and centroid analyses, and corrected for the likelihood of false positives. We evaluated the sensitivity of our detection pipeline on a star-by-star basis by injecting 2000 transit signals into the light curve of each target star. For periods shorter than 50 days, we find 0.56 − 0.05 + 0.06 ? > Earth-size planets (1−1.5 R⊕) and 0.46 − 0.05 + 0.07 ? > super-Earths (1.5−2 R⊕) per M dwarf. In total, we estimate a cumulative planet occurrence rate of 2.5 ± 0.2 planets per M dwarf with radii 1−4 R⊕ and periods shorter than 200 days. Within a conservatively defined habitable zone (HZ) based on the moist greenhouse inner limit and maximum greenhouse outer limit, we estimate an occurrence rate of 0.16 − 0.07 + 0.17 ? > Earth-size planets and 0.12 − 0.05 + 0.10 ? > super-Earths per M dwarf HZ. Adopting the broader insolation boundaries of the recent Venus and early Mars limits yields a higher estimate of 0.24 − 0.08 + 0.18 ? > Earth-size planets and 0.21 − 0.06 + 0.11 ? > super-Earths per M dwarf HZ. This suggests that the nearest potentially habitable non-transiting and transiting Earth-size planets are 2.6 ± 0.4 pc and 10.6 − 1.8 + 1.6 ? > pc away, respectively. If we include super-Earths, these distances diminish to 2.1 ± 0.2 pc and 8.6 − 0.8 + 0.7 ? > pc.
Shifts in the balance of brain tryptophan metabolism due to age and systemic administration of lipopolysaccharide

The kynurenine (KYN) pathway, which is initi-ated by indoleamine 2, 3-dioxygenase (IDO), is a key tryptophan (TRP) metabolic pathway. It shares TRP with the serotonin (5-HT) pathway. Because activation of the KYN pathway by proinflammatory cytokines induces depressive symptoms, shifts in the balance of TRP metabolism to the KYN pathway are closely related to the etiology of depression. In the present study, the influence of age on the effect of the inflammation response system (IRS) on brain TRP metabolism was investigated. Male ICR mice (PND21) were reared for 4 weeks (younger group) or until they reached 1 year of age (older group), and given an intraperitoneal (i.p.) injection of lipopolysaccharide (LPS). The TRP, KYN, and 5-HT levels were measured in the prefrontal cortex, hippocampus, amygdala, and dorsal raphe nuclei. An increase in TRP and 5-HT levels was observed with age in all brain regions, whereas age was associated with decreases in KYN levels in the dorsal raphe nuclei. In all brain regions, LPS increased TRP levels, while it in-creased KYN levels in the prefrontal cortex and amygdala. Reduced KYN/5-HT ratios in all regions were observed with age, whereas increased KYN/5-HT ratios were observed with LPS in all regions except the dorsal raphe nuclei. Thus, age shifted the balance between the KYN and 5-HT pathways toward the 5-HT pathway, and countered the effects of LPS, which shifted the balance to the KYN pathway. These effects are relevant to the etiology of psychiatric disorders in elderly people.
Polarized Suppression and Enhancement of Six-Wave Mixing in Electromagnetically Induced Transparency Window

We show that polarization properties of the suppression and enhancement as well as the Autler-Townes (AT) splitting of two coexisting six-wave mixing (SWM) processes in multi-Zeeman levels atomic system. By scanning the frequency detuning of the dressing field, we observe the suppression and enhancement as well as the AT splitting of the two coexisting SWM processes with the different polarized probe beams. Different polarization states of the probe beam can select different transitions among multi-Zeeman levels and different dressing strengths. The AT splitting separations get slightly large as the probe beam changes from the linearly polarized state to the circularly polarized one. Under the conditions of different dressing fields, the polarization dependence of the SWM enhancement and suppression shows the inverse variation. Theoretical calculations are carried out, which are in good agreement with the experimental results.
Treatment of a patient with end‐stage renal disease with Rituximab: Pharmacokinetic evaluation suggests Rituximab is not eliminated by hemodialysis

The purpose of this study was to determine if therapeutic levels of Rituximab could be achieved in a patient with renal failure being dialyzed and if Rituximab is removed by hemodialysis. A 54‐year‐old man with low‐grade lymphoma and renal failure on hemodialysis received 8 weekly treatments of Rituximab at 375 mg/M2. Serum Rituximab levels were obtained before and after each treatment, before and after dialysis following each treatment, as well as in the dialysate fluid. The serum levels of Rituximab increased gradually with each treatment and were comparable to levels in patients with normal renal function. The postdialysis levels were higher than the predialysis levels as a consequence of hemo‐concentration after dialysis. Rituximab was not detected in the dialysate fluid. The patient developed life‐threatening hyperkalemia after the fourth treatment, which we believe occurred secondary to tumor lysis. Therapeutic levels of Rituximab may be maintained in patients undergoing dialysis. Rituximab is not eliminated by hemodialysis. Am. J. Hematol. 71:219–222, 2002. © 2002 Wiley‐Liss, Inc.
LINKING ATTITUDE TO ACTUAL PURCHASE OF HERBAL PRODUCT IN MALAYSIA: THE MODERATING ROLE OF PERCEIVED RISK

Drawing from Fishbein and Ajzen (1975) theory of planned behavior, this study hypothesized that attitude would each interact with perceived risk to predict actual purchase. Mall intercept survey was used to collect data from six states in Malaysia. A total of 473 out of 573 respondents completed and returned the questionnaire. A seven point Likert scale was used to measure responses. The data were analyzed using Partial Least Squares (PLS) path modeling (Ringle et al., 2015), results suggest that attitude and purchase intention is positively associated with actual purchase. On the contrary, the findings show that perceived risk does not moderate the relationship between attitude and actual purchase.
Barriers to clinical trials: Part III: Knowledge and attitudes of health care providers

The role of clinical trials is becoming extremely important for our understanding of the effects of different therapeutic modalities of cancer treatment and the value of their interactions. Participation of patients in clinical trials remains disappointingly low, with less than 3% of the estimated 1.17 million patients with newly diagnosed cancers entering the studies. Several physician‐based factors hinder accrual of patients—(1) lack of awareness of or access to clinical trials, (2) physician bias that the trial therapy is not as good as the “standard therapy” even though the standard therapy may provide a response rate of less than 20%, (3) physician's concern about losing patients to follow‐up, (4) the complexity of the clinical trial(s), which requires excessive amount of time to discuss, implement, and follow‐up the patient, (5) the lack of equitable compensation for the physician's time and effort, and (6) excessive costs of laboratory and radiologic tests that are not paid by the agency or group sponsoring the study, particularly in Phase I and II trials. These factors are confounded by the lack of institutional review boards in several community hospitals, associated with a complex and lengthy procedure to institute such a board.
Bearing fault diagnosis based on SVD feature extraction and transfer learning classification

This paper presents a transfer learning-based approach for bearing fault diagnosis, where the transfer strategy is proposed to improve diagnostic performance of the bearings under various operating conditions. The main idea of transfer learning is to utilize selective auxiliary data to assist target data classification, where a weight adjustment between them is involved in the TrAdaBoost algorithm for enhanced diagnostic capability. In addition, negative transfer is avoided through the similarity judgment, thus improving accuracy and relaxing computational load of the presented approach. Experimental comparison between transfer learning and traditional machine learning has verified the superiority of the proposed algorithm for bearing fault diagnosis.
Genetic markers of inflammation may not contribute to metabolic traits in Mexican children

Background: Low-grade chronic inflammation is a common feature of obesity and its cardio-metabolic complications. However, little is known about a possible causal role of inflammation in metabolic disorders. Mexico is among the countries with the highest obesity rates in the world and the admixed Mexican population is a relevant sample due to high levels of genetic diversity. Methods: Here, we studied 1,462 Mexican children recruited from Mexico City. Six genetic variants in five inflammation-related genes were genotyped: rs1137101 (leptin receptor (LEPR)), rs7305618 (hepatocyte nuclear factor 1 alpha (HNF1A)), rs1800629 (tumor necrosis factor alpha (TNFA)), rs1800896, rs1800871 (interleukin-10 (IL-10)), rs1862513 (resistin (RETN)). Ten continuous and eight binary traits were assessed. Linear and logistic regression models were used adjusting for age, sex, and recruitment centre. Results: We found that one SNP displayed a nominal evidence of association with a continuous trait: rs1800871 (IL-10) with LDL (beta = −0.068 ± 1.006, P = 0.01). Subsequently, we found one nominal association with a binary trait: rs7305618 (HNF1A) with family history of hypertension (odds-ratio = 1.389 [1.054–1.829], P = 0.02). However, no P-value passed the Bonferroni correction for multiple testing. Discussion: Our data in a Mexican children population are consistent with previous reports in European adults in failing to demonstrate an association between inflammation-associated single nucleotide polymorphisms (SNPs) and metabolic traits.
PATHOGENIC MORTALITY OF FICUS SPP

Ficus nitida Thunb and F. benjamina L. have been widely planted as avenue and home gardens shade trees in Khartoum State, Sudan. They are fast growing and easily pruned into several shapes. It was noticed that both species have been showing symptoms of decline with a characteristic sooty smooth black mass of spores underneath the peeled off tree barks. Therefore they were suspected of being infected with the fungus Nattrassia mangiferae Nattrass which has been reported also as causing nail and skin diseases in humans. In Africa, very little research was conducted on N. mangiferae and most of the research was too old and needs updating [19]. N. mangiferae was also reported as causing skin and nail diseases and fungal keratitis in humans [18] [20]. This study was undertaken with the objective of surveying the incidence of disease in two of the most widely planted avenue and house gardens shade trees in Khartoum State, Sudan. Symptoms included chlorosis and necrosis of leaves, dieback and peeled off barks. Plant and soil samples from underneath infected trees were collected and cultured on PDA. They were dominated with N. mangiferae and some minor saprophytic fungi. Four isolates of N. mangiferae were recognized in terms of spore shape and mycelium. Pathogenicity tests on F. nitida and F. benjamina proved further that the causal organism was N. mangiferae. Ranking of susceptibility was determined for some other tree species.
Antitumor effect of arsenic trioxide in murine xenograft model

Arsenic trioxide, As2O3 (ATO), has been established to be an effective agent for treating acute promyelocytic leukemia, but its effect on solid tumors has not been fully explored. In the present study in a murine xenograft system, we found that ATO significantly inhibited tumor growth of the inoculated human hepatocellular carcinoma cell line HuH7 when administered either intravenously or intratumorally. Pathological examination revealed that ATO induced extensive cell death in the tumor. Some of the dead cells in intratumorally ATO‐treated mice showed characteristic features of apoptosis, such as nuclear condensation and fragmentation, and were TUNEL‐positive. The measurement of arsenic by using particle induced X‐ray emission revealed that arsenic was accumulated more in the tumor than in brain, kidney or liver after the intravenous injection of ATO, which is consistent with the hemorrhagic cell death observed in ATO‐treated tumor tissues. Thus, ATO appears to have potential for the treatment of solid tumors, as well as hematopoietic malignancies.