LLukas22/scidocs huggingface dataset:
The Analysis of a Probabilistic Approach to Nearest Neighbor Searching

Given a set S of n data points in some metric space. Given a query point q in this space, a nearest neighbor query asks for the nearest point of S to q. Throughout we will assume that the space is real d-dimensional space <d, and the metric is Euclidean distance. The goal is to preprocess S into a data structure so that such queries can be answered efficiently. Nearest neighbor searching has applications in many areas, including data mining [7], pattern classification [5], data compression [10]. Because many applications involve large data sets, we are interested in data structures that use linear storage space. Naively, nearest neighbor queries can be answered in O(dn) time through brute-force search. Although nearest neighbor searching can be performed efficiently in lowdimension spaces, for all known exact linear-space data structures, search times grow exponentially as a function of dimension. Thus for reasonably large dimensions, brute-force search is often the most efficient in practice. One approach to reducing the search time is through approximate nearest neighbor search. A number of data structures for approximate nearest neighbor searching have been proposed [1, 3, 11]. The phenomenon of concentration of distance would suggest that approximate nearest neighbor searching is meaningless. Fortunately, the distributions that arise in applications tend to be clustered in lower dimensional subspaces [6]. Good search algorithms take advantage of this low-dimensional clustering. The fundamental problem that motivates this work is the lack of predictability in existing practical approaches to nearest neighbor searching. In high dimensions, exact search is no better than brute-force, and approximate search algorithms are acceptably fast only when the allowed
Relativism about Science

This is the older version of an article that I updated in 2012 and published in the second edition of the Routledge Companion to Philosophy of Science, so I don't think there will be any problems about the copy right.
Rod sensitivity, cone sensitivity, and photoreceptor layer thickness in retinal degenerative diseases.

PURPOSE
To evaluate the effects of selective rod and/or cone loss on frequency-domain optical coherence tomography (fdOCT) measures of photoreceptor structure in patients with retinal degenerative diseases.


METHODS
Six patients with cone dystrophy (CD) and eight patients with retinitis pigmentosa (RP) were recruited from the Southwest Eye Registry on the basis of diagnosis and ERG findings. fdOCT horizontal line scans were segmented to obtain the thicknesses of the outer segments plus RPE (OS+) and the outer nuclear layer (ONL). The normalized product ONL*OS was obtained after dividing by mean ONL*OS values of 23 normal individuals. Visual field sensitivity profiles were obtained with a modified retinal perimeter, from the horizontal midline with short- and long-wave stimuli under dark- and light-adapted conditions.


RESULTS
Patients with CD and normal rod-mediated sensitivity, but decreased cone-mediated sensitivity, showed normal ONL*OS outside the fovea. The total receptor layer was thinned in the fovea, consistent with loss in cone nuclei and Henle's fiber layer. Patients with RP and sensitivity in the dark that was mediated by cones showed ONL*OS thickness that was linearly related to cone sensitivity. ONL*OS thickness was linearly related to rod sensitivity in regions with greater loss of cone than rod sensitivity.


CONCLUSIONS
Both rods and cones can support an intact IS/OS junction and normal photoreceptor thickness measures. The product of ONL and OS thicknesses is proportional to the sensitivity mediated by the less abnormal type of photoreceptor.
Conventional Linear versus Purse-string Skin Closure after Loop Ileostomy Reversal: Comparison of Wound Infection Rates and Operative Outcomes

PURPOSE
Wound infection after an ileostomy reversal is a common problem. To reduce wound-related complications, purse-string skin closure was introduced as an alternative to conventional linear skin closure. This study is designed to compare wound infection rates and operative outcomes between linear and purse-string skin closure after a loop ileostomy reversal.


METHODS
Between December 2002 and October 2010, a total of 48 consecutive patients undergoing a loop ileostomy reversal were enrolled. Outcomes were compared between linear skin closure (group L, n = 30) and purse string closure (group P, n = 18). The operative technique for linear skin closure consisted of an elliptical incision around the stoma, with mobilization, and anastomosis of the ileum. The rectus fascia was repaired with interrupted sutures. Skin closure was performed with vertical mattress interrupted sutures. Purse-string skin closure consisted of a circumstomal incision around the ileostomy using the same procedures as used for the ileum. Fascial closure was identical to linear closure, but the circumstomal skin incision was approximated using a purse-string subcuticular suture (2-0 Polysorb).


RESULTS
Between group L and P, there were no differences of age, gender, body mass index, and American Society of Anesthesiologists (ASA) scores. Original indication for ileostomy was 23 cases of malignancy (76.7%) in group L, and 13 cases of malignancy (77.2%) in group P. The median time duration from ileostomy to reversal was 4.0 months (range, 0.6 to 55.7 months) in group L and 4.1 months (range, 2.2 to 43.9 months) in group P. The median operative time was 103 minutes (range, 45 to 260 minutes) in group L and 100 minutes (range, 30 to 185 minutes) in group P. The median hospital stay was 11 days (range, 5 to 4 days) in group L and 7 days (range, 4 to 14 days) in group P (P < 0.001). Wound infection was found in 5 cases (16.7%) in group L and in one case (5.6%) in group L (P = 0.26).


CONCLUSION
Based on this study, purse-string skin closure after a loop ileostomy reversal showed comparable outcomes, in terms of wound infection rates, to those of linear skin closure. Thus, purse-string skin closure could be a good alternative to the conventional linear closure.
Immunologic response to xenogeneic gp100 DNA in melanoma patients: comparison of particle-mediated epidermal delivery with intramuscular injection.

PURPOSE
Prior studies show that i.m. injection of xenogeneic orthologues of melanosomal antigens (tyrosinase, gp100) induces CD8(+) T-cell responses to the syngeneic protein. To further define the optimal vaccination strategy, we conducted a pilot clinical trial comparing i.m. injection with particle-mediated epidermal delivery (PMED).


EXPERIMENTAL DESIGN
Human leukocyte antigen (HLA)-A*0201(+) disease-free melanoma patients were randomized to the PMED or i.m. arm, receiving eight vaccinations over 4 months. Patients received 4 microg or 2,000 microg per injection, respectively, of mouse gp100 DNA. Peripheral blood mononuclear cells were collected, cultured with gp100 peptides, and analyzed by tetramer and intracellular cytokine staining for responses to HLA-A*0201-restricted gp100 epitopes [gp100(209-217) (ITDQVPFSV) and gp100(280-288) (YLEPGPVTA)].


RESULTS
Twenty-seven patients with stage IIB-IV melanoma were analyzable for immune response. The only common toxicity was grade 1 injection site reaction in nine patients with no intergroup difference, and one dose-limiting toxicity of acute hypersensitivity occurred in a PMED patient with undiagnosed gold allergy. Four of 27 patients produced gp100 tetramer(+)CD8(+) T cells, all carrying the CCR7(lo)CD45RA(lo) effector-memory phenotype. Five of 27 patients generated IFN-gamma(+)CD8(+) T cells, one who was also tetramer-positive. Overall, vaccination induced a response in 30% of patients, which was not significantly associated with study arm or clinical outcome. However, the PMED group showed a trend toward increased IFN-gamma(+)CD8(+) T-cell generation (P = 0.07).


CONCLUSION
A comparable efficacy and safety profile was shown between the i.m. and PMED arms, despite a significantly decreased dose of DNA used for PMED injection.
Submodular Functions, Matroids, and Certain Polyhedra

I The viewpoint of the subject of matroids, and related areas of lattice theory, has always been, in one way or another, abstraction of algebraic dependence or, equivalently, abstraction of the incidence relations in geometric representations of algebra. Often one of the main derived facts is that all bases have the same cardinality. (See Van der Waerden, Section 33.) From the viewpoint of mathematical programming, the equal cardinality of all bases has special meaning — namely, that every basis is an optimum-cardinality basis. We are thus prompted to study this simple property in the context of linear programming. It turns out to be useful to regard " pure matroid theory " , which is only incidentally related to the aspects of algebra which it abstracts, as the study of certain classes of convex polyhedra. (1) A matroid M = (E, F) can be defined as a finite set E and a nonempty family F of so-called independent subsets of E such that (a) Every subset of an independent set is independent, and (b) For every A ⊆ E, every maximal independent subset of A, i.e., every basis of A, has the same cardinality, called the rank, r(A), of A (with respect to M). (This definition is not standard. It is prompted by the present interest).
Recent advances in robust optimization: An overview

This paper provides an overview of developments in robust optimization since 2007. It seeks to give a representative picture of the research topics most explored in recent years, highlight common themes in the investigations of independent research teams and highlight the contributions of rising as well as established researchers both to the theory of robust optimization and its practice. With respect to the theory of robust optimization, this paper reviews recent results on the cases without and with recourse, i.e., the static and dynamic settings, as well as the connection with stochastic optimization and risk theory, the concept of distributionally robust optimization, and findings in robust nonlinear optimization. With respect to the practice of robust optimization, we consider a broad spectrum of applications, in particular inventory and logistics, finance, revenue management, but also queueing networks, machine learning, energy systems and the public good. Key developments in the period from 2007 to present include: (i) an extensive body of work on robust decision-making under uncertainty with uncertain distributions, i.e., ‘‘robustifying’’ stochastic optimization, (ii) a greater connection with decision sciences by linking uncertainty sets to risk theory, (iii) further results on nonlinear optimization and sequential decision-making and (iv) besides more work on established families of examples such as robust inventory and revenue management, the addition to the robust optimization literature of new application areas, especially energy systems and the public good. 2013 Elsevier B.V. All rights reserved.
Context-aware recommender systems for implicit data

Recommender systems are software tools and techniques providing suggestions and recommendations for items to be of use to a user [18, 44, 55, 56]. These suggestions can help users make better decisions on choosing products or services, such as which film to watch, what music to listen to or which travel insurance to buy. When making suggestions, many recommender systems do not consider contextual information, such as location or time [5]. Recommender systems that make use of contextual information are called context-aware recommender systems. Many context-aware recommender systems can not generate reliable recommendations on sparse data. Besides, in most context-aware recommender systems, the contexts are pre-defined and not personalised. These limitations of existing methods usually lead to inaccurate recommendations. In this thesis, new context-aware recommendation methods are presented. In these methods, personalised contexts are defined based on users’ activity patterns. The underlying associations between contexts are analysed, and similar contexts are combined so that the system can make use of existing data collected in similar contexts. Experimental results from two datasets show that the proposed methods can achieve significantly higher recommendation accuracy than existing context-aware recommendation methods.
Towards a Categorical Foundation of Mathematics

This paper is an expanded version of a talk with the same title given at the Logic Colloquium in Haifa in August, 1995. A year later, at the time of writing these lines, one of the papers, [M2], on which the talk was based has appeared in print. The present paper is, primarily, a somewhat philosophical introduction to the research monograph [M3], the other source of the talk. For understanding the story, it is necessary to keep the contents of [M2] in view; some of [M2] will be recapitulated here. The paper is written for readers with at least a slight familiarity with Category Theory. At certain points, we make remarks referring to more advanced notions; however, the understanding of these is not essential for the main part of the paper.
Hematologic toxicity in RTOG 0418: a phase 2 study of postoperative IMRT for gynecologic cancer.

PURPOSE
Intensity modulated radiation therapy (IMRT), compared with conventional 4-field treatment, can reduce the volume of bone marrow irradiated. Pelvic bone marrow sparing has produced a clinically significant reduction in hematologic toxicity (HT). This analysis investigated HT in Radiation Therapy Oncology Group (RTOG) 0418, a prospective study to test the feasibility of delivering postoperative IMRT for cervical and endometrial cancer in a multiinstitutional setting.


METHODS AND MATERIALS
Patients in the RTOG 0418 study were treated with postoperative IMRT to 50.4 Gy to the pelvic lymphatics and vagina. Endometrial cancer patients received IMRT alone, whereas patients with cervical cancer received IMRT and weekly cisplatin (40 mg/m(2)). Pelvic bone marrow was defined within the treatment field by using a computed tomography density-based autocontouring algorithm. The volume of bone marrow receiving 10, 20, 30, and 40 Gy and the median dose to bone marrow were correlated with HT, graded by Common Terminology Criteria for Adverse Events, version 3.0, criteria.


RESULTS
Eighty-three patients were eligible for analysis (43 with endometrial cancer and 40 with cervical cancer). Patients with cervical cancer treated with weekly cisplatin and pelvic IMRT had grades 1-5 HT (23%, 33%, 25%, 0%, and 0% of patients, respectively). Among patients with cervical cancer, 83% received 5 or more cycles of cisplatin, and 90% received at least 4 cycles of cisplatin. The median percentage volume of bone marrow receiving 10, 20, 30, and 40 Gy in all 83 patients, respectively, was 96%, 84%, 61%, and 37%. Among cervical cancer patients with a V40 >37%, 75% had grade 2 or higher HT compared with 40% of patients with a V40 less than or equal to 37% (P =.025). Cervical cancer patients with a median bone marrow dose of >34.2 Gy also had higher rates of grade ≥ 2 HT than did those with a dose of ≤ 34.2 Gy (74% vs 43%, P=.049).


CONCLUSIONS
Pelvic IMRT with weekly cisplatin is associated with low rates of HT and high rates of weekly cisplatin use. The volume of bone marrow receiving 40 Gy and the median dose to bone marrow correlated with higher rates of grade ≥ 2 toxicity among patients receiving weekly cisplatin (cervical cancer patients). Evaluation and limitation of the volume of bone marrow treated with pelvic IMRT is warranted in patients receiving concurrent chemotherapy.
Neglect and perceived stigmatization impact psychological distress of orphans in Tanzania

BACKGROUND
Research has shown that orphans in sub-Saharan Africa are at increased risk for mental health problems. Exposure to maltreatment and HIV/AIDS-related stigmatization are related to orphans' psychological distress. Yet, researchers stress the need for more research in low-income countries to identify which factors of being an orphan may lead to psychological distress.


OBJECTIVES
The present study aims to systematically investigate orphans' experiences of maltreatment and stigmatization to identify factors that relate to their psychological distress.


METHODS
In total, 89 Tanzanian children who had lost at least one parent were compared to 89 matched non-orphans (mean age: 11 years; 51% boys). We measured exposure to maltreatment and perceived stigmatization as an orphan. Mental health was assessed using the Strengths and Difficulties Questionnaire, the Children's Depression Inventory, the UCLA PTSD Index for Children, and the Reactive-Proactive Questionnaire.


RESULTS
Orphans reported significantly more experiences of neglect, but not of abuse. A group comparison revealed more depressive symptoms, posttraumatic stress symptoms, and aggressive behavior among orphans. Neglect, abuse, and stigmatization correlated with orphans' internalizing and externalizing problems, yet only neglect and stigmatization were related to orphans' depression severity. Perceived stigmatization moderated the relationship between neglect and depression.


CONCLUSIONS
Our findings suggest that orphans in Tanzania are at increased risk of experiencing neglect. Maltreatment and perceived stigmatization may play a role in orphans' psychological distress. Culturally appropriate and evidence-based interventions may help to prevent maltreatment and stigmatization of orphans.
Reconstructive surgery for penoscrotal filarial lymphedema: a decade of experience and follow-up.

OBJECTIVES
To present our experience of reconstructive surgery in patients with penoscrotal filarial lymphedema.


METHODS
From January 2000 to December 2009, we treated 48 patients with penile and penoscrotal filarial lymphedema using reconstructive surgery. Isolated penile involvement was seen in 14 patients, and 34 patients had penoscrotal involvement. All the patients had taken multiple courses of antifilarial drug before surgery. For isolated penile involvement, the diseased penile skin was excised and covered with a split-thickness skin graft. In some patients, the inner prepucial skin was preserved and used to cover the penile shaft. For those with penoscrotal involvement, scrotoplasty was performed, after excising the diseased scrotal skin and underlying soft tissue, while sparing the testes and spermatic cords.


RESULTS
The mean patient age was 38 years (range 25-52), and the median follow-up time was 48 months (range 10-120). All 48 patients reported a satisfactory cosmetic appearance after the procedure and noted improvement in their ability to void while standing. Also, all of them could ambulate better and resumed sexual activity. Local groin infection was present in 12 patients; all were cured after proper management.


CONCLUSIONS
In filarial lymphedema of penis and/or scrotum, excision of the diseased tissue and covering with a split-thickness skin graft provided good results. If the inner prepucial skin is healthy, it should be used to cover the distal penile shaft. If the scrotum is involved, scrotoplasty with lateral and posterior mobilized flaps provides satisfactory results.
Arthropod phylogeny: an overview from the perspectives of morphology, molecular data and the fossil record.

Monophyly of Arthropoda is emphatically supported from both morphological and molecular perspectives. Recent work finds Onychophora rather than Tardigrada to be the closest relatives of arthropods. The status of tardigrades as panarthropods (rather than cycloneuralians) is contentious from the perspective of phylogenomic data. A grade of Cambrian taxa in the arthropod stem group includes gilled lobopodians, dinocaridids (e.g., anomalocaridids), fuxianhuiids and canadaspidids that inform on character acquisition between Onychophora and the arthropod crown group. A sister group relationship between Crustacea (itself likely paraphyletic) and Hexapoda is retrieved by diverse kinds of molecular data and is well supported by neuroanatomy. This clade, Tetraconata, can be dated to the early Cambrian by crown group-type mandibles. The rival Atelocerata hypothesis (Myriapoda+Hexapoda) has no molecular support. The basal node in the arthropod crown group is embroiled in a controversy over whether myriapods unite with chelicerates (Paradoxopoda or Myriochelata) or with crustaceans and hexapods (Mandibulata). Both groups find some molecular and morphological support, though Mandibulata is presently the stronger morphological hypothesis. Either hypothesis forces an unsampled ghost lineage for Myriapoda from the Cambrian to the mid Silurian.
Pulmonary Vein Antrum Isolation in Patients With Paroxysmal Atrial Fibrillation: More Than a Decade of Follow-Up.

BACKGROUND
We report the outcome of pulmonary vein (PV) antrum isolation in paroxysmal atrial fibrillation (AF) patients over more than a decade of follow-up.


METHODS AND RESULTS
A total of 513 paroxysmal AF patients (age 54±11 years, 73% males) undergoing catheter ablation at our institutions were included in this analysis. PV antrum isolation extended to the posterior wall between PVs plus empirical isolation of the superior vena cava was performed in all. Non-PV triggers were targeted during repeat procedure(s). Follow-up was performed quarterly for the first year and every 6 to 9 months thereafter. The outcome of this study was freedom from recurrent AF/atrial tachycardia. At 12 years, single-procedure arrhythmia-free survival was achieved in 58.7% of patients. Overall, the rate of recurrent arrhythmia (AF/atrial tachycardia) was 21% at 1 year, 11% between 1 and 3 years, 4% between 3 and 6 years, and 5.3% between 6 and 12 years. Repeat procedure was performed in 74% of patients. Reconnection in the PV antrum was found in 31% of patients after a single procedure and in no patients after 2 procedures. Non-PV triggers were found and targeted in all patients presenting with recurrent arrhythmia after ≥2 procedures. At 12 years, after multiple procedures, freedom from recurrent AF/atrial tachycardia was achieved in 87%.


CONCLUSIONS
In patients with paroxysmal AF undergoing extended PV antrum isolation, the rate of late recurrence is lower than what previously reported with segmental or less extensive antral isolation. However, over more than a decade of follow-up, nearly 14% of patients developed recurrence because of new non-PV triggers.