Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of bphA, Encoding Biphenyl Dioxygenase, in Two Polychlorinated Biphenyl-Degrading Bacteria, Psychrotolerant Pseudomonas Strain Cam-1 and MesophilicBurkholderia Strain LB400

ABSTRACT We investigated induction of biphenyl dioxygenase in the psychrotolerant polychlorinated biphenyl (PCB) degraderPseudomonas strain Cam-1 and in the mesophilic PCB degraderBurkholderia strain LB400. Using a counterselectable gene replacement vector, we inserted a lacZ-Gmrfusion cassette between chromosomal genes encoding the large subunit (bphA) and small subunit (bphE) of biphenyl dioxygenase in Cam-1 and LB400, generating Cam-10 and LB400-1, respectively. Potential inducers of bphA were added to cell suspensions of Cam-10 and LB400-1 incubated at 30°C, and then beta-galactosidase activity was measured. Biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately six times greater than the basal level in cells incubated with pyruvate. In contrast, the beta-galactosidase activities in LB400-1 incubated with biphenyl and in LB400-1 incubated with pyruvate were indistinguishable. At a concentration of 1 mM, most of the 40 potential inducers tested were inhibitory to induction by biphenyl of beta-galactosidase activity in Cam-10. The exceptions were naphthalene, salicylate, 2-chlorobiphenyl, and 4-chlorobiphenyl, which induced beta-galactosidase activity in Cam-10, although at levels that were no more than 30% of the levels induced by biphenyl. After incubation for 24 h at 7°C, biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately four times greater than the basal level in cells incubated with pyruvate. The constitutive level of beta-galactosidase activity in LB400-1 grown at 15°C was approximately five times less than the level in LB400-1 grown at 30°C. Thus, there are substantial differences in the effects of physical and chemical environmental conditions on genetic regulation of PCB degradation in different bacteria.
Decadal‐Scale Riverbed Deformation and Sand Budget of the Last 500 km of the Mississippi River: Insights Into Natural and River Engineering Effects on a Large Alluvial River

Alluvial rivers are shaped by interactions of flow and sediment transport. Their lower reaches to the world's oceans are highly dynamic, often presenting engineering and management challenges. Here we analyzed over 6,000 single‐beam cross‐sectional measurements surveyed in 1992, 2004, and 2013 in the last 500‐km reach of the highly engineered Mississippi River, also known as the lowermost Mississippi River or LmMR, starting from the river's Gulf outlet to its avulsion into the Atchafalaya River. We applied inverse distance weighted interpolation to downscale the survey records into 10 × 10 m digital elevation models. We assessed riverbed deformation from bank to bank and quantified changes in riverbed sediment volume. The goal of our study is to test the hypothesis that the lower reach of a large alluvial river can function as a conduit for sediment transport under the current engineering focus of navigation safety and flood control. Our analysis shows that in the past two decades, nearly 70% of the riverine sand was trapped within the LmMR, and continuous riverbed aggradation occurred below the Mississippi‐Atchafalaya diversion, presenting favorable backwater conditions for avulsion. Backwater effects have mainly controlled riverbed deformation in the LmMR, while flow reduction may have also contributed to the channel aggradation in the uppermost and lowermost reaches. The study reveals the considerable complexity of geomorphic responses of a large alluvial river to human interventions, strongly suggesting that future river engineering and management of the world's alluvial rivers should focus on strategies and solutions that will improve sediment transport.
Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function

Eph receptor tyrosine kinases participate in a variety of normal and pathogenic processes during development and throughout adulthood. This versatility is likely facilitated by the ability of Eph receptors to signal through diverse cellular signalling pathways: primarily by controlling cytoskeletal dynamics, but also by regulating cellular growth, proliferation, and survival. Despite many proteins linked to these signalling pathways interacting with Eph receptors, the specific mechanisms behind such links and their coordination remain to be elucidated. In a proteomics screen for novel EPHB2 multi-effector proteins, we identified human MYC binding protein 2 (MYCBP2 or PAM or Phr1). MYCBP2 is a large signalling hub involved in diverse processes such as neuronal connectivity, synaptic growth, cell division, neuronal survival, and protein ubiquitination. Our biochemical experiments demonstrate that the formation of a complex containing EPHB2 and MYCBP2 is facilitated by FBXO45, a protein known to select substrates for MYCBP2 ubiquitin ligase activity. Formation of the MYCBP2-EPHB2 complex does not require EPHB2 tyrosine kinase activity and is destabilised by binding of ephrin-B ligands, suggesting that the MYCBP2-EPHB2 association is a prelude to EPHB2 signalling. Paradoxically, the loss of MYCBP2 results in increased ubiquitination of EPHB2 and a decrease of its protein levels suggesting that MYCBP2 stabilises EPHB2. Commensurate with this effect, our cellular experiments reveal that MYCBP2 is essential for efficient EPHB2 signalling responses in cell lines and primary neurons. Finally, our genetic studies in Caenorhabditis elegans provide in vivo evidence that the ephrin receptor VAB-1 displays genetic interactions with known MYCBP2 binding proteins. Together, our results align with the similarity of neurodevelopmental phenotypes caused by MYCBP2 and EPHB2 loss of function, and couple EPHB2 to a signalling effector that controls diverse cellular functions.
Mirror neurons: action observation treatment as a tool in stroke rehabilitation.

BACKGROUND The observation of actions performed by others activate in an observer the same neural structures (including mirror neurons) as when he/she actually performs the same actions. AIM The aim of the present study was to assess whether action observation treatment may improve upper limb motor impairment in chronic stroke patients. DESIGN This was an observational study. SETTING Patients were recruited by three Italian Centres for Neurorehabilitation between 2006 and 2008. POPULATION Twenty-eight chronic stroke patients with upper limb impairment have undergone for four weeks, five days a week, a rehabilitation treatment based on observation of video-clips presenting hand daily actions, followed by the imitation of those same actions with the affected limb. METHODS Functional evaluation by means of Modified Barthel Index (MBI), Frenchay Arm Test (FAT) and Fugl Meyer (FM) was carried out twice before treatment (BT1 and BT2), at an interval of 15 days, then after treatment (AT1) and finally at a two-month follow-up (AT2). Wilcoxon Signed Rank test was applied to test differences between scores obtained from functional scales before and after treatment (BT1 vs. BT2; BT2 vs. AT1; AT1 vs. AT2). RESULTS In all scales, scores did not differ when comparing BT1 with BT2. Scores improved significantly in all scales at AT1 as compared to BT2 (MBI, P=0.026; FAT, P=0.005; FM, P=0.001). This improvement was still present at the two-month follow-up as testified by no score difference between AT1 and AT2. CONCLUSION Action Observation Treatment may become a useful strategy in the rehabilitation of stroke patients. CLINICAL REHABILITATION IMPACT The present preliminary study suggests that stimulation of neural structures (including mirror neurons), activated when the patients actually perform the same actions as those observed could constitute a good alternative rehabilitative approach in chronic stroke patients.
Treating Post-traumatic Stress Disorder in Patients with Multiple Sclerosis: A Randomized Controlled Trial Comparing the Efficacy of Eye Movement Desensitization and Reprocessing and Relaxation Therapy

Objective: Multiple Sclerosis (MS) is a demyelinating autoimmune disease that imposes a significant emotional burden with heavy psychosocial consequences. Several studies have investigated the association between MS and mental disorders such as depression and anxiety, and recently researchers have focused also on Post-traumatic Stress Disorder (PTSD). This is the first study that investigates the usefulness of proposing a treatment for PTSD to patients with MS. Methods: A randomized controlled trial with patients with MS diagnosed with PTSD comparing Eye Movement Desensitization and Reprocessing (EMDR; n = 20) and Relaxation Therapy (RT; n = 22). The primary outcome measure was the proportion of participants that no longer meet PTSD diagnosis as measured with Clinician Administered PTSD Scale 6-months after the treatment. Results: The majority of patients were able to overcome their PTSD diagnosis after only 10 therapy sessions. EMDR treatment appears to be more effective than RT in reducing the proportion of patients with MS suffering from PTSD. Both treatments are effective in reducing PTSD severity, anxiety and depression symptoms, and to improve Quality of Life. Conclusion: Although our results can only be considered preliminary, this study suggests that it is essential that PTSD symptoms are detected and that brief and cost-effective interventions to reduce PTSD and associated psychological symptoms are offered to patients, in order to help them to reduce the psychological burden associated with their neurological condition. Trial registration: NCT01743664, https://clinicaltrials.gov/ct2/show/NCT01743664
Constraint-Based Typing for ML via Semiunification Computer Science Technical Report CS-2008-10 Brad

We characterize ML type inference as a constraint satisfaction based on a new generalization of the semiunification problem, based on a new class of constraint variables that we call unknowns (we call the semiunification problem with unknowns USUP). Unlike previous characterizations based on ordinary semiunification, ours maintains a one-to-one correspondence between terms in the source language and constraints in the problem instance. This correspondence promises to facilitate reasoning about types by backward propagation of information back to the original source program—for example, unsolvable constraint sets could be directly translated back into specific type error information. Previous formulations of ML type inference in terms of semiunification have been less direct, thereby making practical adoption more difficult. We show that our syntax-directed formulation of ML type inference in terms of USUP is sound and complete. We give a solution semiprocedure for USUP, and show that the USUP image of any ML program is decidable. Through these contributions we wish to establish semiunification as a viable alternative to existing constraint-based typing systems for ML.
Drug-eluting bead therapy in primary and metastatic disease of the liver.

BACKGROUND Drug-eluting bead transarterial chemoembolization (DEB-TACE) is a novel therapy for the treatment of hypervascuarized tumours. Through the intra-arterial delivery of microspheres, DEB-TACE allows for embolization as well as local release of chemotherapy in the treatment of hepatic malignancy, providing an alternative therapeutic option in unresectable tumours. Its role as an adjunct to surgical resection or radiofrequency ablation (RFA) is less clear. The purpose of this review is to summarize recent studies investigating DEB-TACE in order to better define safety, efficacy and outcomes associated with its use. METHODS A systematic review of all published articles and trials identified nine clinical trials and 23 abstracts. These were reviewed for tumour histology, stage of treatment, delivery technique, outcome at follow-up, complications and mortality rates. RESULTS Publications involved treatment of hepatocellular carcinoma (HCC), metastatic colorectal carcinoma (MCRC), metastatic neuroendocrine (MNE) disease and cholangiocarcinoma (CCA). Using Response Evaluation Criteria in Solid Tumours (RECIST) or European Association for the Study of the Liver (EASL) criteria, studies treating HCC reported complete response (CR) rates of 5% (5/101) at 1 month, 9% (8/91) at 4 months, 14% (19/138) at 6 months and 25% (2/8) at 10 months. Partial response (PR) was reported as 58% (76/131) at 1 month, 50% (67/119) at 4 months, 57% (62/108) at 6-7 months and 63% (5/8) at 10 months. Studies involving MCRC, CCA and MNE disease were less valuable in terms of response rate because there is a lack of comparative data. The most common procedure-associated complications included fever (46-72%), nausea and vomiting (42-47%), abdominal pain (44-80%) and liver abscess (2-3%). Rather than reporting individual symptoms, two studies reported rates of post-embolic syndrome (PES), consisting of fever, abdominal pain, and nausea and vomiting, at 82% (75/91). Six of eight studies reported length of hospital stay, which averaged 2.3 days per procedure. Mortality was reported as occurring in 10 of 456 (2%) procedures, or 10 of 214 (5%) patients. CONCLUSIONS Drug-eluting bead TACE is becoming more widely utilized in primary and liver-dominant metastatic disease of the liver. Outcomes of success must be expanded beyond response rates because these are not a reliable surrogate for progression-free survival or overall survival. Ongoing clinical trials will further clarify the optimal timing and strategy of this technology.
Picturing perspectives: development of perspective-taking abilities in 4- to 8-year-olds

Although the development of perspective taking has been well researched, there is no uniform methodology for assessing this ability across a wide age span when frames of reference conflict. To address this gap, we created scenes of toy photographers taking pictures of layouts of objects from different angles, and presented them to 4- to 8-year-olds (N = 80). Children were asked to choose which one of four pictures could have been taken from a specific viewpoint. Results showed that this new technique confirmed the classic pattern of developmental progress on this kind of spatial skill: (1) 4-year-olds responded near chance level, regardless of layout complexity, (2) there was a growing ability to inhibit egocentric choices around age 6 with layouts of low complexity (one object), (3) performance increased and egocentric responses decreased dramatically around age 7, (4) even at age 8, children still showed considerable individual variability. This perspective taking task can thus be used to address important questions about the supports for early spatial development and the structure of early intellect.
The influence of upper airways diameter on the intensity of obstructive sleep apnea.

INTRODUCTION AND OBJECTIVE Obstructive sleep apnea (OSA) is characterized by at least 5 ten-second-long episodes of apnea or hypopnea, per hour of sleep. This disease may lead to severe, life-threatening complications. Therefore, risk analysis and its influence on disease intensity is crucial for proper implementation of preventive treatments. OBJECTIVE To determine the relation between the intensity of OSA expressed in Apnea-Hypopnea Index (AHI), and the anterior-posterior diameter of upper airways at the levels of soft palate and tongue base. MATERIAL AND METHOD Medical records of 41 patients with sleep apnea (AHI>4) diagnosed through polysomnographic examination obstructive were used for the study. The data consisted of: age and gender, polysomnographic examination results (AHI), lateral cephalogram with cephalomertic analysis, together with measurements of the upper and lower pharyngeal depth according to McNamara. Statistical analysis was carried out in accordance with Pearson's r correlation coefficient test (Statistica 8.0 software package). RESULTS Analysis of the influence of upper airways diameter on the intensity of OSA showed that the value of upper Airways diameter at the tongue base level had no statistically significant impact on the value of AHI (p=0.795). However, a statistically significant impact of the value of upper airways diameter on the AHI value (p=0.008) at the soft palate level was observed. Patients with OSA have narrowed upper airways diameter. The value of AHI increases with the decrease of upper diameter and is not dependent on a lower diameter value. Patients with a decreased upper airways diameter should be informed about potential breathing disorders during sleep.
A Universal Circuit for Studying and Generating Chaos-Part 11 : Strange Attractors

Manuscript received May 15, 1993; revised August 10, 1993. This paper was recommended by Guest Editor L. 0. Chua. This work was supported by the Office of Naval Research under grant N00014-89-J-1402 and by the National Science Foundation under grant MIP 86-14000. The authors are with the Electronics Research Laboratory and Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720. IEEE Log Number 921 1612. In [3], it was proved that (1) is topologically conjugate to a large class of 3-D systems C = C\€o, where C is the class of odd-symmetric continuous three-region piecewise-linear 3D vector fields, and Eo is a measure zero set. The reader is referred to [l] for the definition of lo. The algorithm for finding the parameters that make a Chua’s oscjllator topologically conjugate to a particular vector field in C is as follows: Algorithm 1: Calculate the eigenvalues ( p i , p h ~ p$) and (U: , U:, vi) associated with the linear and affine vector fields, respectively, of the circuit or system candidate whose attractor is being reproduced by Chua’s oscillator, up to a linear conjugacy. Find a set of circuit parameters
Turbulence Characteristic of Flow Near Laboratory Experiment Groin Fields

Groin is hydraulic structure utilized to protect riverbank from erosion. Groin will shift away flow. Area just downstream of groin structure will be occupied by low velocity flow hence there will be sediment deposition. Turbulence mechanism between primary flow region and groin field having important role in sediment exchange needs to be investigated. Instantaneous flow measurement was conducted in order to investigate turbulence relation between series groin under various groin spacing. Laboratory experiment employed turbulence flow having Reynolds number range between 31,935-32,500 and Froude number range between 0.051-0.053. A MicroADV 16-MHz was used to measure 3D instantaneous velocity. The experiment findings expressed that Reynolds stress involving vertical velocity and did not show any specific distributions except at the lowest measurement elevation, while Reynolds stress showed specific distributions. Turbulence value difference between groin field and primary flow region at upstream of the groin field was significant. As the area was getting downstream, area containing high turbulence was wider. This work indicated that bed shear stress value tended to grow at downstream area of groin field. High difference bed shear stress value between primary flow region and groin field seized second groin field and third groin field.
Neurourology and Urodynamics

Correspondence Allen F. Morey, MD, Department of Urology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390‐9110. Email: allen.morey@utsouthwestern.edu Abstract Aims: We sought to compare in‐office physical exam findings via standing cough test (SCT) versus 24‐hour pad weights among men seeking treatment for postprostatectomy stress urinary incontinence (SUI). Methods: A retrospective review of a single surgeon database of incontinence procedures was performed. Documentation of SUI severity (grades 0‐4) was completed by SCT preoperatively utilizing the Male Stress Incontinence Grading Scale (MSIGS). All patients had pads per day (PPD) and 24‐hour pad weights obtained. We determined the Spearman’s correlation coefficient between these variables. Results: We identified 104 men who underwent anti‐incontinence surgery (AdVance Sling or artificial urinary sphincter [AUS]). In the sling group (65 patients), nearly all (97%) had minimal incontinence with SCT (MSIGS = 0‐2). In the AUS group (39 patients), most patients (69%) had an MSIGS 3 or 4 with SCT. Spearman’s coefficient between quantification of SCT and pad weight for the overall group was ρ= . 68 (P< .0001) demonstrating a strong positive correlation. PPD was also strongly correlated with pad weight (ρ= .55, P< .0001). As seen previously, SCT and PPD were correlated (ρ= .47, P< .0001). In a multivariable model predicting pad weight, the effect of SCT was greater than PPD (β= 83 [54‐111], P< .0001 vs 45 [2169], P= .0004). Conclusions: SCT findings strongly correlate to 24‐hour pad weights in the evaluation of male SUI. The SCT shows promise as a rapid, reliable, noninvasive measure of SUI severity before anti‐incontinence surgery.
Horticulture for Pollinator Conservation

Pollinating insects are integral to the health of all terrestrial ecosystems and worldwide agriculture. Urbanization has greatly influenced this loss of nutritional resources and habitat. This can be reconciled through targeted landscape practices, such as providing nectarand pollenrich plants and managing pollinator habitat in urban areas, like home landscapes. As homeowners attempt to conserve pollinators through horticultural practices, they seek the advice and guidance of garden center employees. The knowledge retail employees have about pollinators and the recommendations they are giving customers on the subject is unknown. Here, a nationwide survey was developed and distributed to gauge current knowledge levels of horticulture retail employees about pollinator science and conservation practices. Our findings suggest overall knowledge level and recommendations are fairly good, but room for improvement exists in specific groups of retail employees. Specifically, employees without any type of horticultural certification and part time employees should be the focus on educational
Tunable surface-normal modulators operating near 1550 nm with a high-extinction ratio at high temperatures

We present high-performance surface-normal modulators based on unique properties of stepped quantum wells at an eye-safe wavelength of 1550 nm. Fabricated devices show higher efficiency and a 7-dB higher extinction ratio compared with devices with coupled quantum-well active layers. Moreover, the energy band edge of the device can be tuned over 70 nm while maintaining a 3-dB modulation depth. Such a wide tuning range eliminates the need for a thermoelectric cooler and is a critical advantage for many applications such as unmanned aerial vehicles and dynamic optical tags. The devices show good performance up to the maximum measured temperature of 70/spl deg/C.
Getting to the Top of Mind : How Reminders Increase Saving

We provide evidence from field experiments with three different banks, that reminder messages increase commitment attainment for clients who recently opened commitment savings accounts. Messages that mention both savings goals and financial incentives are particularly effective, while other content variations such as gain versus loss framing do not have significantly different effects. Nor do we find evidence that receiving additional late reminders has an additive effect. These empirical results do not map neatly into existing models, so we provide a simple model where limited attention to exceptional expenses can generate under-saving that is in turn mitigated by reminders.
Computational Learning Theory

Da die Zahl 0 durch die obige Darstellung nicht kodierbar ist, wird anstelle von x ∈ N die Zahl x + 1 kodiert. Diese Kodierung erlaubt es, Folgen(x1, . . . , xt) von natürlichen Zahlen effizient zu kodieren, nämlich durch das Wort code(x1) · · · code(xt). Eine Dekodierung ist stets möglich: Suche die erste Bitfolge b2i−1b2i = 01 und bestimme die Anzahl der Bits der ersten Zahl. Damit erhalten wir x1. Wir wiederholen dieses Verfahren für die folgenden Zahlen.