LLukas22/scidocs huggingface dataset:
BEDTools: a flexible suite of utilities for comparing genomic features

MOTIVATION
Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner.


RESULTS
This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.


AVAILABILITY AND IMPLEMENTATION
BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools


CONTACT
aaronquinlan@gmail.com; imh4y@virginia.edu


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Prevention of compensatory hyperhidrosis after thoracoscopic sympathectomy for hyperhidrosis

Background: Compensatory hyperhidrosis is a troublesome complication of thoracoscopic sympathectomy for hyperhidrosis. After extensive resection of the second through the fourth ganglion (T2-4), as well as after limited resection of the second ganglion (T2), the reported incidence of compensatory hyperhidrosis ranges as high as 50-97%. The purpose of this study was to determine whether the incidence of compensatory hyperhidrosis can be reduced by limiting the thoracoscopic sympathectomy to another level, the third ganglion. Methods: We analyzed 28 thoracoscopic sympathectomies for palmar and/or axillary hyperhidrosis. In all patients, the sympathetic chain was transected cranially and caudally to the third ganglion (T3 dissection). Long-term follow-up was conducted by interviewing patients using standardized questionnaires. Results: The surgery was effective in all patients. After a median follow-up of 3.5 years, compensatory hyperhidrosis was not recorded in any of the patients. There were no recurrences of hyperhidrosis. Conclusion: Limited thoracoscopic sympathectomy at the level of the third ganglion is effective and seems to prevent compensatory hyperhidrosis.
Implementation of construction industry best practices into workflow management systems

Several research studies have confirmed that identification and adoption of industry best practices drive performance improvements in terms of cost, schedule, and productivity. Best practices specifications facilitate the reuse of experience within a domain. However, they typically offer abstract suggestions and recommendations that include not only explicit, but also tacit knowledge. Key approaches of adopting and promoting best practices include socialization and face to face interactions, such as meetings, workshops, and training. These approaches, however, are not easily scalable to large capital projects, to provide systematic and consistent adoption of best practices throughout different phases of a project or among different projects. An alternative solution is to transform best practices into processes implementable into workflow management systems. In this paper, well-known best practices in the domain of the construction industry and their common characteristics are investigated. A framework is then established for transforming best practices into structured processes implementable into workflow management systems. Only parts of a best practice can be transformed into a structured process. The proposed framework describes which components of a best practice are more suitable for this transformation. The result is a process with the essence of a best practice that can be embedded into and automated through workflow management systems. This approach of integrating construction industry best practices into workflow management systems, not only facilitates consistent implementation of best practices throughout the project lifecycle and within projects, but also improves conformance to those practices, with the end result of improved capital project performance.
Expectation-based syntactic comprehension

This paper investigates the role of resource allocation as a source of processing difficulty in human sentence comprehension. The paper proposes a simple information-theoretic characterization of processing difficulty as the work incurred by resource reallocation during parallel, incremental, probabilistic disambiguation in sentence comprehension, and demonstrates its equivalence to the theory of Hale [Hale, J. (2001). A probabilistic Earley parser as a psycholinguistic model. In Proceedings of NAACL (Vol. 2, pp. 159-166)], in which the difficulty of a word is proportional to its surprisal (its negative log-probability) in the context within which it appears. This proposal subsumes and clarifies findings that high-constraint contexts can facilitate lexical processing, and connects these findings to well-known models of parallel constraint-based comprehension. In addition, the theory leads to a number of specific predictions about the role of expectation in syntactic comprehension, including the reversal of locality-based difficulty patterns in syntactically constrained contexts, and conditions under which increased ambiguity facilitates processing. The paper examines a range of established results bearing on these predictions, and shows that they are largely consistent with the surprisal theory.
Photodynamic therapy outcome for T1/T2 N0 oral squamous cell carcinoma.

INTRODUCTION
This new prospective clinical study assessed the oncological outcomes following surface illumination mTHPC-photodynamic therapy of T1/T2 N0 oral squamous cell carcinoma (OSCC) patients.


MATERIAL/METHODS
Thirty-eight patients participated in this study. Their mean age at the first diagnosis of OSCC was 58.0 years. Common clinical presentation was an ulcer mainly identified in the tongue, floor of mouth (FOM), or buccal mucosa. Current and ex-smokers represented 89.5% of the cohort; while current and ex-drinkers were 86.8%. Clinically nine patients had T1 disease while 29 had T2 disease.


RESULTS
Pathological analysis revealed that 12 patients had well differentiated SCC, 16 moderately differentiated and 10 had poorly-differentiated cancer. All patients were discussed in a multidisciplinary meeting and, subsequently, underwent mTHPC-PDT. PDT was repeated in 6- to 7-month period following the first round when residual tumor was identified in the treated site. At last clinic review post-PDT, 26/38 patients showed complete normal clinical appearance of their oral mucosa in the primary tumor site. Recent surgical biopsies from the study cohort showed that 17 had normal mucosa, five with hyperkeratinization, 10 with dysplastic changes and six showed recurrent SCC. The overall recurrence was 15.8% and the 5-year survival was 84.2%. Death from loco-regional and distant disease spread was identified in three patients. The recurrence group comprised six patients. Most common presentation was an ulcer involving the buccal mucosa or retromolar area, identified in current or ex-smokers and current drinkers. The surgical margins in this group were also evaluated following laser or surgical excision and reconstruction.


CONCLUSIONS
mTHPC-photodynamic therapy (up to three rounds) is a comparable modality to other traditional interventions in the management of low-risk tumors of the oral cavity. Although, sometimes, multiple rounds of the treatment is required, morbidity following PDT is far less when compared to the three conventional modalities: surgery, radiotherapy, and chemotherapy.
The Robustness of LWPP and WPP, with an Application to Graph Reconstruction

We show that the counting class LWPP [8] remains unchanged even if one allows a polynomial number of gap values rather than one. On the other hand, we show that it is impossible to improve this from polynomially many gap values to a superpolynomial number of gap values by relativizable proof techniques. The first of these results implies that the Legitimate Deck Problem (from the study of graph reconstruction) is in LWPP (and thus low for PP, i.e., PPLegitimate Deck = PP) if the weakened version of the Reconstruction Conjecture holds in which the number of nonisomorphic preimages is assumed merely to be polynomially bounded. This strengthens the 1992 result of Köbler, Schöning, and Torán [15] that the Legitimate Deck Problem is in LWPP if the Reconstruction Conjecture holds, and provides strengthened evidence that the Legitimate Deck Problem is not NP-hard. We additionally show on the one hand that our main LWPP robustness result also holds for WPP, and also holds even when one allows both the rejectionand acceptancegap-value targets to simultaneously be polynomial-sized lists; yet on the other hand, we show that for the #P-based analog of LWPP the behavior much differs in that, in some relativized worlds, even two target values already yield a richer class than one value does. 2012 ACM Subject Classification Theory of computation → Complexity classes
Prolonged release melatonin in the treatment of primary insomnia: evaluation of the age cut-off for short- and long-term response.

OBJECTIVES
The authors recently reported on efficacy and safety of prolonged-release melatonin formulation (PRM; Circadin 2  mg) in elderly insomnia patients. The age cut-off for response to PRM and the long-term maintenance of efficacy and safety were further evaluated by looking at the total cohort (age 18-80 years) from that study and subsets of patients aged 18-54 and 55-80 years (for whom the drug is currently indicated).


DESIGN
Randomised, double-blind, placebo controlled trial.


SETTING
Multicentre, outpatients, primary care setting.


METHODS
A total of 930 males and females aged 18-80 years with primary insomnia who reported mean nightly sleep latency (SL) >20  min were enrolled and 791 entered the active phase of the study. The study comprised a 2-week, single-blind placebo run-in period followed by 3 week's double-blind treatment with PRM or placebo, one tablet per day at 2 hours before bedtime. PRM patients continued whereas placebo completers were re-randomised 1:1 to PRM or placebo for 26 weeks followed by 2-weeks run-out on placebo.


MAIN OUTCOME MEASURES
SL and other sleep variables derived from sleep diary, Pittsburgh Sleep Quality Index (PSQI), Quality of life (WHO-5), Clinical Global Impression of Improvement (CGI-I) and adverse effects, recorded each visit, withdrawal and rebound effects during run-out.


RESULTS
In all, 746 patients completed the 3-week and 555 (421 PRM, 134 placebo) completed the 6-month period. The principal reason for drop-out was patient decision. At 3 weeks, significant differences in SL (diary, primary variable) in favour of PRM vs. placebo treatment were found for the 55-80-year group (-15.4 vs. -5.5  min, p = 0.014) but not the 18-80-year cut-off which included younger patients. Other variables (SL-PSQI, PSQI, WHO-5, CGI-I scores) improved significantly with PRM in the 18-80-year population, more so than in the 55-80-year age group. Improvements were maintained or enhanced over the 6-month period with no signs of tolerance. No withdrawal symptoms or rebound insomnia were detected. Most adverse events were mild with no significant differences between PRM and placebo groups in any safety outcome.


CONCLUSIONS
The results demonstrate short- and long-term efficacy of PRM in insomnia patients aged 18-80 years, particularly those aged 55 and over. PRM was well-tolerated over the entire 6-month period with no rebound or withdrawal symptoms following discontinuation. Study Registry No: ClinicalTrials.gov ID: NCT00397189.
Association of metallothionein expression and clinical response to cisplatin based chemotherapy in testicular germ cell tumors

INTRODUCTION
The protective roles of metallothioneins (MT) against metal toxicity suggest that MT may have a functional role in cisplatin resistance. The aim of this study was to investigate the expression of MT in specimens of germ cell tumors and compare it with clinical sensitivity to cisplatin based chemotherapy.


MATERIAL AND METHODS
Tissue blocks of primary GCT specimens obtained from 39 patients were examined immunohistochemically for MT expression. Staining intensity was evaluated according to the percentage of MT positive cells and graded as [-], [+] and [++]. The staining characteristics were compared with the clinical response to chemotherapy.


RESULTS
Of the 39 tumors, 3 evidenced no MT expression while 26 and 10 specimens showed [+] and [++] staining, respectively. Although seminomas tend to stain weaker than non-seminomas, the difference of staining between them was not significant (p = 0.19). Of the 39 patients, 23 underwent cisplatin based chemotherapy. Of those, 6 progressed and 17 achieved complete remission. Of the non-responders, 5 showed [+] and 1 showed [++] staining. Six of the responders showed [+], 10 had [++] and 1 showed no staining. No association was found between MT staining and chemo-sensitivity (p = 0.53).


CONCLUSIONS
MT expression in primary germ cell tumors did not differ between responding and non-responding patients and therefore may not be useful in predicting response to chemotherapy.
Prognostic impact of clinical variables on surgically resected small-cell lung cancer: Results of a retrospective multicenter analysis (FIGHT002A and HOT1301A).

OBJECTIVES
Several American and Japanese guidelines recommend surgery for patients with c-stage I small-cell lung cancer (SCLC), whereas the European Society of Medical Oncology (ESMO) guidelines recommend surgery for patients with not only c-stage I but also c-stage II (T2N1) SCLC. In addition, previous studies identified various factors other than clinical stage that are related to survival in these patients. Thus, further validation and examination of the association of clinical stage and other clinical variables with survival are required for establishing practical management of early-stage SCLC.


PATIENTS AND METHODS
We reviewed the clinical courses of 156 SCLC patients who had undergone surgery at 17 institutions between January 2003 and January 2013.


RESULTS
Clinical stages (tumor-node-metastasis [TNM] version 7) of the 156 patients were 98 cases in IA, 14 in IB, 16 in IIA, 7 in IIB, 18 in IIIA, and 3 in IIIB. Median overall survival (OS) was 33.3 months (95% confidence interval: 20.9-45.8). Multivariate analysis revealed that OS was longer in patients either at c-stage II and under, with a maximum tumor diameter of <20mm, with preoperative diagnosis, without a history or presence of other types of cancer, or who underwent prophylactic cranial irradiation (PCI).


CONCLUSION
These results indicate that a history or presence of other types of cancer might be a major decisive factor for surgery. Patients with c-stages I and II (c-T2N1) can be considered for surgery, and PCI may be useful in patients undergoing surgery in a practical setting, partly supporting the ESMO guidelines.(1).
Prednisone inhibits formation of cortical bone in sham-operated and ovariectomized female rats

Prednisone inhibits bone formation and causes bone loss. To investigate possible mechanisms and sites, the effects of sham operation, ovariectomy, and prednisone were determined on bone and mineral metabolism in 7-week-old growing female rats. Forty animals were divided into groups of 10 each. Sham operation and ovariectomy were performed. One week later, pellets containing 5 mg prednisone or drug free were implanted S.C. at the back of the neck. Four weeks later, animals were sacrificed and tibiae were removed for histomorphometric analysis of the middiaphysis and proximal metaphysis. In both sham-operated and ovariectomized rats, prednisone (1) reduced weight gain (P<0.02) and did not alter uterine weight; (2) lowered serum magnesium (Mg) (P<0.001) and did not change serum calcium (Ca), phosphate (P), 25-hydroxyvitamin D (25OHD), or 1,25-dihydroxyvitamin D [1,25(OH)2D]; (3) produced striking increases in calcified cartilage, reduced cross-sectional area (P<0.05) and cortical area (P<0.01) and did not change medullary area of the tibial diaphysis; (4) lowered periosteal and endocortical bone formation and apposition rates; and (5) increased mean cancellous bone area (P<0.05) and cancellous bone perimeter (P<0.01) of the tibial metaphysis. In both control and prednisone-treated rats, ovariectomy (1) reduced uterine weight (P<0.001); (2) did not change serum Ca, P, Mg, 25OHD, or 1,25(OH)2D; (3) did not change mean cross-sectional, medullary, or cortical areas; (4) increased periosteal bone formation and apposition rates (P<0.01) and did not alter endosteal bone formation and apposition rates, and (5) decreased cancellous bone area (P<0.01) and cancellous bone perimeter (P<0.01). Thus, in short-term studies, prednisone increased calcified cartilage and inhibited the formation of cortical bone at periosteal and endosteal surfaces and reduced cortical bone of the tibia in both sham-operated and ovariectomized, rapidly growing animals.
Design and Implementation of Cloud-Like Soft Drone S-Cloud

This study presents a new drone, called S-CLOUD, developed for safe and long flight time. It provides 3-axial (x, y, and z)translational motion and stable hovering for more than an hour after takeoff. S-CLOUD consists of two parts; soft blimp part and driving one. The soft blimp is a center-pierced torus-shaped part filled with Helium gas. Thus, it is safe to fly near people because it is light and soft, and all its rotating parts are at the center of the vehicle, which does not get damaged on collision. The driving part is plugged into the center of the soft blimp and includes the flow control mechanism, which consists of co-axial rotors and 2-axis crossed flaps. It controls the altitude, attitude, and translational movements of the vehicle. Its dynamic and reaction features against disturbances are derived using Newton-Euler formulation, and the simulation results are discussed. Finally, a prototype of S-CLOUD is fabricated and its feasibility is experimentally validated with practical applications.
Effects of Bone Marrow Stromal Cell-conditioned Medium on Primary Cultures of Peripheral Nerve Tissues and Cells

Implantation of bone marrow stromal cells (MSCs) produces an improved functional outcome of peripheral nerve repair. In this study, rat dorsal root ganglion (DRG) explants, rat DRG neurons, and rat Schwann cells (SCs) were treated with monkey MSC-conditioned medium, respectively, and then subjected to MTT assay, Bromodeoxyuridine/Hoechst 33342 double staining, flow cytometry, immunohistochemistry, real-time quantitative PCR, and Western blot analysis, respectively. The results showed that MSC-conditioned medium enhanced axon growth and neurogenesis in cultured DRG explants, augmented cell survival of and expression of NF and GAP-43 by cultured DRG neurons, promoted cell survival and proliferation of cultured SCs, and increased the expression of NGF, BDNF, and bFGF in cultured SCs. We also found that mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (Erk) 1/2 pathway was involved in the enhanced cell proliferation of SCs evoked by MSC-conditioned medium. The data of this study might help the understanding of MSCs-based treatment for peripheral nerve repair.
Monitoring of Large-Area IoT Sensors Using a LoRa Wireless Mesh Network System: Design and Evaluation

Although many techniques exist to transfer data from the widely distributed sensors that make up the Internet of Things (IoT) (e.g., using 3G/4G networks or cables), these methods are associated with prohibitively high costs, making them impractical for real-life applications. Recently, several emerging wireless technologies have been proposed to provide long-range communication for IoT sensors. Among these, LoRa has been examined for long-range performance. Although LoRa shows good performance for long-range transmission in the countryside, its radio signals can be attenuated over distance, and buildings, trees, and other radio signal sources may interfere with the signals. Our observations show that in urban areas, LoRa requires dense deployment of LoRa gateways (GWs) to ensure that indoor LoRa devices can successfully transfer data back to remote GWs. Wireless mesh networking is a solution for increasing communication range and packet delivery ratio (PDR) without the need to install additional GWs. This paper presents a LoRa mesh networking system for large-area monitoring of IoT applications. We deployed 19 LoRa mesh networking devices over an  $800\,\,\text {m} \times 600$  m area on our university campus and installed a GW that collected data at 1-min intervals. The proposed LoRa mesh networking system achieved an average 88.49% PDR, whereas the star-network topology used by LoRa achieved only 58.7% under the same settings. To the best of our knowledge, this is the first academic study discussing LoRa mesh networking in detail and evaluating its performance via real experiments.
The Rise and Fall of Economic History at MIT

This article recalls the unity of economics and history at MIT before the Second World War and their divergence thereafter. Economic history at MIT reached its peak in the 1970s, with three teachers of the subject to graduates and undergraduates alike. It declined until economic history vanished both from the faculty and from the graduate program around 2010. The cost of this decline to current education and scholarship is suggested at the end of the narrative.
Chronic disease management for tobacco dependence: a randomized, controlled trial.

BACKGROUND
Tobacco dependence disorder is a chronic relapsing condition, yet treatment is delivered in discrete episodes of care that yield disappointing long-term quit rates.


METHODS
We conducted a randomized controlled trial from June 1, 2004, through May 31, 2009, to compare telephone-based chronic disease management (1 year; longitudinal care [LC]) with evidence-based treatment (8 weeks; usual care [UC]) for tobacco dependence. A total of 443 smokers each received 5 telephone counseling calls and nicotine replacement therapy by mail for 4 weeks. They were then randomized to UC (2 additional calls) or LC (continued counseling and nicotine replacement therapy for an additional 48 weeks). Longitudinal care targeted repeat quit attempts and interim smoking reduction for relapsers. The primary outcome was 6 months of prolonged abstinence measured at 18 months of follow-up.


RESULTS
At 18 months, 30.2% of LC participants reported 6 months of abstinence from smoking, compared with 23.5% in UC (unadjusted, P = .13). Multivariate analysis showed that LC (adjusted odds ratio, 1.74; 95% CI, 1.08-2.80), quit attempts in past year (1.75; 1.06-2.89), baseline cigarettes per day (0.95; 0.92-0.99), and smoking in the 14- to 21-day interval post-quit (0.23; 0.14-0.38) predicted prolonged abstinence at 18 months. The LC participants who did not quit reduced smoking more than UC participants (significant only at 12 months). The LC participants received more counseling calls than UC participants (mean, 16.5 vs 5.8 calls; P < .001), longer total duration of counseling (283 vs 117 minutes; P < .001), and more nicotine replacement therapy (4.7 vs 2.4 boxes of patches; P < .001).


CONCLUSION
A chronic disease management approach increases both short- and long-term abstinence from smoking.


TRIAL REGISTRATION
clinicaltrials.gov Identifier: NCT00309296.